The protein structure visualization programs usually show the amino acid sequence and allow you to select specific residues in the sequence to highlight in the structure visualization.

In order to define the N and C terminal you have to install VMD. Follow the link: http://www.ks.uiuc.edu/Research/vmd/current/ig/ig.html

If you're looking at a protein molecule in a graphics programme like pymol, then the amino acid with the lowest residue number is the "visible" N-terminus and the one with the highest residue number is the "visible" C-terminus.

If you're looking at a pdb file instead, you'll see lines that look like this:

ATOM   1  N   LYS A 122      48.634 -28.081  21.272  1.00 44.28       N 

ATOM   2  CA  LYS A 122      47.475 -28.583  20.498  1.00 49.73       C 

ATOM   3  C   LYS A 122      46.238 -27.671  20.520  1.00 38.88       C 

ATOM   4  O   LYS A 122      45.871 -27.078  21.534  1.00 42.39       O 

ATOM   5  CB  LYS A 122      47.118 -29.995  20.929  1.00 55.26       C 

ATOM   6  CG  LYS A 122      46.105 -30.107  22.042  1.00 57.09       C 

ATOM   7  CD  LYS A 122      45.791 -31.570  22.263  1.00 66.89       C 

ATOM   8  CE  LYS A 122      44.770 -32.043  21.242  1.00 69.87       C 

ATOM   9  NZ  LYS A 122      44.677 -33.516  21.162  1.00 74.29       N 

I have highlighted the important bits by making them bold. If we concentrate on the second line: this means you're looking at atom number 2 in this pdb file, which is a carbon atom and belongs to a lysine residue, which is residue number 122 of chain A.

CA: this is the name of the atom. The atom type is mentioned at the end of the line (in this case it is C). As an amino acid has several atoms of the same type, they are given different names to distinguish them. For example CA, C, CB, CG, CD and CE are all carbon atoms and all have the identifier C at the end of the line, but they have different names after the atom number.

LYS: this is the name of the amino acid in three letter code that the atom belongs to (in this case lysine).

A: this is the name of the chain. There might be more than one molecule of the same protein in a crystal structure and therefore each protein molecule in a pdb file is generally given its own chain letter to distinguish between them.

122: this is the residue number allocated to the amino acid. This is the number you need to check. The amino acid with the lowest number will have the N-terminus. Remember that other atoms such as water molecules or ligand molecules that interact with a protein molecule are also included in the chain of that protein molecule. So make sure you are looking at an amino acid residue and don't just try to find the highest number in a chain, as that might belong to something else .

The amino acid with the highest residue number inside a chain will contain the C-terminus.

If you want to find the exact atom that forms the terminus rather than the whole residue, then look for the atom of type N with atom name N (as opposed to NZ, for example) in the N-terminal residue and the atom of type C with atom name C (as opposed to CA, CG, etc...) in the C-terminal residue.

Remember that often the residues at either terminus are disordered and therefore not visible in the crystal structure even though they are actually there. Hence, you need to distinguish between the "visible" termini and the "real" termini.

Also, sometimes the numbering can be a bit confusing. For example, very few proteins in crystal structures have "true" N- or C-termini that are identical to the corresponding sequence of the native protein deposited in a data bank. Because you need a lot of protein to make a protein crystal, the protein is generally expressed as recombinant protein with an affinity tag at either the N- or C-terminus. Even if the tag is removed before crystallisation, one or two extra amino acid residues remain that are not present in the native protein sequence. Therefore, you might have a structure that starts at residue -12 (e.g a protein with an N-terminal 6His-tag) or -2 (e.g where an N-terminal tag has been removed but two extra residues remain that are part of the recognition site needed by the protease used to remove the tag).

I hope this wasn't too confusing.

Thank you all for answering the question. 

Hi I have a PDB file for viral envelope and an inhibitor peptide. Now I want to see the binding of that peptide with viral envelope at C and N terminal  Which software to use? Can anyone suggest something easier?