Contacts of the helix formed by residues 80 - 103 (chain n) 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 LEU 80 (chain n).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13m TRP* 4.2 14.1 - - + -
19m ILE* 4.4 10.1 - - + -
22m ILE* 4.7 10.5 - - + -
120m THR* 6.0 0.2 - - - +
150m SER* 5.6 11.4 - - - +
152m ASN* 6.1 4.3 - - + +
29n ALA* 4.9 4.8 + - + +
79n GLY* 1.3 68.6 - - - -
81n LEU* 1.3 68.2 + - - +
82n ALA* 4.5 11.4 - - + +
83n ASP* 3.3 17.3 + - - +
84n ALA* 3.1 18.2 + - - +
129n ARG* 3.7 26.9 - - - +
132n GLY* 2.7 22.5 + - - +
133n CYS* 4.0 0.9 - - - +
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Residues in contact with LEU 81 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152m ASN* 3.6 28.9 - - - +
63n ASN* 3.6 24.0 - - + +
64n LYS 4.8 3.6 - - - +
65n ARG* 4.1 34.1 - - + +
67n PHE* 5.4 2.7 - - + -
77n VAL* 4.2 16.8 - - + -
79n GLY 3.0 7.0 + - - +
80n LEU* 1.3 74.5 - - - +
82n ALA* 1.3 65.8 + - - +
84n ALA* 2.9 7.5 + - + +
85n ARG* 2.9 54.4 + - + +
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Residues in contact with ALA 82 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117m GLN* 3.9 20.6 - - + +
120m THR* 5.5 1.6 - - - +
150m SER 3.5 24.9 - - - +
151m ALA 4.1 16.4 - - - +
152m ASN* 4.3 6.4 - - + +
80n LEU* 4.5 9.4 - - + +
81n LEU* 1.3 77.4 - - - +
83n ASP* 1.3 66.9 + - - +
85n ARG* 3.1 10.5 + - - +
86n SER* 3.0 22.9 + - - -
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Residues in contact with ASP 83 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117m GLN* 3.3 17.0 + - - +
120m THR* 4.7 1.0 + - - -
80n LEU* 3.3 20.3 + - - +
81n LEU 3.2 0.2 - - - -
82n ALA* 1.3 82.8 - - - +
84n ALA* 1.3 59.0 + - - +
86n SER* 2.5 24.6 + - - -
87n LEU* 2.9 17.8 + - - +
129n ARG* 2.3 38.3 + - - -
131n PHE* 3.8 16.3 - - + -
132n GLY* 2.8 19.3 + - - +
133n CYS* 3.9 11.9 - - - -
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Residues in contact with ALA 84 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67n PHE* 4.6 3.4 - - + -
75n MET* 4.0 4.9 - - - +
77n VAL* 3.7 37.9 - - + -
78n ALA 5.4 1.3 - - - +
80n LEU 3.1 9.3 + - - +
81n LEU* 2.9 19.6 + - + +
83n ASP* 1.3 79.5 - - - +
85n ARG* 1.3 56.2 + - - +
87n LEU* 3.3 5.0 + - - +
88n ALA* 2.9 27.0 + - - +
133n CYS* 3.9 14.7 - - + -
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Residues in contact with ARG 85 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113m GLY* 6.2 0.2 - - - -
151m ALA 4.6 1.7 + - - -
152m ASN* 2.9 31.1 + - - +
153m TYR* 3.1 68.3 + - - +
63n ASN* 3.9 15.0 - - - +
64n LYS 4.6 6.0 + - - +
67n PHE* 4.0 22.0 - - + -
81n LEU* 2.9 42.9 + - + +
82n ALA* 3.1 9.4 + - - +
84n ALA* 1.3 72.7 - - - +
86n SER* 1.3 65.9 + - - +
88n ALA* 3.0 9.1 + - - +
89n ASP* 2.9 29.4 + - - +
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Residues in contact with SER 86 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114m SER* 6.5 1.6 - - - +
117m GLN* 3.7 23.2 + - - -
121m GLN* 5.7 0.2 - - - -
82n ALA 3.0 10.4 + - - -
83n ASP* 2.5 27.9 + - - -
85n ARG* 1.3 75.9 - - - +
87n LEU* 1.3 60.1 + - - +
89n ASP* 3.1 11.1 + - - +
90n ILE* 2.9 38.6 + - - +
131n PHE* 3.7 14.9 - - - -
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Residues in contact with LEU 87 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75n MET* 4.2 12.3 - - + +
83n ASP 2.9 10.8 + - - +
84n ALA* 3.7 5.6 - - - +
86n SER* 1.3 81.1 + - - +
