Contacts of the helix formed by residues 80 - 103 (chain A) in PDB entry 3N6J
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 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A ARG* 4.3 10.3 - - + -
77A PRO* 3.0 37.5 + - + +
79A SER* 1.3 82.1 - - - +
81A LEU* 1.3 59.8 + - - +
82A ASN* 3.3 2.7 - - - -
83A LYS* 3.0 27.3 + - + +
84A ILE* 3.0 38.0 + - + +
131B VAL* 3.6 23.8 - - + -
135B GLU* 3.7 17.9 - - + +
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Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ILE 3.4 18.7 + - - +
79A SER 3.5 4.1 - - - +
80A ILE* 1.3 72.2 - - - +
82A ASN* 1.3 90.7 + - - +
83A LYS 3.0 1.6 - - - -
84A ILE* 3.9 11.3 - - - +
85A VAL* 3.0 30.3 + - + +
118A GLU* 5.1 3.6 - - + +
121A LEU* 3.4 53.8 - - + +
122A LEU* 4.2 16.6 - - + +
125A MSE 4.4 19.5 - - + -
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Residues in contact with ASN 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A SER 5.3 1.6 + - - -
80A ILE* 3.3 1.5 - - - -
81A LEU* 1.3 91.9 - - - +
83A LYS* 1.3 57.2 - - - +
85A VAL* 4.0 5.4 - - - +
86A ASN* 3.2 19.8 + - - +
118A GLU* 5.8 0.3 - - - +
321A THR* 5.1 10.6 - - - +
135B GLU 2.9 28.2 + - - +
136B LEU* 3.7 21.6 + - - +
138B GLY 3.7 21.1 + - - +
139B PRO* 3.0 20.3 - - - +
140B GLY* 4.1 0.7 - - - +
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Residues in contact with LYS 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ILE* 3.0 30.4 + - + +
81A LEU 3.0 0.4 - - - -
82A ASN* 1.3 75.1 - - - +
84A ILE* 1.3 68.2 + - - +
85A VAL 3.0 1.1 - - - -
86A ASN* 2.8 14.0 + - - -
87A ASP* 2.8 36.0 + - - +
135B GLU* 3.4 34.0 + - - +
139B PRO 4.1 6.5 - - - +
141B LYS* 3.3 40.7 + - - +
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Residues in contact with ILE 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ILE* 4.3 11.2 - - + -
72A HIS* 3.7 21.6 - - + +
73A VAL* 4.1 17.5 - - + +
76A ARG* 4.1 23.8 - - + -
77A PRO 3.9 14.1 - - - +
80A ILE* 3.0 32.7 + - + +
81A LEU* 3.8 11.2 - - - +
83A LYS* 1.3 77.0 - - - +
85A VAL* 1.3 60.0 + - - +
87A ASP* 4.0 10.9 + - - +
88A MSE 3.7 16.8 + - - +
117A LEU* 4.3 11.0 - - + +
121A LEU* 4.3 15.0 - - + -
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Residues in contact with VAL 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A LEU* 3.0 19.2 + - + +
82A ASN* 4.0 5.6 - - - +
83A LYS 3.0 0.8 - - - -
84A ILE* 1.3 76.1 - - - +
86A ASN* 1.3 62.9 + - + +
88A MSE 3.3 8.0 + - - +
89A HIS* 3.0 25.5 + - + +
114A VAL* 3.7 22.7 - - + +
117A LEU* 4.7 6.7 - - + -
118A GLU* 3.8 53.6 - - + +
121A LEU* 4.2 11.9 - - + -
319A THR* 5.4 2.9 - - + -
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Residues in contact with ASN 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A ASN 3.2 18.8 + - - +
83A LYS* 2.8 10.5 + - - +
85A VAL* 1.3 72.9 - - - +
87A ASP* 1.3 64.9 + - - +
89A HIS* 3.3 18.5 + - - +
90A ASN* 3.0 44.2 + - - +
139B PRO* 3.4 36.7 - - - +
142B GLN* 3.9 12.5 + - - +
360B PRO* 5.9 0.7 - - - +
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Residues in contact with ASP 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A LYS* 2.8 41.6 + - - +
