Contacts of the helix formed by residues 79 - 102 (chain j) in PDB entry 5GJQ
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 ILE 79 (chain j).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12i PHE* 4.5 10.8 - - + -
16i GLY 5.0 2.2 - - - +
18i LEU* 4.4 18.2 - - + -
21i ILE* 5.9 1.3 - - + -
151i SER* 5.3 8.3 - - - +
27j ALA* 4.1 22.2 - - + -
78j GLY* 1.3 73.3 - - - -
80j THR* 1.3 64.9 + - - +
81j SER* 3.3 23.1 + - - +
82j ASP* 3.4 16.6 + - - +
83j ALA* 3.2 4.9 + - - +
131j GLY* 2.9 34.9 + - - +
132j VAL* 3.2 20.8 - - - +
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Residues in contact with THR 80 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153i ALA* 3.1 26.1 - - - +
155i PHE* 5.5 5.4 - - + -
64j LYS* 6.4 2.0 - - - -
66j TYR* 4.5 3.1 + - - -
76j VAL* 5.7 5.4 - - + -
78j GLY 4.2 9.2 - - - +
79j ILE* 1.3 73.6 - - - +
81j SER* 1.3 61.9 + - - +
83j ALA* 3.1 12.2 + - - +
84j ASN* 2.9 34.4 + - - +
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Residues in contact with SER 81 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118i GLN* 3.8 11.1 - - - +
151i SER* 2.9 32.2 + - - -
152i GLY 3.7 17.7 - - - -
153i ALA* 3.9 2.0 - - - -
79j ILE* 3.3 11.8 - - - +
80j THR* 1.3 79.2 + - - +
82j ASP* 1.3 80.1 + - - +
84j ASN* 3.0 24.5 + - - +
85j VAL* 3.0 16.1 + - - +
128j ARG* 5.2 0.7 + - - -
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Residues in contact with ASP 82 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118i GLN* 3.6 5.1 + - - +
79j ILE* 3.4 22.8 + - - +
80j THR 3.3 0.2 - - - -
81j SER* 1.3 86.5 + - - +
83j ALA* 1.3 57.6 + - - +
85j VAL* 3.3 9.9 + - - +
86j LEU* 3.0 32.6 + - - +
128j ARG* 2.7 42.7 + - - -
130j PHE* 3.7 18.5 - - + -
131j GLY* 3.3 15.8 + - - -
132j VAL* 3.7 12.8 - - + -
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Residues in contact with ALA 83 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66j TYR* 4.5 6.5 - - + +
76j VAL* 3.5 42.2 - - + -
79j ILE 3.2 7.9 + - - +
80j THR* 3.1 17.4 + - - +
82j ASP* 1.3 77.7 - - - +
84j ASN* 1.3 51.3 + - - +
86j LEU* 3.9 4.1 - - - +
87j THR* 2.6 42.3 + - - +
132j VAL* 3.7 6.0 - - + +
134j LEU* 6.1 0.2 - - - -
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Residues in contact with ASN 84 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114i ALA* 5.3 1.8 - - - +
115i SER* 5.9 2.9 - - - +
152i GLY 4.2 6.9 + - - -
153i ALA* 5.0 1.8 - - - +
154i TYR* 3.6 33.7 + - - -
66j TYR* 2.8 29.5 + - - -
80j THR* 2.9 20.5 + - - +
81j SER* 3.0 14.7 + - - +
83j ALA* 1.3 75.8 - - - +
85j VAL* 1.3 62.6 + - + +
87j THR* 2.9 17.9 + - - -
88j ASN* 3.0 16.2 + - - +
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Residues in contact with VAL 85 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115i SER* 6.1 3.8 - - - +
118i GLN* 3.3 41.5 - - + +
81j SER 3.0 10.1 + - - +
82j ASP* 3.4 8.7 - - - +
84j ASN* 1.3 77.2 - - + +
86j LEU* 1.3 67.1 + - + +
88j ASN* 3.4 8.9 + - - +
89j GLU* 3.0 22.7 + - + +
130j PHE* 4.2 24.0 - - + -
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Residues in contact with LEU 86 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82j ASP 3.0 18.4 + - - +
83j ALA* 4.0 3.8 - - - +
85j VAL* 1.3 79.7 - - + +
87j THR* 1.3 58.9 + - - +
89j GLU* 3.3 5.5 + - + +
90j LEU* 2.9 33.0 + - - +
114j LEU* 3.9 28.6 - - + +
117j ILE* 4.2 11.7 - - + -
118j LYS* 3.9 20.9 - - + -
