Contacts of the helix formed by residues 39 - 66 (chain I) in PDB entry 3GHG
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 39 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97H VAL* 4.4 20.8 - - + +
101H ASN* 5.2 1.6 + - - +
34I THR 3.8 1.2 + - - -
35I LYS* 3.2 40.4 + - - +
36I VAL* 2.7 10.4 + - - +
38I LYS* 1.3 70.6 - - - +
40I LEU* 1.3 65.5 + - + +
41I GLN 3.1 2.2 - - - -
42I SER* 3.2 28.0 + - - +
43I LEU* 3.6 12.3 - - - +
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Residues in contact with LEU 40 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62G PHE* 4.3 19.3 - - + +
65G ARG* 3.3 50.6 + - + +
66G ILE* 5.1 14.1 - - + -
69G LEU* 5.9 8.0 - - + +
93H ILE* 6.3 0.4 - - + -
97H VAL* 4.0 27.6 - - + -
36I VAL* 2.6 15.2 + - + +
37I ASP 3.1 13.6 + - - +
39I ASP* 1.3 79.2 - - - +
41I GLN* 1.3 55.5 + - - +
42I SER 3.3 0.2 - - - -
43I LEU* 3.6 16.0 + - + +
44I GLU* 3.0 29.5 + - - +
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Residues in contact with GLN 41 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65G ARG* 3.6 20.6 - - - +
37I ASP* 3.6 1.6 + - - +
38I LYS* 3.8 41.8 - - + +
39I ASP 3.1 0.4 - - - -
40I LEU* 1.3 76.6 - - - +
42I SER* 1.3 65.2 + - - +
44I GLU* 4.0 11.2 + - - +
45I ASP* 2.9 60.0 + - - +
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Residues in contact with SER 42 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38I LYS 5.0 1.3 + - - -
39I ASP* 3.2 25.5 + - - +
41I GLN* 1.3 75.9 - - - +
43I LEU* 1.3 65.0 + - - +
46I ILE* 2.8 48.3 + - - +
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Residues in contact with LEU 43 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G LEU* 4.7 12.0 - - + +
97H VAL* 4.2 7.6 - - + +
100H LEU* 3.1 45.3 - - + +
101H ASN* 3.0 28.9 - - - +
104H VAL* 4.7 8.7 - - + +
105H GLU* 4.2 11.0 - - - +
39I ASP* 3.6 26.5 - - - +
40I LEU* 3.6 17.2 + - + +
42I SER* 1.3 85.4 - - - +
44I GLU* 1.3 61.2 + - - +
46I ILE* 4.0 7.3 - - - +
47I LEU* 3.3 23.7 + - - +
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Residues in contact with GLU 44 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65G ARG* 2.8 38.2 + - - +
69G LEU* 4.7 13.9 - - + +
40I LEU 3.0 17.7 + - - +
41I GLN* 4.0 16.5 + - - +
43I LEU* 1.3 73.4 - - - +
45I ASP* 1.3 59.4 + - - +
46I ILE 3.1 1.1 - - - -
47I LEU* 2.7 27.1 + - + +
48I HIS* 2.9 43.5 + - + +
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Residues in contact with ASP 45 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41I GLN* 2.9 42.3 + - - +
42I SER 4.5 0.4 - - - +
44I GLU* 1.3 74.7 - - - +
46I ILE* 1.3 66.8 + - + +
47I LEU 3.2 0.2 - - - -
48I HIS* 3.3 24.6 - - + -
49I GLN* 2.7 32.9 + - - +
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Residues in contact with ILE 46 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104H VAL* 4.0 14.4 - - + -
105H GLU* 3.1 28.9 - - + +
112H SER* 5.7 0.2 - - - +
41I GLN 4.9 0.4 - - - +
42I SER* 2.8 41.4 + - - +
43I LEU 4.0 2.2 - - - +
45I ASP* 1.3 80.6 - - + +
47I LEU* 1.3 57.8 + - - +
48I HIS 3.5 0.2 - - - -
49I GLN* 3.8 5.0 + - - +
50I VAL* 3.0 32.6 + - + +
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Residues in contact with LEU 47 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G LEU* 4.2 35.7 - - + +
72G SER* 4.9 8.3 - - - -
73G LEU* 4.9 13.0 - - + +
76G TYR* 4.3 25.4 - - + -
104H VAL* 4.8 17.0 - - + -
43I LEU 3.3 12.5 + - - +
44I GLU* 2.7 14.5 + - + +
46I ILE* 1.3 76.9 - - - +
48I HIS* 1.3 60.3 + - + +
