Contacts of the helix formed by residues 88 - 117 (chain A) in PDB entry 1JI5
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 THR 88 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A GLY 3.9 1.8 + - - -
87A GLU* 1.3 73.1 - - - +
89A ALA* 1.3 66.9 + - - +
90A GLU* 3.4 28.5 - - + +
91A GLY* 3.4 15.9 - - - -
92A MET* 2.7 39.0 + - - +
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Residues in contact with ALA 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A VAL* 4.0 21.5 - - + +
31A LYS 3.5 26.7 + - - +
34A GLN* 5.2 11.9 - - + -
38A LEU* 5.3 3.3 - - + +
42A PHE* 4.8 1.2 - - - -
88A THR* 1.3 77.3 - - + +
90A GLU* 1.3 78.9 + - - +
92A MET* 3.2 6.0 + - - +
93A VAL* 3.1 26.6 + - - +
143A PHE* 5.9 1.3 - - + -
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Residues in contact with GLU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A GLN* 5.4 8.3 - - - +
88A THR* 3.4 19.4 - - + +
89A ALA* 1.3 87.1 - - - +
91A GLY* 1.3 58.7 + - - +
93A VAL* 3.2 9.2 + - - +
94A GLU* 2.8 37.3 + - - +
143A PHE* 5.0 10.3 - - - -
144A LEU* 4.4 16.6 - - + +
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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
----------------------------------------------------------
87A GLU* 5.0 6.1 - - - -
88A THR* 3.1 23.5 + - - -
90A GLU* 1.3 79.1 - - - +
92A MET* 1.3 51.6 + - - +
94A GLU* 3.3 13.2 + - - +
95A ALA* 2.6 36.6 + - - +
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Residues in contact with MET 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ASN* 4.5 1.8 - - - +
26A PHE* 3.3 67.1 - - + -
29A TYR* 3.9 15.7 - - + +
30A VAL* 3.9 40.6 - - - +
42A PHE* 3.7 7.4 - - + -
85A TYR 5.1 2.7 - - - +
87A GLU* 3.8 22.9 - - + +
88A THR 2.7 26.0 + - - +
89A ALA* 3.5 4.7 - - - +
91A GLY* 1.3 70.7 - - - +
93A VAL* 1.3 62.4 + - - +
95A ALA* 3.1 3.0 + - - +
96A ILE* 2.9 30.2 + - - +
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Residues in contact with VAL 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 4.0 18.4 - - + -
42A PHE* 4.5 6.1 - - + -
89A ALA 3.1 16.9 + - - +
90A GLU* 3.6 4.9 - - - +
92A MET* 1.3 75.2 - - - +
94A GLU* 1.3 61.8 + - - +
96A ILE* 2.7 24.5 - - - +
97A MET* 3.1 13.9 + - - +
140A LEU* 3.6 31.0 - - + +
143A PHE* 3.7 32.3 - - + -
144A LEU* 3.6 23.3 - - + -
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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
----------------------------------------------------------
90A GLU* 2.8 20.4 + - - +
91A GLY* 3.4 11.6 - - - +
93A VAL* 1.3 78.2 - - - +
95A ALA* 1.3 62.9 + - - +
97A MET* 3.5 11.2 - - + +
98A LYS* 3.1 48.6 + - + +
144A LEU* 4.2 18.1 - - + +
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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
----------------------------------------------------------
22A LYS* 4.8 8.2 + - - +
26A PHE* 3.8 21.1 - - + -
87A GLU* 4.4 9.6 - - - +
91A GLY 2.6 20.9 + - - +
92A MET* 3.1 6.0 + - - +
94A GLU* 1.3 73.7 - - - +
96A ILE* 1.3 62.7 + - - +
98A LYS* 3.4 17.7 + - - +
99A ASP* 3.1 25.1 + - - +
102A MET* 5.4 0.2 - - - +
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Residues in contact with ILE 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 5.2 5.4 - - + -
22A LYS* 5.1 5.8 - - + -
23A LEU* 4.1 23.3 - - + -
26A PHE* 3.4 31.9 - - + -
42A PHE* 4.5 9.4 - - + -
45A LEU* 4.9 3.6 - - + -
92A MET 2.9 17.7 + - - +
93A VAL* 2.7 38.8 - - - +
95A ALA* 1.3 70.8 - - - +
97A MET* 1.3 61.6 + - - +
99A ASP* 3.1 15.1 + - + +
100A TYR* 2.8 46.8 + - + -
140A LEU* 4.1 20.0 - - + -
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Residues in contact with MET 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A VAL 3.1 20.7 + - - +
94A GLU* 3.5 13.9 - - + +
95A ALA 3.2 0.2 - - - -
96A ILE* 1.3 82.2 - - - +
98A LYS* 1.3 71.6 + - + +
100A TYR* 3.3 5.5 + - - +
101A GLU* 3.1 48.3 + - - +
137A ALA* 4.3 8.5 - - - +