130j PHE* 3.8 49.1 - - + -
132j VAL* 4.0 20.6 - - + -
134j LEU* 4.4 8.7 - - + -
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Residues in contact with THR 87 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66j TYR* 3.4 52.6 - - + -
68j LEU* 4.3 4.3 - - + +
74j CYS* 4.0 14.8 - - - -
76j VAL* 5.5 0.7 - - + -
83j ALA* 2.6 29.2 + - + +
84j ASN* 2.9 17.3 + - - -
86j LEU* 1.3 70.6 - - - +
88j ASN* 1.3 63.2 + - - +
90j LEU* 3.2 10.8 + - + +
91j ARG* 2.9 32.8 + - - +
134j LEU* 5.0 5.4 - - + -
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Residues in contact with ASN 88 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115i SER* 5.9 1.0 + - - -
84j ASN 3.0 18.6 + - - +
85j VAL* 3.4 8.2 + - - +
87j THR* 1.3 74.8 + - - +
89j GLU* 1.3 68.1 + - - +
91j ARG* 3.1 14.0 + - - +
92j LEU* 3.1 32.1 + - - +
77q LYS* 2.8 36.2 + - - +
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Residues in contact with GLU 89 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85j VAL* 3.0 15.3 + - + +
86j LEU* 3.7 7.9 - - + +
88j ASN* 1.3 84.9 + - - +
90j LEU* 1.3 57.3 + - - +
92j LEU* 3.1 16.5 + - - +
93j ILE* 2.9 33.0 + - + +
96j ARG* 3.4 30.1 + - - -
114j LEU* 4.8 1.8 - - + -
117j ILE* 3.4 33.2 - - + +
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Residues in contact with LEU 90 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68j LEU* 3.9 28.0 - - + -
74j CYS* 4.6 0.7 - - - -
86j LEU 2.9 20.5 + - - +
87j THR* 3.4 15.7 - - - +
89j GLU* 1.3 71.2 - - - +
91j ARG* 1.3 67.7 + - - +
93j ILE* 3.2 8.5 + - + +
94j ALA* 3.0 24.0 + - - +
110j LEU* 3.6 36.3 - - + +
114j LEU* 3.5 40.8 - - + +
134j LEU* 4.0 16.2 - - + -
136j TYR* 4.1 11.0 - - + -
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Residues in contact with ARG 91 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111i GLN* 5.6 2.0 + - - -
66j TYR* 4.1 23.5 - - - -
67j LYS* 3.1 30.4 + - - +
68j LEU* 3.9 19.4 - - - +
87j THR* 2.9 23.1 + - - +
88j ASN* 3.1 12.2 + - - +
90j LEU* 1.3 75.8 - - - +
92j LEU* 1.3 64.8 + - - +
94j ALA* 3.2 4.0 + - - +
95j GLN* 2.9 28.2 + - - +
73q LEU* 4.0 13.2 - - + -
76q LEU* 3.4 60.7 + - + +
77q LYS* 3.7 22.1 + - - +
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Residues in contact with LEU 92 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88j ASN* 3.1 24.3 + - - +
89j GLU* 3.1 25.1 + - - +
91j ARG* 1.3 81.4 - - - +
93j ILE* 1.3 57.0 + - - +
95j GLN* 3.3 3.5 + - + +
96j ARG* 2.8 60.4 + - - +
69q PHE* 4.5 14.6 - - + -
73q LEU* 3.3 37.5 - - + -
77q LYS* 5.4 1.6 - - - +
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Residues in contact with ILE 93 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89j GLU* 2.9 34.1 + - + +
90j LEU* 3.6 9.2 - - - +
92j LEU* 1.3 75.4 - - - +
94j ALA* 1.3 64.0 + - - +
96j ARG* 3.0 22.5 + - - +
97j TYR* 3.0 22.5 + - + +
105j ILE* 4.2 9.2 - - + -
110j LEU* 3.5 16.8 - - + -
113j ALA* 3.7 43.7 - - + +
114j LEU* 4.1 5.8 - - + +
117j ILE* 4.3 6.7 - - + -
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Residues in contact with ALA 94 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68j LEU 4.2 15.0 - - - +
69j ASN* 4.4 14.1 + - + +
90j LEU 3.0 12.6 + - - +
91j ARG 3.5 7.6 - - - +
93j ILE* 1.3 78.3 - - - +
95j GLN* 1.3 61.0 + - - +
97j TYR* 3.3 4.2 + - - +
98j LEU* 3.0 26.0 + - - +
105j ILE* 3.8 29.7 + - + +
110j LEU* 4.3 9.0 - - + -