49I GLN 3.2 2.0 - - - -
50I VAL* 4.1 9.2 - - + -
51I GLU* 2.8 34.3 + - + +
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Residues in contact with HIS 48 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44I GLU* 2.9 42.3 + - + +
45I ASP* 3.3 31.2 + - + +
46I ILE 3.5 0.2 - - - -
47I LEU* 1.3 84.3 - - + +
49I GLN* 1.3 67.7 + - - +
51I GLU* 3.0 33.7 - - + +
52I ASN* 3.1 10.7 + - - +
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Residues in contact with GLN 49 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45I ASP* 2.7 27.6 + - - +
46I ILE* 4.0 7.6 - - - +
47I LEU 3.2 0.4 - - - -
48I HIS* 1.3 86.4 + - - +
50I VAL* 1.3 61.8 + - + +
51I GLU 3.1 1.6 - - - -
52I ASN* 2.9 10.7 + - + +
53I LYS* 2.8 44.6 + - - +
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Residues in contact with VAL 50 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76G TYR* 5.5 11.7 - - + -
104H VAL* 5.5 3.4 - - + -
108H SER* 4.2 23.1 - - - +
112H SER* 3.0 29.2 - - - +
115H PHE* 3.2 35.2 - - + -
46I ILE* 3.0 28.1 + - + +
47I LEU* 3.4 11.9 + - + +
49I GLN* 1.3 75.4 - - + +
51I GLU* 1.3 58.0 + - - +
53I LYS* 3.7 7.7 - - + +
54I THR* 3.5 7.1 + - - +
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Residues in contact with GLU 51 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76G TYR* 4.0 31.4 + - + +
47I LEU* 2.8 24.1 + - + +
48I HIS* 3.0 31.9 - - - +
50I VAL* 1.3 71.2 - - - +
52I ASN* 1.3 86.7 + - - +
53I LYS 3.1 1.6 - - - -
54I THR* 2.2 31.9 + - - -
55I SER* 3.1 17.8 + - - -
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Residues in contact with ASN 52 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48I HIS 3.1 14.7 + - - +
49I GLN* 2.9 13.9 + - - +
51I GLU* 1.3 90.0 + - - +
53I LYS* 1.3 76.5 + - - +
55I SER* 3.6 15.9 + - - -
56I GLU* 3.3 25.2 + - - +
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Residues in contact with LYS 53 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112H SER* 5.3 10.8 - - - +
115H PHE* 3.5 30.5 - - + -
116H GLN* 5.0 19.5 - - + -
49I GLN* 2.8 31.7 + - - +
50I VAL* 3.7 5.8 - - + +
52I ASN* 1.3 93.5 + - - +
54I THR* 1.3 59.3 + - - +
56I GLU* 3.4 7.0 + - + +
57I VAL* 3.0 36.7 + - + +
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Residues in contact with THR 54 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76G TYR* 4.2 19.4 + - + -
79G ASN* 4.0 21.5 - - - +
115H PHE* 3.0 38.8 - - + -
50I VAL 3.5 7.9 - - - +
51I GLU* 2.2 33.0 + - - +
53I LYS* 1.3 74.7 - - - +
55I SER* 1.3 64.4 + - - +
57I VAL* 4.0 2.4 - - - +
58I LYS* 3.1 40.7 + - - +
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Residues in contact with SER 55 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51I GLU* 3.1 19.8 + - - -
52I ASN* 3.6 26.0 + - - -
54I THR* 1.3 81.6 + - - +
56I GLU* 1.3 60.0 + - - +
58I LYS* 3.5 17.5 + - - +
59I GLN* 3.2 41.0 + - - +
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Residues in contact with GLU 56 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119H TYR* 5.3 8.1 - - - +
52I ASN* 3.3 18.8 + - - +
53I LYS* 3.4 9.2 + - + +
54I THR 3.3 0.2 - - - -
55I SER* 1.3 79.6 - - - +
57I VAL* 1.3 60.9 + - + +
59I GLN* 3.5 23.7 + - - +
60I LEU* 3.1 38.3 + - + +
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Residues in contact with VAL 57 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83G SER* 5.3 11.9 - - - -
115H PHE* 2.9 46.2 - - + +
116H GLN* 4.2 7.2 - - + +
118H MET* 4.8 10.3 - - + -
53I LYS* 3.0 21.0 + - - +