140A LEU* 4.2 20.2 - - + -
141A ARG* 3.8 42.0 - - + +
144A LEU* 4.2 13.7 - - + -
145A ASN* 6.4 0.2 - - - +
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Residues in contact with LYS 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLU* 3.1 39.1 + - + +
95A ALA* 3.6 14.8 - - - +
97A MET* 1.3 82.6 - - + +
99A ASP* 1.3 61.4 + - - +
101A GLU* 3.1 15.4 + - - +
102A MET* 2.8 51.9 + - + +
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Residues in contact with ASP 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 4.1 11.5 - - + +
22A LYS* 2.8 38.7 + - - +
80A ILE* 3.9 33.2 - - + +
81A GLN* 4.8 4.2 + - - +
95A ALA 3.1 15.1 + - - +
96A ILE* 3.1 14.8 + - - +
98A LYS* 1.3 77.1 - - - +
100A TYR* 1.3 63.9 + - + +
102A MET* 3.4 22.0 + - - +
103A MET* 3.1 24.1 + - - +
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Residues in contact with TYR 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TRP* 4.2 24.4 - + - -
19A LEU* 4.6 14.6 - - + -
23A LEU* 4.5 8.1 - - + +
45A LEU* 3.1 34.0 + - + +
48A GLU* 5.1 1.7 + - - +
96A ILE* 2.8 30.8 + - + +
97A MET* 3.6 5.6 - - - +
99A ASP* 1.3 77.4 - - + +
101A GLU* 1.3 58.2 + - + +
103A MET* 2.9 23.6 + - - +
104A LEU* 3.0 16.6 + - - +
133A LEU* 4.1 35.0 - - + +
136A HIS* 3.8 37.0 - + + -
137A ALA* 4.7 5.8 - - + -
140A LEU* 4.3 17.9 - - + -
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Residues in contact with GLU 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A MET* 3.1 33.9 + - - +
98A LYS* 3.6 17.4 - - - +
100A TYR* 1.3 76.0 - - - +
102A MET* 1.3 63.4 + - + +
104A LEU* 3.0 32.2 + - + +
105A VAL* 3.5 10.2 + - - +
137A ALA* 4.5 10.5 - - + -
141A ARG* 2.3 37.4 + - - +
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Residues in contact with MET 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ILE* 6.0 3.1 - - + -
98A LYS* 2.8 44.3 + - + +
99A ASP* 3.4 28.7 - - - +
101A GLU* 1.3 73.4 - - + +
103A MET* 1.3 57.0 + - - +
105A VAL* 3.0 30.4 - - + +
106A GLU* 3.7 9.0 + - - +
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Residues in contact with MET 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLN* 2.9 45.1 - - - +
15A ASP* 4.5 15.5 - - + +
16A TRP* 3.3 37.2 - - + +
19A LEU* 4.4 16.6 - - - -
80A ILE* 5.2 4.7 - - + -
99A ASP 3.1 12.6 + - - +
100A TYR* 2.9 14.0 + - - +
102A MET* 1.3 77.1 - - - +
104A LEU* 1.3 64.1 + - - +
105A VAL 3.2 1.8 - - - -
106A GLU* 3.3 9.2 + - + +
107A LEU* 2.9 44.0 + - + +
129A ILE* 4.4 0.2 - - + -
133A LEU* 4.0 7.6 - - + -
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Residues in contact with LEU 104 (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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100A TYR 3.0 15.9 + - - +
101A GLU* 3.0 23.1 + - + +
103A MET* 1.3 77.5 - - - +
105A VAL* 1.3 65.0 + - + +
107A LEU* 3.0 7.9 + - + +
108A LYS* 2.9 26.6 + - - +
130A TYR* 3.4 57.3 - - + +
133A LEU* 4.0 15.5 - - + -
134A GLU* 3.8 26.9 - - + +
137A ALA* 5.5 3.8 - - + -
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Residues in contact with VAL 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A GLU 3.8 11.7 - - - +
102A MET* 3.0 22.7 - - - +
104A LEU* 1.3 76.8 - - + +
106A GLU* 1.3 82.1 + - + +
108A LYS* 3.2 12.4 + - + +
109A LYS* 3.0 38.5 + - - +
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Residues in contact with GLU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 4.8 5.7 - - - +
11A LYS* 2.9 46.3 - - - +
12A GLN* 5.3 5.7 + - - +
15A ASP* 3.4 10.0 - - - +
79A SER* 3.6 7.9 + - - -
102A MET 4.0 11.5 - - - +
103A MET* 3.3 14.4 + - + +
105A VAL* 1.3 86.5 - - + +
107A LEU* 1.3 57.7 + - - +
109A LYS* 3.6 14.0 - - + +
110A GLY* 2.9 22.2 + - - -
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Residues in contact with LEU 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 6.1 0.7 - - + -
12A GLN* 3.8 22.0 - - + +
103A MET* 2.9 40.0 + - + +
104A LEU* 3.3 10.5 - - - +
