Contacts of the helix formed by residues 90 - 119 (chain A) in PDB entry 1JIG
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 SER 90 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A THR* 5.8 2.7 - - - -
88A LYS 3.9 0.8 + - - -
89A GLU* 1.3 76.6 - - - +
91A ALA* 1.3 65.4 + - - +
92A GLU* 3.5 11.8 + - - +
93A GLU* 2.9 28.3 + - - +
94A MET* 3.0 23.3 + - - +
147D LYS* 5.8 5.6 - - - -
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Residues in contact with ALA 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A VAL* 5.2 1.1 - - + -
33A THR* 3.7 28.3 + - - +
34A GLY* 5.7 0.4 - - - -
36A HIS* 5.5 4.5 - - + -
40A LEU* 3.7 24.9 - - + +
90A SER* 1.3 74.2 - - - +
92A GLU* 1.3 62.6 + - - +
94A MET* 3.3 13.5 + - - +
95A VAL* 3.1 28.7 + - - +
145A PHE* 6.0 2.0 - - + -
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Residues in contact with GLU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A SER* 3.5 9.9 + - - +
91A ALA* 1.3 78.9 - - - +
93A GLU* 1.3 75.3 + - - +
95A VAL* 2.7 28.2 - - - +
96A GLN* 3.0 29.3 + - + +
145A PHE* 6.0 1.3 - - - -
146A LEU* 4.1 15.5 - - + -
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Residues in contact with GLU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A GLU* 3.2 24.4 - - + +
90A SER* 2.9 26.2 + - - +
92A GLU* 1.3 95.2 - - - +
94A MET* 1.3 54.9 + - - +
96A GLN* 3.4 6.2 + - - +
97A THR* 2.6 41.6 + - - +
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Residues in contact with MET 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR* 3.5 42.8 - - + -
31A TYR* 3.6 40.8 - - + +
32A VAL* 3.2 30.3 - - - +
44A PHE* 4.2 7.0 - - + -
88A LYS 5.7 0.4 - - - +
89A GLU* 3.5 35.9 - - + +
90A SER 3.0 15.2 + - - +
91A ALA* 3.6 9.2 - - - +
93A GLU* 1.3 77.8 - - - +
95A VAL* 1.3 62.5 + - - +
97A THR* 3.3 0.9 + - - -
98A LEU* 3.0 31.7 + - - +
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Residues in contact with VAL 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 4.1 30.3 - - + -
44A PHE* 4.2 7.4 - - + -
91A ALA 3.1 13.7 + - - +
92A GLU* 2.7 26.2 - - - +
94A MET* 1.3 76.9 - - - +
96A GLN* 1.3 60.0 + - - +
98A LEU* 3.2 9.6 + - - +
99A VAL* 2.9 33.6 + - - +
142A LEU* 4.3 19.5 - - + +
145A PHE* 4.3 13.5 - - + -
146A LEU* 3.1 31.9 - - + -
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Residues in contact with GLN 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A GLU* 3.0 34.4 + - + +
93A GLU* 3.8 6.3 - - - +
95A VAL* 1.3 77.2 - - - +
97A THR* 1.3 57.5 + - - +
99A VAL* 3.2 8.5 + - - +
100A ASN* 2.9 42.0 + - - +
146A LEU* 3.0 38.1 - - + +
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Residues in contact with THR 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LYS* 3.4 16.4 - - - +
28A TYR* 3.5 21.6 + - + +
83A ASN* 4.9 5.6 - - - +
89A GLU* 4.9 2.9 + - - +
93A GLU* 2.6 27.9 + - - +
94A MET 3.5 4.3 - - - -
96A GLN* 1.3 76.8 - - - +
98A LEU* 1.3 53.6 + - - +
100A ASN* 3.2 11.7 + - + +
101A ASP* 2.7 49.9 + - - +
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Residues in contact with LEU 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU* 5.5 3.8 - - + -
24A LYS* 5.1 4.7 - - + -
25A LEU* 4.0 21.1 - - + -
28A TYR* 3.3 33.7 - - + -
44A PHE* 3.3 40.2 - - + -
47A PHE* 4.4 8.1 - - + -
94A MET 3.0 14.7 + - - +
95A VAL* 3.2 6.7 + - - +
97A THR* 1.3 75.2 - - - +
99A VAL* 1.3 56.9 + - - +
101A ASP* 4.2 13.0 - - + +
102A TYR* 2.7 54.4 + - + +
142A LEU* 5.3 5.8 - - + -
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Residues in contact with VAL 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A VAL 2.9 21.6 + - - +
96A GLN* 3.5 13.7 - - - +
98A LEU* 1.3 75.4 - - - +
100A ASN* 1.3 61.2 + - - +
102A TYR* 3.8 5.6 - - - +
103A SER* 2.8 46.3 + - - +
139A VAL* 4.3 11.1 - - + +
142A LEU* 3.6 28.3 - - + -
143A SER* 3.7 26.2 - - - +
146A LEU* 4.4 6.3 - - + -
