Contacts of the helix formed by residues 88 - 116 (chain A) in PDB entry 1JI4
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 88 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A VAL* 4.3 6.3 - - - +
29A LYS 4.2 5.7 + - - -
32A ASP* 2.5 41.9 + - - -
36A VAL* 4.6 3.1 - - - -
87A HIS* 1.3 69.8 + - - +
89A LYS* 1.3 64.6 + - - +
91A ILE* 3.1 13.7 + - - +
92A PHE* 3.1 43.7 + - - -
142A HIS* 3.8 5.2 + - - -
31J THR* 5.3 2.8 - - - +
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Residues in contact with LYS 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A HIS* 3.0 5.7 + - + +
88A SER* 1.3 78.8 + - - +
90A ASP* 1.3 72.1 + - - +
92A PHE* 3.4 2.6 + - - -
93A LYS* 3.1 56.9 + - - +
142A HIS* 5.6 1.3 - - - -
143A LEU* 3.9 18.4 - - + +
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Residues in contact with ASP 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PHE* 5.9 0.2 - - - -
86A PHE* 5.0 11.6 - - + -
87A HIS* 3.0 26.1 + - - +
89A LYS* 1.3 81.4 + - - +
91A ILE* 1.3 66.3 + - - +
93A LYS* 3.4 13.7 + - - +
94A GLU* 3.1 26.7 + - - +
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Residues in contact with ILE 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PHE* 3.7 49.8 - - + +
28A VAL* 3.4 33.0 - - + -
36A VAL* 4.0 7.9 - - + -
40A THR* 4.7 6.5 - - + -
86A PHE* 3.6 28.0 - - + -
87A HIS 3.4 6.0 + - - +
88A SER* 3.1 8.4 + - - +
90A ASP* 1.3 78.0 - - - +
92A PHE* 1.3 64.2 + - + +
94A GLU* 3.4 3.5 + - - +
95A ILE* 3.0 47.8 + - + +
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Residues in contact with PHE 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ASP* 4.6 2.2 - - - -
35A ASN 6.0 0.2 - - - -
36A VAL* 4.2 24.7 - - + -
39A ALA* 5.3 11.4 - - + -
40A THR* 5.9 1.8 - - + -
43A ILE* 5.8 3.4 - - + -
88A SER* 3.1 34.2 + - - +
89A LYS 4.0 3.8 - - - +
91A ILE* 1.3 82.6 - - + +
93A LYS* 1.3 62.1 + - - +
95A ILE* 4.1 13.0 - - + +
96A LEU* 3.0 29.8 + - - +
139A LEU* 3.7 27.0 - - + +
142A HIS* 3.1 43.1 - + + -
143A LEU* 4.0 19.3 - - + +
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Residues in contact with LYS 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LYS* 3.1 57.3 + - + +
90A ASP* 3.8 13.6 + - - +
91A ILE 3.3 0.4 - - - -
92A PHE* 1.3 75.8 - - - +
94A GLU* 1.3 53.2 + - - +
96A LEU* 3.3 2.1 + - - +
97A GLU* 2.6 50.6 + - - +
143A LEU* 4.2 20.9 - - + -
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Residues in contact with GLU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LYS* 2.7 36.2 + - - -
24A PHE* 3.6 19.1 - - + -
81A GLU* 2.8 38.5 - - - +
86A PHE* 4.8 1.4 - - - -
90A ASP 3.1 16.1 + - - +
91A ILE 3.7 3.8 - - - +
92A PHE 3.3 0.2 - - - -
93A LYS* 1.3 77.3 - - + +
95A ILE* 1.3 65.4 + - - +
97A GLU* 3.1 12.4 + - + +
98A ASP* 2.9 29.0 + - - +
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Residues in contact with ILE 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A VAL* 4.8 9.4 - - + -
24A PHE* 3.8 20.4 - - + -
40A THR* 4.6 7.6 - - + -
43A ILE* 4.1 23.6 - - + -
91A ILE* 3.0 35.4 + - + +
92A PHE* 4.1 14.4 - - + +
94A GLU* 1.3 75.1 - - - +
96A LEU* 1.3 58.0 + - - +
98A ASP* 3.3 7.2 + - - -
99A TYR* 2.8 60.6 + - + +
139A LEU* 4.1 13.9 - - + -
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Residues in contact with LEU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A PHE 3.0 19.7 + - - +
93A LYS* 3.4 4.9 - - - +
95A ILE* 1.3 78.4 - - - +
97A GLU* 1.3 69.3 + - - +
99A TYR* 3.3 3.6 + - + +
100A LYS* 3.0 50.9 + - + +
136A ILE* 4.1 20.6 - - + -
139A LEU* 3.9 23.1 - - + +
140A GLN* 3.9 19.5 - - + -
143A LEU* 4.0 18.2 - - + -
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Residues in contact with GLU 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A LYS* 2.6 47.6 + - - +
94A GLU* 3.1 13.4 + - + +
96A LEU* 1.3 86.8 - - - +
98A ASP* 1.3 64.9 + - - +
100A LYS* 3.4 9.9 + - - +
101A TYR* 3.2 20.6 + - - +
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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