105A VAL 3.0 0.2 - - - -
106A GLU* 1.3 76.2 - - - +
108A LYS* 1.3 65.9 + - - +
110A GLY* 2.8 12.6 + - - -
111A MET* 2.8 21.9 + - + +
126A LEU* 3.7 39.7 - - + +
129A ILE* 4.4 5.2 - - + -
130A TYR* 3.9 34.5 - - + +
133A LEU* 4.3 8.1 - - + -
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Residues in contact with LYS 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LEU* 2.9 12.6 + - + +
105A VAL* 3.6 12.3 - - + +
107A LEU* 1.3 74.1 - - - +
109A LYS* 1.3 65.9 + - + +
111A MET* 3.0 17.6 + - + +
112A GLU* 3.0 23.7 + - - +
130A TYR* 3.2 39.2 + - + +
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Residues in contact with LYS 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A VAL* 3.0 30.0 + - - +
106A GLU* 3.6 15.3 - - + +
108A LYS* 1.3 76.2 - - + +
110A GLY* 1.3 60.4 + - - +
112A GLU* 3.0 19.3 + - - +
113A ILE* 2.9 21.8 - - + +
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Residues in contact with GLY 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A VAL* 5.4 0.3 - - - +
8A VAL* 3.7 24.5 - - - +
106A GLU 2.9 13.6 + - - -
107A LEU* 2.8 9.7 + - - -
109A LYS* 1.3 76.5 - - - +
111A MET* 1.3 55.8 + - - -
113A ILE* 3.5 9.4 - - - +
114A ALA* 3.1 27.2 + - - +
126A LEU* 3.8 10.3 - - - +
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Residues in contact with MET 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LEU* 2.8 15.9 + - + +
108A LYS* 3.0 30.5 + - + +
110A GLY* 1.3 72.0 - - - +
112A GLU* 1.3 66.7 + - - +
114A ALA* 3.6 3.9 - - - +
115A GLN* 2.9 36.9 + - - +
123A SER* 3.5 28.0 - - - +
126A LEU* 3.9 10.5 - - + -
127A LEU* 3.9 29.4 - - + +
130A TYR* 3.7 31.2 - - + -
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Residues in contact with GLU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A LYS 3.0 12.8 + - - +
109A LYS* 3.1 15.3 - - - +
111A MET* 1.3 79.7 - - - +
113A ILE* 1.3 58.4 + - - +
115A GLN* 3.1 12.1 + - - +
116A ASN* 2.8 56.5 + - - +
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Residues in contact with ILE 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A GLN* 4.5 7.6 - - - +
5A VAL* 3.4 39.3 - - + -
8A VAL* 3.7 18.6 - - + -
109A LYS* 2.9 19.7 - - + +
110A GLY* 3.5 13.5 - - - +
112A GLU* 1.3 71.9 - - + +
114A ALA* 1.3 63.6 + - - +
116A ASN* 3.6 10.9 - - - +
117A SER* 2.8 42.5 + - - +
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Residues in contact with ALA 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A VAL* 4.2 20.0 - - + -
110A GLY 3.1 20.1 + - - +
111A MET* 3.6 5.4 - - - +
113A ILE* 1.3 82.1 - - - +
115A GLN* 1.3 57.1 + - - +
117A SER 3.2 6.4 + - - -
119A ASP* 2.8 48.6 + - + +
122A THR* 4.5 3.6 - - + -
123A SER* 4.0 16.4 - - - +
126A LEU* 5.2 0.2 - - + -
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Residues in contact with GLN 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A MET* 2.9 31.6 + - - +
112A GLU* 3.4 15.1 + - - +
114A ALA* 1.3 77.6 - - - +
116A ASN* 1.3 61.6 + - - +
118A ASP* 3.0 19.2 + - - -
119A ASP 4.4 5.4 - - - +
120A GLU* 4.9 10.8 + - + +
123A SER* 3.8 20.5 + - - +
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Residues in contact with ASN 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A GLU* 2.8 44.4 + - - +
113A ILE* 3.6 9.8 + - - +
115A GLN* 1.3 80.3 - - - +
117A SER* 1.3 58.9 + - - +
118A ASP* 3.1 3.6 + - - +
----------------------------------------------------------
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Residues in contact with SER 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A GLN* 4.5 7.7 + - - -
5A VAL* 3.8 22.3 - - - +
113A ILE* 2.8 23.8 + - - +
114A ALA 3.2 3.6 + - - -
115A GLN 3.2 0.2 - - - -
116A ASN* 1.3 75.7 - - - +
118A ASP* 1.3 71.7 + - - +
119A ASP* 3.4 4.7 + - - +
----------------------------------------------------------
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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