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Residues in contact with ASN 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A GLN* 2.9 26.1 + - - +
97A THR* 3.3 11.9 - - + +
99A VAL* 1.3 85.1 - - - +
101A ASP* 1.3 59.6 + - - +
103A SER* 3.4 5.9 + - - -
104A ALA* 3.0 30.1 + - - +
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Residues in contact with ASP 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU* 4.5 17.5 - - + +
24A LYS* 2.7 33.4 + - - +
82A VAL* 4.9 13.8 - - + +
83A ASN* 3.3 19.1 + - - -
97A THR* 2.7 29.5 + - - +
98A LEU* 3.8 9.4 - - - +
100A ASN* 1.3 73.3 - - - +
102A TYR* 1.3 67.9 + - + +
104A ALA* 3.3 5.7 + - - +
105A LEU* 3.0 29.9 + - + +
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Residues in contact with TYR 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A TRP* 5.6 3.6 - + - -
21A LEU* 4.9 14.6 - - + -
25A LEU* 4.1 10.0 - - + +
47A PHE* 3.3 46.6 + + - +
98A LEU* 2.7 38.9 + - + +
99A VAL* 4.9 0.9 - - - -
101A ASP* 1.3 75.6 - - + +
103A SER* 1.3 53.1 + - - +
105A LEU* 3.1 13.3 + - + +
106A ILE* 2.7 39.6 + - - +
135A LEU* 3.8 32.0 - - + +
138A HIS* 3.8 35.5 - + + -
139A VAL* 3.6 19.3 - - + -
142A LEU* 5.3 3.8 - - + -
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Residues in contact with SER 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A VAL* 2.8 31.8 + - - +
100A ASN* 3.5 8.1 - - - -
102A TYR* 1.3 77.6 - - - +
104A ALA* 1.3 61.4 + - - +
106A ILE* 3.2 11.1 + - - +
107A GLN* 3.1 25.6 + - - +
139A VAL* 4.1 11.2 - - - +
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Residues in contact with ALA 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A SER* 6.1 1.3 - - - +
82A VAL* 6.4 1.1 - - + -
100A ASN 3.0 17.2 + - - +
101A ASP* 3.7 6.7 - - - +
103A SER* 1.3 72.7 - - - +
105A LEU* 1.3 63.7 + - + +
107A GLN* 3.1 10.9 + - - +
108A GLU* 2.9 33.7 + - + +
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Residues in contact with LEU 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLN* 4.1 5.4 - - - +
17A ASN* 3.7 28.5 - - + +
18A TRP* 4.3 23.1 - - + +
21A LEU* 4.3 21.3 - - + -
81A SER* 4.9 2.5 - - - +
82A VAL* 3.9 18.2 - - + -
101A ASP 3.0 24.0 + - - +
102A TYR* 3.1 15.9 + - + +
104A ALA* 1.3 75.2 - - + +
106A ILE* 1.3 57.6 + - - +
108A GLU* 3.1 8.7 + - + +
109A LEU* 2.7 43.3 + - + +
135A LEU* 3.7 16.8 - - + -
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Residues in contact with ILE 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A TYR 2.7 20.9 + - - +
103A SER* 3.3 12.6 - - - +
105A LEU* 1.3 76.1 - - - +
107A GLN* 1.3 62.8 + - - +
109A LEU* 3.3 5.8 + - - +
110A LYS* 3.0 53.2 + - + +
132A HIS* 3.3 40.0 - - + +
135A LEU* 3.3 23.1 - - + +
136A GLU* 3.4 22.9 - - + +
139A VAL* 5.0 3.4 - - + -
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Residues in contact with GLN 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A SER 3.1 12.2 + - - +
104A ALA* 3.1 12.6 + - - +
106A ILE* 1.3 83.2 - - + +
108A GLU* 1.3 62.4 + - + +
110A LYS* 3.5 27.3 + - - +
111A GLU* 3.3 33.2 + - - +
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Residues in contact with GLU 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LYS* 3.2 24.7 - - + +
14A GLN* 3.5 22.4 + - - +
17A ASN* 4.2 1.2 + - - -
81A SER* 2.8 28.9 + - - -
104A ALA* 3.0 19.0 - - - +
105A LEU* 3.1 15.2 + - + +
107A GLN* 1.3 74.5 - - + +
109A LEU* 1.3 60.9 + - - +
111A GLU* 3.3 14.9 + - - +
112A GLY* 2.8 26.9 + - - -
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Residues in contact with LEU 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLN* 4.3 14.6 - - + +
18A TRP* 4.0 15.5 - - + -
105A LEU* 2.7 40.2 + - + +
106A ILE* 3.6 7.6 - - - +
108A GLU* 1.3 76.7 - - - +
110A LYS* 1.3 52.4 + - - +
112A GLY* 3.5 1.9 - - - -
113A MET* 2.7 41.4 + - + +
128A LEU* 3.8 25.5 - - + +