----------------------------------------------------------
17A LEU* 3.8 24.0 - - + +
20A LYS* 2.9 39.1 + - - +
24A PHE* 5.7 0.3 - - - -
78A VAL* 3.9 14.0 - - + +
79A LYS 5.3 0.5 + - - -
94A GLU* 2.9 20.6 + - - +
95A ILE* 3.8 6.8 - - - +
97A GLU* 1.3 77.7 - - - +
99A TYR* 1.3 63.0 + - + +
101A TYR* 3.3 11.0 + - - +
102A LEU* 3.0 31.2 + - - +
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Residues in contact with TYR 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A VAL* 6.2 0.2 - - + -
43A ILE* 3.3 29.6 - - + +
47A PHE* 3.7 25.8 - + - -
95A ILE* 2.8 36.0 + - + +
96A LEU* 3.6 5.8 - - - +
98A ASP* 1.3 77.4 - - + +
100A LYS* 1.3 61.6 + - - +
102A LEU* 3.2 5.6 + - + +
103A GLU* 2.9 28.6 + - - +
132A LEU* 4.0 20.8 - - + +
135A SER* 3.5 29.6 - - - -
136A ILE* 3.9 17.8 - - + +
139A LEU* 3.6 20.9 - - + -
700A MPD 3.3 28.7 + - + +
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Residues in contact with LYS 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A LEU* 3.0 41.4 + - + +
97A GLU* 3.7 8.7 - - - +
98A ASP 3.3 0.2 - - - -
99A TYR* 1.3 76.5 - - - +
101A TYR* 1.3 60.9 + - - +
103A GLU* 3.4 12.2 + - - +
104A LYS* 3.3 33.9 + - - +
136A ILE* 4.0 19.2 - - + +
140A GLN* 3.0 27.3 + - - -
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Residues in contact with TYR 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A HIS* 5.4 0.3 - - - +
10A LEU* 5.1 0.2 - - - +
13A ASP* 2.5 36.7 + - - -
77A ARG* 2.9 47.7 + - + +
78A VAL* 3.9 17.3 - - + -
97A GLU 3.2 12.1 + - - +
98A ASP* 3.4 15.3 - - - +
99A TYR 3.2 0.8 - - - -
100A LYS* 1.3 75.5 - - - +
102A LEU* 1.3 73.4 + - + +
104A LYS* 3.2 14.4 + - + +
105A GLU* 3.2 53.4 + - + +
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Residues in contact with LEU 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 4.1 22.0 - - + -
13A ASP* 4.2 13.9 - - + -
17A LEU* 4.1 9.2 - - + -
47A PHE* 3.6 34.1 - - + -
50A MET* 4.4 14.1 - - + -
98A ASP 3.0 17.8 + - - +
99A TYR* 3.2 11.2 + - + +
101A TYR* 1.3 90.2 - - + +
103A GLU* 1.3 58.0 + - - +
105A GLU* 3.2 4.3 + - - +
106A PHE* 2.9 35.8 + - + -
132A LEU* 4.0 25.6 - - + -
700A MPD 4.6 2.0 - - + -
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Residues in contact with GLU 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A TYR 2.9 13.4 + - - +
100A LYS* 3.6 16.8 + - - +
101A TYR 3.2 0.2 - - - -
102A LEU* 1.3 76.5 - - - +
104A LYS* 1.3 64.6 + - + +
106A PHE 3.4 0.7 + - - -
107A LYS* 3.0 47.0 + - + +
129A LEU* 3.5 12.6 - - + +
132A LEU* 3.9 13.4 - - + +
133A GLN* 3.1 32.9 + - + +
136A ILE* 3.6 24.3 - - + +
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Residues in contact with LYS 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LYS* 3.3 19.8 + - - +
101A TYR* 3.2 15.8 + - + +
103A GLU* 1.3 78.9 - - + +
105A GLU* 1.3 66.0 + - + +
107A LYS* 3.2 11.8 + - + +
108A GLU* 3.1 29.8 + - + +
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Residues in contact with GLU 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 4.7 6.6 - - - +
6A ILE* 4.0 14.2 - - - +
9A HIS* 5.8 1.3 - - - +
10A LEU* 3.5 27.1 - - + +
77A ARG* 3.0 29.7 + - - -
101A TYR* 3.2 44.6 + - + +
102A LEU 3.2 4.5 + - - +
104A LYS* 1.3 80.8 - - - +
106A PHE* 1.3 57.8 + - - +
108A GLU* 3.3 13.7 + - - +
109A LEU* 2.9 26.0 + - - +
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Residues in contact with PHE 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 4.0 26.0 - - + -
50A MET* 4.1 27.1 - - + -
54A LEU* 4.6 2.2 - - + -
102A LEU* 2.9 31.7 + - + +
105A GLU* 1.3 73.5 - - - +
107A LYS* 1.3 61.1 + - - +
109A LEU* 3.5 22.2 - - + +
110A SER* 2.9 28.1 + - - -
124A TYR* 3.9 18.4 - + - -
125A ALA* 3.7 11.4 - - - +
128A GLN* 3.6 38.1 - - + -
129A LEU* 3.6 23.4 - - + +
132A LEU* 3.6 18.4 - - + -
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Residues in contact with LYS 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A GLU* 3.0 46.6 + - + +
104A LYS* 3.5 12.6 - - + +
105A GLU 3.2 0.2 - - - -
