Contacts of the helix formed by residues 77 - 106 (chain A) in PDB entry 1N1J
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 ALA 77 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ILE* 1.3 76.0 - - - +
78A LYS* 1.3 66.9 + - - +
79A ASP* 4.2 10.1 - - + +
80A ALA* 2.9 17.3 + - + +
81A LYS* 3.1 9.7 + - - +
95B THR* 3.6 16.4 - - + +
96B LEU 3.1 20.0 + - - +
97B GLN* 4.7 8.7 - - + -
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Residues in contact with LYS 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ILE* 5.1 9.0 - - + -
76A ILE 3.6 2.4 + - - -
77A ALA* 1.3 72.0 - - - +
79A ASP* 1.3 63.0 + - - +
81A LYS* 3.1 17.7 + - + +
82A GLU* 2.8 58.6 + - + +
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Residues in contact with ASP 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ALA* 3.1 7.6 - - + +
78A LYS* 1.3 81.4 - - - +
80A ALA* 1.3 56.3 + - - +
82A GLU* 3.5 14.7 + - - +
83A CYS* 3.0 22.2 + - - +
98B ARG* 2.9 56.5 + - - +
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Residues in contact with ALA 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A MET* 4.5 1.8 - - - -
76A ILE* 3.9 4.5 - - + -
77A ALA* 2.9 12.2 + - + +
79A ASP* 1.3 75.3 + - - +
81A LYS* 1.3 67.7 + - - +
83A CYS* 3.2 8.6 + - - +
84A VAL* 2.9 26.9 + - - +
96B LEU* 3.4 43.3 - - + +
97B GLN* 4.0 11.0 - - - -
98B ARG 4.4 4.0 - - - +
101B ILE* 3.6 2.4 - - + +
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Residues in contact with LYS 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ILE* 3.9 24.2 - - + +
62A VAL* 4.3 3.5 - - + +
63A ALA* 3.9 30.5 - - + +
66A MET* 4.1 13.2 - - - -
76A ILE* 3.6 42.1 + - + -
77A ALA 3.1 5.2 + - - +
78A LYS* 3.1 16.2 + - + +
80A ALA* 1.3 75.8 - - - +
82A GLU* 1.3 58.5 + - - +
84A VAL* 3.2 3.8 + - - +
85A GLN* 2.9 30.5 + - - +
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Residues in contact with GLU 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A TYR* 5.9 0.2 - - - -
59A ILE* 4.2 9.9 - - + +
78A LYS* 2.8 47.7 + - + +
79A ASP* 3.7 19.8 + - - +
81A LYS* 1.3 76.7 - - - +
83A CYS* 1.3 62.0 + - - +
85A GLN* 3.2 23.5 + - - +
86A GLU* 3.0 35.8 + - - +
98B ARG* 4.5 1.7 + - - +
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Residues in contact with CYS 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ASP 3.0 15.0 + - - +
80A ALA* 3.4 9.9 - - - +
81A LYS 3.2 0.2 - - - -
82A GLU* 1.3 76.5 - - - +
84A VAL* 1.3 57.1 + - - +
86A GLU* 3.1 10.2 + - - +
87A CYS* 2.9 30.6 + - - -
98B ARG* 3.6 25.5 - - + +
101B ILE* 3.7 26.0 - - + -
118B VAL* 3.6 40.8 - - - -
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Residues in contact with VAL 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A VAL* 3.6 20.6 - - + -
66A MET* 3.5 25.6 - - + -
80A ALA 2.9 16.7 + - - +
81A LYS 3.7 6.7 - - - +
83A CYS* 1.3 76.3 - - - +
85A GLN* 1.3 64.4 + - - +
87A CYS* 3.1 6.6 + - - +
88A VAL* 2.8 24.3 + - + +
77B ILE* 4.1 26.5 - - + -
80B LEU* 4.2 20.9 - - + -
81B THR* 4.7 4.3 - - - +
101B ILE* 3.8 14.6 - - + -
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Residues in contact with GLN 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A TYR* 3.6 38.7 - - + +