84A ILE* 4.0 9.1 + - - +
86A ASN* 1.3 78.5 - - - +
88A MSE 1.3 61.4 + - - +
90A ASN* 4.1 3.7 + - - +
91A GLY* 3.8 12.3 + - - -
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Residues in contact with MSE 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ALA 3.9 21.5 - - - +
66A LEU* 4.4 5.6 - - + -
69A ALA* 4.0 16.4 - - + -
84A ILE 3.7 9.7 + - - +
85A VAL 3.3 10.5 + - - +
87A ASP* 1.3 77.1 - - - +
89A HIS* 1.3 67.8 + - - +
91A GLY* 3.1 11.3 + - - -
92A TYR* 3.3 39.3 + - + -
113A ALA* 3.8 30.5 - - + -
114A VAL* 3.8 22.7 - - + +
117A LEU* 3.6 28.5 - - - -
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Residues in contact with HIS 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A VAL* 3.0 19.1 + - + +
86A ASN* 3.3 16.5 + - - +
88A MSE 1.3 73.9 - - - +
90A ASN* 1.3 54.9 + - - +
92A TYR* 2.8 24.8 + - + -
93A LEU* 2.8 40.7 + - + +
111A VAL* 3.3 32.1 - - + +
114A VAL* 4.2 14.0 - - + +
318A TRP 5.7 2.0 - - - -
319A THR* 4.5 20.7 - - + +
332B GLU* 5.9 3.6 - - - -
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Residues in contact with ASN 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ASN* 3.0 36.6 + - - +
87A ASP* 4.4 3.4 - - - +
89A HIS* 1.3 77.2 - - - +
91A GLY* 1.3 61.5 + - - +
92A TYR 3.3 0.7 + - - -
93A LEU* 3.5 26.3 + - + +
94A ASP* 4.0 7.8 + - - +
142B GLN* 5.5 2.8 + - - -
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Residues in contact with GLY 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ASP 3.8 7.0 + - - -
88A MSE 3.1 9.0 + - - -
89A HIS 3.0 1.4 + - - -
90A ASN* 1.3 78.0 - - - +
92A TYR* 1.3 68.3 + - - +
94A ASP* 4.8 7.3 + - - +
95A ALA* 5.1 3.1 + - - +
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Residues in contact with TYR 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ALA* 3.6 31.0 + - + +
68A GLU* 3.3 26.5 + - - +
69A ALA* 5.9 0.6 - - + +
88A MSE 3.3 50.2 + - + +
89A HIS* 2.8 12.7 + - + +
91A GLY* 1.3 78.0 - - - +
93A LEU* 1.3 62.9 + - - +
94A ASP 3.3 2.2 - - - -
95A ALA* 3.6 8.1 + - + +
96A ASP* 3.2 29.0 + - - +
110A ARG* 3.8 40.2 - - + -
111A VAL* 5.4 1.1 - - + +
114A VAL* 4.4 9.9 - - + -
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Residues in contact with LEU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A HIS* 2.8 37.5 + - + +
90A ASN* 3.5 19.8 + - + +
92A TYR* 1.3 77.1 - - - +
94A ASP* 1.3 67.3 + - + +
96A ASP* 3.7 5.7 + - - +
97A TYR* 3.2 56.4 + - + +
111A VAL* 5.9 0.9 - - - -
332B GLU* 5.8 6.1 - - + +
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Residues in contact with ASP 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ASN 4.0 7.4 + - - +
91A GLY 4.9 5.2 - - - +
92A TYR 3.3 0.2 - - - -
93A LEU* 1.3 86.3 - - + +
95A ALA* 1.3 63.4 + - - +
96A ASP 3.4 0.2 + - - -
97A TYR* 3.6 7.6 + - - +
98A ASP* 3.5 18.9 + - - +
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Residues in contact with ALA 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A GLY 5.1 2.2 + - - +
92A TYR* 3.6 13.9 + - + +
93A LEU 3.5 0.2 - - - -