106A PHE* 1.3 76.5 - - - +
108A GLU* 1.3 61.8 + - + +
110A SER* 3.4 3.8 + - - -
111A ASN* 2.9 39.2 + - - +
129A LEU* 4.1 15.9 - - + -
133A GLN* 4.0 12.7 - - - +
117K GLY 6.0 1.8 - - - -
119K LYS* 4.9 9.8 - - + +
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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
----------------------------------------------------------
1A MET* 6.4 1.3 - - + -
6A ILE* 4.2 10.8 - - + -
104A LYS* 3.1 18.7 + - + +
105A GLU* 3.6 16.6 - - - +
107A LYS* 1.3 76.3 - - - +
109A LEU* 1.3 57.2 + - - +
111A ASN* 3.1 11.5 + - - +
112A THR* 2.7 44.4 + - + +
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Residues in contact with LEU 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A THR* 3.8 19.3 - - + +
6A ILE* 3.9 20.3 - - + +
7A LEU* 3.7 28.7 - - + -
10A LEU* 4.2 2.7 - - + -
105A GLU 2.9 14.1 + - - +
106A PHE* 3.5 28.5 - - + +
108A GLU* 1.3 76.6 - - - +
110A SER* 1.3 56.7 + - - +
113A ALA* 2.9 35.6 + - - +
121A THR* 3.5 26.9 - - + +
124A TYR* 4.6 4.0 - - + -
125A ALA* 3.5 23.6 - - + -
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Residues in contact with SER 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A PHE 2.9 17.9 + - - -
107A LYS* 3.6 6.3 - - - -
108A GLU 3.2 0.2 - - - -
109A LEU* 1.3 76.0 - - - +
111A ASN* 1.3 63.0 + - - +
113A ALA* 4.6 2.5 - - - -
114A GLU* 3.1 24.6 + - - +
122A VAL* 3.7 11.7 - - - +
125A ALA* 3.8 10.7 - - - +
126A ASP* 2.6 29.3 + - - -
129A LEU* 4.6 2.0 - - - -
119K LYS* 3.0 24.9 + - - -
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Residues in contact with ASN 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LYS* 2.9 25.3 + - - +
108A GLU* 3.6 13.2 - - - +
110A SER* 1.3 76.8 - - - +
112A THR* 1.3 63.4 - - + +
114A GLU* 3.4 7.0 + - - +
115A LYS* 3.3 39.7 + - - +
119K LYS* 3.1 31.4 - - - +
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Residues in contact with THR 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET 4.0 12.1 + - - +
3A THR* 3.5 17.7 + - - -
6A ILE* 3.5 27.5 - - + +
108A GLU* 2.7 26.3 + - + +
109A LEU 4.2 0.5 + - - -
111A ASN* 1.3 73.5 - - + +
113A ALA* 1.3 66.3 + - - +
115A LYS* 3.3 16.0 + - - +
116A GLU* 3.2 28.7 + - - +
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Residues in contact with ALA 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A THR* 3.4 16.8 - - - +
109A LEU* 2.9 20.5 + - + +
112A THR* 1.3 77.7 + - - +
114A GLU* 1.3 61.5 + - - +
116A GLU* 3.3 2.2 + - - -
117A GLY 3.1 3.6 + - - -
118A ASP* 2.8 35.6 + - + +
121A THR* 4.0 23.8 - - + -
122A VAL* 3.6 19.3 - - + +
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Residues in contact with GLU 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A SER 3.1 15.3 + - - +
111A ASN* 3.5 7.6 + - - +
112A THR 3.2 0.2 - - - -
113A ALA* 1.3 77.8 - - - +
115A LYS* 1.3 63.6 + - + +
117A GLY* 3.0 14.1 + - - -
118A ASP 4.8 0.9 - - - +
122A VAL* 3.4 18.6 - - + +
114H GLU* 5.5 3.1 - - - +
114K GLU* 5.5 2.3 - - - +
119K LYS* 3.3 24.1 + - - -
----------------------------------------------------------
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Residues in contact with LYS 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ASN* 3.3 27.4 + - - +
112A THR* 3.3 15.9 + - - +
114A GLU* 1.3 78.8 - - + +
116A GLU* 1.3 62.3 + - + +
117A GLY* 3.2 0.9 + - - -
----------------------------------------------------------
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Residues in contact with GLU 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET 4.9 0.2 - - - +
2A LYS* 3.8 12.0 - - - +
3A THR* 2.7 48.5 + - - -
112A THR* 3.2 13.4 + - - +
113A ALA* 3.7 6.7 - - - +
114A GLU 3.2 0.6 - - - -
115A LYS* 1.3 78.7 - - + +
117A GLY* 1.3 59.3 + - - +
118A ASP* 3.6 9.0 + - + +
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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
------------------------------------------------------------
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