57A LEU* 2.8 29.7 + - - +
58A PRO* 4.5 0.2 - - - +
59A ILE* 3.3 34.8 + - - +
62A VAL* 4.0 17.0 - - + +
81A LYS 2.9 13.2 + - - +
82A GLU* 3.3 29.8 - - - +
84A VAL* 1.3 77.8 - - - +
86A GLU* 1.3 61.5 + - - +
88A VAL* 3.3 6.1 + - - +
89A SER* 3.2 19.4 + - - -
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Residues in contact with GLU 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A TYR* 3.9 31.4 + - + +
82A GLU* 3.0 22.8 + - - +
83A CYS* 3.3 7.1 - - - +
85A GLN* 1.3 77.3 - - - +
87A CYS* 1.3 63.2 + - - +
89A SER* 3.4 3.6 + - - -
90A GLU* 3.0 23.3 + - - +
98B ARG* 3.2 39.0 + - - -
117B ILE* 4.7 21.0 - - + +
118B VAL* 5.0 0.7 - - + +
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Residues in contact with CYS 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A CYS* 2.9 23.4 + - - +
84A VAL 3.1 6.7 + - - +
86A GLU* 1.3 77.9 - - - +
88A VAL* 1.3 57.5 + - - +
90A GLU* 3.2 3.3 + - - +
91A PHE* 2.8 28.2 + - - +
76B PHE* 3.7 9.2 - - + -
80B LEU* 3.8 28.3 - - + -
101B ILE* 4.5 0.7 - - - -
105B ILE* 4.5 4.3 - - - -
114B LEU* 4.0 27.1 - - + +
117B ILE* 5.0 1.3 - - - -
118B VAL* 3.7 28.0 - - - -
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Residues in contact with VAL 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LEU* 3.4 33.9 - - + -
62A VAL* 5.1 2.2 - - + -
84A VAL* 2.8 26.7 + - + +
85A GLN* 3.7 6.7 - - - +
86A GLU 3.3 0.2 - - - -
87A CYS* 1.3 69.0 - - - +
89A SER* 1.3 67.3 + - - +
91A PHE* 3.1 5.3 + - + +
92A ILE* 2.9 32.4 + - + +
73B ALA* 4.3 10.8 - - + -
76B PHE* 3.9 16.4 - - + -
77B ILE* 3.4 36.3 - - + -
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Residues in contact with SER 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ILE 2.8 26.7 + - - -
56A TYR* 3.6 16.4 - - - -
57A LEU 4.7 0.5 + - - -
85A GLN 3.2 9.3 + - - -
86A GLU 3.9 3.8 - - - -
88A VAL* 1.3 80.0 - - - +
90A GLU* 1.3 57.2 + - - +
92A ILE* 3.3 3.9 + - - +
93A SER* 3.0 34.1 + - - -
51B ILE* 3.5 25.3 - - - +
54B LEU* 6.1 1.3 - - - -
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Residues in contact with GLU 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A GLU 3.0 14.9 + - - +
87A CYS* 3.5 8.5 - - - +
89A SER* 1.3 76.2 - - - +
91A PHE* 1.3 58.2 + - - +
93A SER* 3.8 8.9 - - - -
94A PHE* 2.9 32.6 + - + +
113B PHE* 3.9 11.9 - - + +
114B LEU* 3.9 15.0 - - + -
117B ILE* 3.8 40.1 - - + +
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Residues in contact with PHE 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A CYS 2.8 13.7 + - - +
88A VAL* 3.3 11.7 - - + +
90A GLU* 1.3 73.5 - - - +
92A ILE* 1.3 73.8 + - + +
94A PHE* 3.3 2.4 + + - +
95A ILE* 3.1 44.1 + - + +
120A MET* 4.3 11.4 - - + -
125A PHE* 3.5 33.7 - + - -
128A TYR* 3.8 22.7 - + - -
69B PHE* 4.6 6.1 - + - -
72B ALA* 3.9 29.8 - - + -
73B ALA* 4.6 4.3 - - - -
76B PHE* 4.0 30.7 - + + -
113B PHE* 3.6 22.4 - + + -
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Residues in contact with ILE 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LEU* 4.9 3.4 - - + -
88A VAL* 2.9 34.2 + - + +
89A SER 3.3 4.2 + - - +