94A ASP* 1.3 80.0 - - - +
96A ASP* 1.3 58.6 + - - +
98A ASP* 3.2 10.2 + - - +
99A THR* 3.0 33.2 + - + +
110A ARG* 3.6 28.0 - - - +
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Residues in contact with ASP 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A TYR 3.2 18.3 + - - +
93A LEU* 4.0 6.7 - - - +
94A ASP 3.3 0.4 - - - -
95A ALA* 1.3 74.4 - - - +
97A TYR* 1.3 60.3 + - - +
99A THR* 3.7 5.0 + - - -
100A PHE* 3.0 33.3 + - - +
109A LEU* 3.7 16.9 - - + +
110A ARG* 3.2 47.7 + - - +
111A VAL* 3.4 29.8 + - + +
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Residues in contact with TYR 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A LEU* 3.2 51.3 + - + +
94A ASP* 3.9 7.4 - - - +
95A ALA 3.5 0.4 - - - -
96A ASP* 1.3 75.1 - - - +
98A ASP* 1.3 65.0 + - - +
100A PHE* 4.2 3.3 - - - +
101A GLY* 3.3 17.5 + - - -
295A ASN* 3.5 33.5 + - + +
297A ARG* 3.4 57.2 + - - +
298A GLU* 5.8 1.3 - - + -
332B GLU* 6.1 1.4 - - - +
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Residues in contact with ASP 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A ASP* 3.5 11.8 + - - +
95A ALA* 3.2 13.6 + - - +
97A TYR* 1.3 80.3 - - - +
99A THR* 1.3 55.2 + - + +
101A GLY 3.8 0.2 - - - -
102A LYS* 2.8 52.4 + - - +
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Residues in contact with THR 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A ALA* 3.0 15.8 + - + +
96A ASP* 3.7 5.7 + - - -
98A ASP* 1.3 77.0 - - + +
100A PHE* 1.3 56.2 + - - +
102A LYS* 4.0 14.8 - - - +
103A GLY 2.5 28.1 + - - +
104A ALA* 2.7 20.1 - - - +
108A GLU* 5.5 4.4 + - - -
109A LEU* 3.7 20.3 - - - +
110A ARG* 3.5 23.0 + - - +
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Residues in contact with PHE 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A ASP 3.0 18.9 + - - +
97A TYR* 4.3 4.3 - - - +
99A THR* 1.3 80.4 + - - +
101A GLY* 1.3 60.4 + - - +
103A GLY 3.7 1.7 - - - +
104A ALA* 3.3 37.9 + - - +
106A THR* 4.0 22.7 - - - -
109A LEU* 3.8 24.9 - - + -
291A MSE 4.2 11.7 - - + -
294A THR* 3.4 39.3 - - + -
295A ASN* 5.5 2.2 - - - -
298A GLU* 3.6 20.9 - - - -
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Residues in contact with GLY 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A TYR 3.3 13.7 + - - -
98A ASP 4.0 1.6 - - - -
100A PHE* 1.3 75.3 - - - +
102A LYS* 1.3 65.4 + - - +
103A GLY 3.5 6.2 - - - +
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Residues in contact with LYS 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A ASP* 2.8 34.4 + - - +
99A THR* 4.0 11.0 - - - +
101A GLY* 1.3 76.1 - - - +
103A GLY* 1.3 63.4 + - - +
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Residues in contact with GLY 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A THR* 2.5 15.2 + - - +
100A PHE 3.7 5.1 - - - +
101A GLY 3.5 8.1 - - - +
102A LYS* 1.3 81.7 - - - +
104A ALA* 1.3 60.0 + - - -
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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
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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