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Residues in contact with GLN 95 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68j LEU 5.1 4.4 + - - -
69j ASN* 4.1 18.8 - - - +
91j ARG 2.9 19.1 + - - +
92j LEU* 3.8 5.4 - - - +
94j ALA* 1.3 79.6 - - - +
96j ARG* 1.3 58.2 + - - +
98j LEU* 3.4 19.5 - - - +
99j LEU* 2.9 27.9 + - - +
69q PHE* 4.1 37.4 - - + +
72q ASN* 3.4 42.4 + - + +
73q LEU* 4.5 14.8 - - + +
76q LEU* 5.1 5.9 - - + +
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Residues in contact with ARG 96 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89j GLU* 3.4 26.5 + - - -
92j LEU* 2.8 44.9 + - - +
93j ILE* 3.0 26.8 + - + +
95j GLN* 1.3 73.4 - - - +
97j TYR* 1.3 66.4 + - - +
99j LEU* 3.2 8.8 + - + +
100j GLN* 2.9 26.6 + - - +
69q PHE* 4.3 17.6 - - + -
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Residues in contact with TYR 97 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93j ILE* 3.0 11.1 + - + +
94j ALA 3.6 7.9 - - - +
96j ARG* 1.3 77.0 - - - +
98j LEU* 1.3 57.6 + - - +
100j GLN* 3.1 2.4 + - - -
101j TYR* 2.9 65.7 + + + +
103j GLU* 3.2 37.6 + - + -
104j PRO 3.5 9.2 - - - -
105j ILE* 3.4 33.2 - - + -
106j PRO* 3.4 14.5 - - + +
109j GLN* 3.2 25.4 - - + -
67r TYR* 2.5 26.3 + + - -
75r LEU* 5.0 1.6 - - - +
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Residues in contact with LEU 98 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69j ASN* 5.6 4.9 - - - +
94j ALA 3.0 17.7 + - - +
95j GLN* 3.4 29.6 - - - +
96j ARG 3.2 0.2 - - - -
97j TYR* 1.3 78.0 - - + +
99j LEU* 1.3 55.5 + - - +
102j GLN* 2.8 47.4 + - - +
103j GLU* 3.7 35.2 - - - +
104j PRO* 4.4 9.0 - - + -
105j ILE 5.7 0.2 - - - +
68q LYS* 5.0 10.8 - - + -
69q PHE* 6.2 0.2 - - - -
72q ASN* 3.8 15.7 - - - +
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Residues in contact with LEU 99 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95j GLN 2.9 17.3 + - - +
96j ARG* 3.5 8.3 - - + +
98j LEU* 1.3 77.0 - - - +
100j GLN* 1.3 66.5 + - - +
102j GLN* 3.6 12.7 + - - +
65q GLN* 4.0 27.6 - - + +
66q ARG* 4.3 24.2 - - + +
69q PHE* 4.0 27.4 - - + -
82r ASN* 5.6 0.3 - - - +
86r ARG* 3.7 43.6 + - - +
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Residues in contact with GLN 100 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96j ARG 2.9 16.4 + - - +
97j TYR* 3.9 2.2 - - - +
99j LEU* 1.3 84.1 - - - +
101j TYR* 1.3 70.1 + - + +
82r ASN* 3.6 8.9 - - - +
83r PHE* 3.0 62.8 + - + -
86r ARG* 4.2 19.0 - - + +
87r ASN* 4.0 15.6 + - - +
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Residues in contact with TYR 101 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97j TYR* 2.9 64.5 + + + +
100j GLN* 1.3 80.4 - - + +
102j GLN* 1.3 69.8 + - - +
103j GLU* 3.1 4.5 + - + +
63r ASN 5.4 2.4 + - - -
67r TYR* 3.8 21.7 - + - +
75r LEU* 4.4 17.0 - - + -
78r THR* 5.3 0.5 - - - +
79r ALA* 3.5 50.8 + - + +
82r ASN* 4.0 5.7 + - - +
83r PHE* 3.4 40.8 - + + -
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Residues in contact with GLN 102 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98j LEU* 2.8 42.1 + - - +
99j LEU* 3.6 16.1 - - - +
101j TYR* 1.3 78.1 - - - +
103j GLU* 1.3 60.7 + - - +
65q GLN* 3.7 34.4 - - - +
68q LYS* 5.9 6.4 - - - +
78r THR* 5.3 5.5 - - + +
82r ASN* 3.3 34.1 - - + +
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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