91A PHE* 1.3 81.2 - - + +
93A SER* 1.3 54.7 + - - +
96A THR* 2.7 38.3 + - - +
48B ILE* 4.5 21.3 - - + +
51B ILE* 4.0 33.7 - - + -
52B MET* 3.7 29.8 - - + +
69B PHE* 3.6 32.9 - - + +
73B ALA* 5.4 4.7 - - + -
----------------------------------------------------------
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Residues in contact with SER 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A SER* 3.0 19.5 + - - -
90A GLU* 3.8 11.7 - - - -
92A ILE* 1.3 73.8 - - - +
94A PHE* 1.3 60.8 + - - +
96A THR* 3.8 5.4 - - - -
97A SER* 2.9 37.6 + - - -
51B ILE* 4.2 17.1 + - - +
52B MET* 6.0 1.1 - - - +
54B LEU* 5.5 5.4 - - - +
55B ASP* 6.4 3.1 - - - -
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Residues in contact with PHE 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A GLU* 2.9 20.0 + - + +
91A PHE 3.5 3.8 - - - +
93A SER* 1.3 77.9 - - - +
95A ILE* 1.3 64.2 + - + +
97A SER* 3.5 10.7 + - - -
98A GLU* 3.5 8.1 + - - +
123A LEU* 3.5 40.0 - - + +
125A PHE* 3.7 31.6 - + - -
113B PHE* 3.6 47.6 - + + -
----------------------------------------------------------
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Residues in contact with ILE 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A PHE* 3.1 34.8 + - + +
94A PHE* 1.3 77.9 - - + +
96A THR* 1.3 59.2 + - - +
98A GLU 3.2 2.3 + - - -
99A ALA* 2.9 24.3 + - - +
116A ILE* 4.0 9.0 - - + +
119A ALA* 3.5 13.2 - - + +
120A MET* 3.9 30.5 - - + -
123A LEU* 3.6 15.7 - - + -
125A PHE* 3.6 37.0 - - + -
69B PHE* 3.7 24.9 - - + -
----------------------------------------------------------
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Residues in contact with THR 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ILE 2.7 26.9 + - - -
93A SER* 3.8 5.6 - - - -
95A ILE* 1.3 75.2 - - - +
97A SER* 1.3 57.8 + - - +
99A ALA* 3.6 6.8 - - + +
100A SER* 2.8 28.6 + - - -
111A ILE* 4.3 5.6 - - + -
116A ILE* 4.9 0.9 - - - -
52B MET* 3.6 37.6 - - + +
55B ASP* 5.4 2.0 - - + -
58B VAL* 3.8 25.6 - - + -
69B PHE* 3.4 20.9 - - - -
----------------------------------------------------------
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Residues in contact with SER 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A SER* 2.9 21.8 + - - -
94A PHE* 3.8 7.3 - - - -
95A ILE 3.3 0.2 - - - -
96A THR* 1.3 77.5 - - - +
98A GLU* 1.3 63.4 + - - +
100A SER* 3.3 6.2 + - - -
101A GLU* 3.2 19.6 + - - +
55B ASP* 3.4 23.0 + - - +
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Residues in contact with GLU 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A PHE 3.5 2.5 + - - +
95A ILE 3.2 7.9 + - - +
97A SER* 1.3 75.8 - - - +
99A ALA* 1.3 66.4 + - - +
101A GLU* 3.2 17.1 + - - +
102A ARG* 3.0 22.5 + - - +
118A PHE* 4.1 17.1 - - + -
119A ALA* 3.8 20.2 - - + -
122A THR* 4.1 15.1 - - + +
123A LEU* 3.7 33.1 - - + +
----------------------------------------------------------
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Residues in contact with ALA 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ILE 2.9 16.8 + - - +
96A THR* 3.2 4.7 + - - +
98A GLU* 1.3 76.3 - - - +
100A SER* 1.3 57.9 + - - +