88n ALA* 1.3 57.8 + - - +
90n ILE* 3.4 14.9 + - + +
91n ALA* 2.9 29.3 + - - +
115n VAL* 4.9 7.8 - - + +
118n TYR* 4.4 5.4 - - + -
119n VAL* 3.8 18.2 - - + -
131n PHE* 3.7 43.7 - - + -
133n CYS* 3.2 32.8 - - - +
135n PHE* 3.6 21.8 - - + -
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Residues in contact with ALA 88 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67n PHE* 4.1 25.6 - - + -
69n VAL* 4.6 2.5 - - + +
75n MET* 3.9 23.3 - - - +
84n ALA 2.9 14.3 + - - +
85n ARG* 3.2 10.8 - - - +
87n LEU* 1.3 75.4 - - - +
89n ASP* 1.3 63.4 + - - +
91n ALA* 3.3 3.1 + - - +
92n ARG* 2.9 39.0 + - - +
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Residues in contact with ASP 89 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114m SER* 3.7 18.9 + - - -
85n ARG* 2.9 20.3 + - - +
86n SER* 3.1 10.3 + - - +
88n ALA* 1.3 76.3 - - - +
90n ILE* 1.3 65.0 + - + +
92n ARG* 3.3 29.9 + - - +
93n GLU* 3.0 23.4 + - - +
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Residues in contact with ILE 90 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86n SER* 2.9 35.1 + - - +
87n LEU* 3.6 18.4 - - + +
88n ALA 3.3 0.2 - - - -
89n ASP* 1.3 75.8 - - - +
91n ALA* 1.3 66.2 + - - +
93n GLU* 3.2 6.6 + - - +
94n GLU* 2.9 25.3 + - + +
115n VAL* 4.7 11.2 - - + -
118n TYR* 3.4 61.5 - - + +
131n PHE* 4.7 3.6 - - + -
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Residues in contact with ALA 91 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69n VAL* 3.8 26.9 - - + -
75n MET* 4.9 3.4 - - + -
87n LEU 2.9 18.2 + - - +
88n ALA* 3.5 5.6 - - - +
90n ILE* 1.3 76.8 - - - +
92n ARG* 1.3 63.0 + - - +
94n GLU* 3.1 3.9 + - - +
95n ALA* 3.0 21.7 + - - +
111n LEU* 3.6 8.5 - - + +
115n VAL* 3.9 26.0 - - + -
135n PHE* 6.1 0.4 - - + -
137n LEU* 5.4 3.6 - - + -
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Residues in contact with ARG 92 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67n PHE* 5.4 9.2 - - - -
68n ASN 2.9 25.8 + - - +
69n VAL* 3.3 28.1 - - - +
88n ALA* 2.9 23.2 + - - +
89n ASP* 3.4 30.4 + - - +
91n ALA* 1.3 76.0 - - - +
93n GLU* 1.3 57.7 + - - +
95n ALA* 3.3 2.9 + - - +
96n SER* 2.9 29.0 + - - -
73u ASP* 5.0 8.5 + - - +
76u LEU* 3.3 33.8 + - + +
77u LEU* 3.1 38.0 - - - +
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Residues in contact with GLU 93 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89n ASP 3.0 15.8 + - - +
90n ILE* 3.7 7.0 - - - +
91n ALA 3.2 0.2 - - - -
92n ARG* 1.3 72.5 - - - +
94n GLU* 1.3 66.7 + - - +
96n SER* 3.6 6.0 - - - -
97n ASN* 2.9 52.0 + - - +
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Residues in contact with GLU 94 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90n ILE* 2.9 17.7 + - + +
91n ALA* 3.1 9.8 + - - +
93n GLU* 1.3 77.3 - - - +
95n ALA* 1.3 57.1 + - - +
97n ASN* 3.5 10.1 + - - +
98n PHE* 3.0 29.6 + - - +
106n ILE* 4.7 5.1 - - + +
110n HIS* 5.5 1.7 - - - -
111n LEU* 4.1 13.0 - - + -
114n ARG* 2.7 66.6 + - + +
115n VAL* 4.8 3.1 - - + -
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Residues in contact with ALA 95 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69n VAL* 4.6 7.0 - - + +
70n ASP* 3.4 36.6 - - + +
91n ALA 3.0 12.7 + - - +
92n ARG* 3.6 8.5 - - - +
94n GLU* 1.3 76.6 - - - +
96n SER* 1.3 65.0 + - - +
98n PHE* 3.2 3.3 + - - +
99n ARG* 3.0 22.6 + - - +
106n ILE* 3.8 25.1 + - + +
111n LEU* 4.4 2.0 - - + +