131A ILE* 3.4 35.4 - - + -
132A HIS* 4.1 17.0 - - + -
135A LEU* 4.1 15.0 - - + -
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Residues in contact with LYS 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ILE* 3.0 25.3 + - - +
107A GLN* 3.6 32.3 - - - +
108A GLU 3.3 0.2 - - - -
109A LEU* 1.3 76.0 - - - +
111A GLU* 1.3 61.1 + - + +
113A MET* 3.3 8.3 + - - +
114A GLU* 2.9 30.8 + - - +
132A HIS* 2.7 42.5 + - + +
136A GLU* 4.2 6.5 + - - -
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Residues in contact with GLU 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A GLN* 3.3 21.4 - - - +
108A GLU* 3.3 15.8 + - - +
109A LEU 3.3 0.2 - - - -
110A LYS* 1.3 76.2 - - + +
112A GLY* 1.3 58.9 + - - +
114A GLU* 2.9 35.5 + - + +
115A VAL* 3.0 13.3 + - + +
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Residues in contact with GLY 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 4.4 23.7 - - - +
108A GLU 2.8 15.6 + - - -
109A LEU* 3.1 4.9 + - - -
111A GLU* 1.3 76.7 - - - +
113A MET* 1.3 60.4 + - - +
115A VAL* 3.4 3.2 + - - +
116A ALA* 3.1 19.6 + - - +
128A LEU* 3.6 20.5 - - - +
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Residues in contact with MET 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A LEU 2.7 24.4 + - - +
110A LYS* 3.7 8.1 - - - +
112A GLY* 1.3 71.1 - - - +
114A GLU* 1.3 66.0 + - - +
116A ALA* 4.0 4.0 - - - +
117A GLY* 3.0 20.1 + - - -
125A ALA* 3.5 27.3 - - + +
128A LEU* 3.7 13.9 - - + -
129A LEU* 3.4 57.0 - - + -
132A HIS* 4.8 9.6 - - - -
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Residues in contact with GLU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LYS* 2.9 26.2 + - - +
111A GLU* 2.9 18.3 + - + +
113A MET* 1.3 79.2 - - - +
115A VAL* 1.3 59.3 + - + +
117A GLY* 3.2 2.3 + - - -
118A GLU* 2.8 47.1 + - - +
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Residues in contact with VAL 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SER* 2.7 41.8 + - - +
6A ASN* 3.7 31.2 - - + -
7A VAL* 4.1 4.7 - - + +
10A VAL* 3.9 25.4 - - + -
111A GLU* 3.0 14.9 + - + +
112A GLY 3.7 7.4 - - - +
114A GLU* 1.3 78.1 - - + +
116A ALA* 1.3 62.8 + - - +
118A GLU* 4.6 0.7 - - - -
119A ALA* 3.1 3.6 + - - +
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Residues in contact with ALA 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 3.9 16.8 - - + +
112A GLY 3.1 14.8 + - - +
113A MET 4.0 0.9 - - - +
114A GLU 3.4 0.2 - - - -
115A VAL* 1.3 79.2 - - - +
117A GLY* 1.3 61.0 + - - +
119A ALA 3.2 4.9 + - - -
121A ASP* 2.8 36.1 + - - +
124A SER* 3.0 27.8 - - - +
125A ALA* 3.8 15.3 - - + +
128A LEU* 4.8 2.2 - - + -
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Residues in contact with GLY 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A MET 3.0 16.0 + - - -
114A GLU 3.6 2.9 - - - -
116A ALA* 1.3 77.4 - - - +
118A GLU* 1.3 58.1 + - - +
119A ALA 3.1 0.2 - - - -
120A GLY* 3.1 17.7 + - - -
121A ASP 4.6 4.0 + - - -
122A ALA* 6.3 0.2 - - - -
125A ALA* 4.6 5.1 - - - +
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Residues in contact with GLU 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SER* 3.2 35.7 + - - +
114A GLU* 2.8 29.0 + - - +
115A VAL* 3.3 0.6 + - - -
117A GLY* 1.3 75.5 - - - +
119A ALA* 1.3 56.2 + - - +
120A GLY 3.3 1.6 - - - -
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Residues in contact with ALA 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SER* 3.3 34.3 - - - +
3A THR 3.9 5.4 - - - +
4A LYS* 4.8 1.6 - - - +
7A VAL* 3.6 21.5 - - + -
115A VAL 3.1 8.5 + - - +
116A ALA 3.6 3.6 - - - +
117A GLY 3.1 1.0 - - - -
118A GLU* 1.3 77.8 - - - +
120A GLY* 1.3 61.8 + - - +
121A ASP* 3.5 3.6 + - + +
----------------------------------------------------------
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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