102A ARG* 3.4 3.8 + - - +
103A CYS* 2.9 28.2 + - - +
111A ILE* 3.7 22.4 - - + +
115A ASP* 3.5 31.7 - - - +
116A ILE* 3.8 13.0 - - + -
119A ALA* 3.7 2.8 - - + +
----------------------------------------------------------
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Residues in contact with SER 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A THR 2.8 17.1 + - - -
97A SER* 3.5 7.4 - - - -
98A GLU 3.2 0.2 - - - -
99A ALA* 1.3 75.6 - - - +
101A GLU* 1.3 65.3 + - - +
103A CYS* 3.4 3.2 + - - +
104A HIS* 3.0 23.4 + - - +
111A ILE* 3.7 24.9 - - - +
55B ASP* 5.6 0.7 - - - -
57B ASP* 4.1 19.9 + - - +
58B VAL* 4.2 9.5 - - - +
----------------------------------------------------------
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Residues in contact with GLU 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A SER 3.2 9.4 + - - +
98A GLU* 3.2 22.3 + - - +
100A SER* 1.3 79.1 - - - +
102A ARG* 1.3 57.1 + - - +
104A HIS* 3.2 10.4 + - - +
105A GLN* 2.9 64.7 + - + +
----------------------------------------------------------
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Residues in contact with ARG 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A GLU* 3.0 13.7 + - - +
99A ALA* 3.6 10.1 - - - +
101A GLU* 1.3 78.4 - - - +
103A CYS* 1.3 62.0 + - - +
105A GLN* 3.1 9.2 + - - +
106A GLU* 3.0 60.7 + - + +
108A ARG* 5.3 0.2 - - - +
114A GLU 5.5 1.0 + - - -
115A ASP* 3.4 23.1 + - - +
118A PHE* 3.6 62.9 - - + +
----------------------------------------------------------
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Residues in contact with CYS 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ALA 2.9 14.9 + - - +
100A SER 3.5 6.7 - - - +
102A ARG* 1.3 76.6 - - - +
104A HIS* 1.3 60.1 + - - +
106A GLU* 3.1 8.8 + - - +
108A ARG* 3.0 54.3 + - - +
109A LYS* 3.6 7.0 - - - -
110A THR 3.6 31.6 - - - -
111A ILE* 3.7 9.0 - - + -
115A ASP* 3.4 21.5 - - - +
----------------------------------------------------------
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Residues in contact with HIS 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A SER 3.0 13.6 + - - +
101A GLU* 3.5 13.4 + - - +
103A CYS* 1.3 77.6 - - - +
105A GLN* 1.3 77.2 + - - +
107A LYS* 3.0 21.1 + - - +
108A ARG 3.9 9.6 - - - -
----------------------------------------------------------
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Residues in contact with GLN 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A GLU* 2.9 45.0 + - + +
102A ARG* 3.6 10.5 - - - +
104A HIS* 1.3 95.7 + - - +
106A GLU* 1.3 65.5 + - - +
107A LYS* 3.1 14.8 + - - +
----------------------------------------------------------
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Residues in contact with GLU 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ARG* 3.0 54.5 + - - +
103A CYS 3.1 2.4 + - - +
104A HIS 3.1 0.2 - - - -
105A GLN* 1.3 82.5 - - - +
107A LYS* 1.3 70.6 + - - +
108A ARG* 3.3 38.2 + - - +
----------------------------------------------------------
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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