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Residues in contact with SER 96 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92n ARG 2.9 17.9 + - - -
93n GLU* 3.6 8.5 - - - -
94n GLU 3.3 0.2 - - - -
95n ALA* 1.3 75.6 - - - +
97n ASN* 1.3 68.9 + - - +
99n ARG* 3.0 14.9 + - - +
100n SER* 3.0 16.6 + - - -
69u GLN* 2.9 43.8 + - - +
72u ILE* 6.4 0.2 - - - -
73u ASP* 4.8 4.2 + - - -
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Residues in contact with ASN 97 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93n GLU* 2.9 44.6 + - - +
94n GLU* 3.9 9.9 + - - +
96n SER* 1.3 82.7 + - - +
98n PHE* 1.3 62.9 + - - +
100n SER* 3.3 5.5 + - - +
101n ASN* 3.0 40.3 + - - +
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Residues in contact with PHE 98 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94n GLU* 3.0 16.2 + - - +
95n ALA 3.5 8.5 - - - +
96n SER 3.1 0.2 - - - -
97n ASN* 1.3 77.5 - - - +
99n ARG* 1.3 63.4 + - - +
101n ASN* 5.0 0.4 - - - +
102n PHE* 2.9 43.5 + + + +
104n TYR* 3.7 31.6 - + - -
106n ILE* 3.5 27.1 - - + -
107n PRO* 3.6 24.9 - - + -
110n HIS* 3.3 34.8 - + - -
66o HIS* 3.1 37.7 - + - -
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Residues in contact with ARG 99 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70n ASP* 3.0 40.1 + - - -
71n ARG* 3.8 30.3 - - - +
95n ALA 3.0 11.6 + - - +
96n SER* 3.0 10.1 + - - +
98n PHE* 1.3 77.1 - - - +
100n SER* 1.3 59.8 + - - +
103n GLY* 2.7 38.1 + - - +
104n TYR 3.7 19.1 - - - +
105n ASN* 4.1 19.9 + - - +
106n ILE 5.7 0.4 - - - +
69u GLN* 3.0 26.5 + - - +
72u ILE* 3.1 28.7 - - - +
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Residues in contact with SER 100 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96n SER* 3.0 15.5 + - - -
97n ASN* 3.3 6.5 + - - -
99n ARG* 1.3 80.0 - - - +
101n ASN* 1.3 63.4 + - - +
103n GLY* 4.8 1.0 + - - -
81o SER* 5.9 1.0 - - - -
84o LYS* 4.9 1.4 + - - -
85o GLU* 3.8 20.7 - - - +
65u GLN* 3.8 35.0 + - - +
69u GLN* 4.0 18.2 + - - +
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Residues in contact with ASN 101 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97n ASN* 3.0 30.4 + - - +
100n SER* 1.3 83.5 - - - +
102n PHE* 1.3 70.8 + - + +
81o SER* 4.6 4.2 - - - +
82o LEU* 2.7 39.2 + - + +
85o GLU* 4.6 13.5 - - - +
89o ARG* 5.6 5.9 + - - -
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Residues in contact with PHE 102 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98n PHE* 2.9 54.1 + + + +
101n ASN* 1.3 92.7 - - + +
103n GLY* 1.3 61.7 + - - +
104n TYR* 3.4 12.8 - - + -
110n HIS* 5.7 1.1 - + - -
62o GLN* 5.0 5.8 - - + -
66o HIS* 3.3 39.5 - + + -
77o HIS* 4.4 1.4 + - - -
78o THR* 3.4 42.5 - - + -
81o SER* 4.0 7.9 + - - -
82o LEU* 3.9 23.6 - - + -
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Residues in contact with GLY 103 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99n ARG* 2.7 29.8 + - - +
100n SER 4.6 1.3 - - - -
102n PHE* 1.3 72.8 - - - +
104n TYR* 1.3 58.7 + - - +
77o HIS* 4.2 16.5 - - - -
81o SER* 4.2 12.6 - - - -
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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
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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) + - + + + + + -
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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