54I THR* 3.4 5.4 + - - +
56I GLU* 1.3 78.4 - - + +
58I LYS* 1.3 60.6 + - - +
59I GLN 3.3 0.4 - - - -
60I LEU* 3.3 7.7 + - + +
61I ILE* 3.1 40.6 + - + +
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Residues in contact with LYS 58 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76G TYR* 6.2 1.4 - - - -
54I THR* 3.1 32.9 + - - +
55I SER* 3.5 22.2 + - - +
57I VAL* 1.3 74.6 - - - +
59I GLN* 1.3 65.7 + - + +
61I ILE* 3.5 7.5 + - - +
62I LYS* 3.1 47.2 + - - +
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Residues in contact with GLN 59 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55I SER* 3.2 28.9 + - - +
56I GLU* 3.5 27.9 + - - +
57I VAL 3.3 0.4 - - - -
58I LYS* 1.3 79.5 - - + +
60I LEU* 1.3 62.7 + - + +
62I LYS* 3.6 13.8 + - + +
63I ALA* 3.3 24.3 + - - +
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Residues in contact with LEU 60 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116H GLN* 6.1 1.8 - - + -
118H MET* 3.9 19.3 - - + -
119H TYR* 5.0 21.3 - - + +
122H LYS* 3.0 30.3 - - + +
123H ASP* 5.2 7.2 - - - +
56I GLU* 3.1 27.4 + - + +
57I VAL* 3.5 10.5 - - + +
58I LYS 3.3 0.8 - - - -
59I GLN* 1.3 79.2 - - - +
61I ILE* 1.3 56.9 + - - +
63I ALA* 3.6 2.8 + - - +
64I ILE* 3.0 44.0 + - + +
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Residues in contact with ILE 61 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118H MET* 4.5 4.3 - - - -
122H LYS* 3.1 33.4 - - - +
57I VAL* 3.1 27.1 + - + +
58I LYS* 4.1 7.9 - - - +
59I GLN 3.4 0.2 - - - -
60I LEU* 1.3 72.6 - - - +
62I LYS* 1.3 65.4 + - + +
64I ILE* 4.0 7.3 - - + +
65I GLN* 3.3 41.4 + - + +
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Residues in contact with LYS 62 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58I LYS* 3.1 36.5 + - - +
59I GLN* 3.8 13.8 - - + +
60I LEU 3.3 0.2 - - - -
61I ILE* 1.3 80.2 - - + +
63I ALA* 1.3 60.2 + - - +
65I GLN* 3.6 8.1 + - - +
66I LEU* 3.5 19.9 + - - +
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Residues in contact with ALA 63 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59I GLN 3.3 15.3 + - - +
60I LEU* 4.2 4.0 - - - +
62I LYS* 1.3 76.4 - - - +
64I ILE* 1.3 65.7 + - + +
65I GLN 3.5 0.2 - - - -
66I LEU* 3.7 8.5 + - - +
67I THR* 2.9 31.2 + - + +
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Residues in contact with ILE 64 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122H LYS* 4.1 29.2 - - + +
123H ASP* 5.7 1.6 - - - +
125H TRP* 5.6 9.4 - - + +
126H GLN* 5.0 14.4 - - - +
60I LEU* 3.0 37.5 + - + +
61I ILE* 4.0 10.1 - - + +
62I LYS 3.3 0.4 - - - -
63I ALA* 1.3 81.2 - - + +
65I GLN* 1.3 61.8 + - + +
67I THR* 2.9 11.6 + - - +
68I TYR* 2.8 39.9 + - + +
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Residues in contact with GLN 65 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61I ILE* 3.3 30.8 + - + +
62I LYS* 4.0 7.2 - - - +
63I ALA 3.5 0.2 - - - -
64I ILE* 1.3 81.8 - - + +
66I LEU* 1.3 58.6 + - - +
67I THR 3.6 0.2 + - - -
68I TYR* 4.2 9.6 - - + +
69I ASN* 3.7 21.1 + - - +
----------------------------------------------------------
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Residues in contact with LEU 66 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62I LYS 3.5 11.3 + - - +
63I ALA* 4.0 11.4 - - - +
64I ILE 3.2 0.8 - - - -
65I GLN* 1.3 77.2 - - - +
67I THR* 1.3 64.4 + - + +
68I TYR 3.6 0.4 - - - -
69I ASN* 5.5 0.9 - - - -
70I PRO* 3.3 19.6 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il