Contacts of the helix formed by residues 92 - 119 (chain A) in PDB entry 1RCE
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 GLY 92 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A PHE* 3.9 12.7 - - - -
47A PHE* 3.6 27.7 - - - -
91A ASN* 1.3 70.3 - - - +
93A LEU* 1.3 61.7 + - - +
95A ALA* 3.5 2.4 + - - +
96A LEU* 3.0 24.1 + - - +
151A LEU* 3.9 7.9 - - - -
163A GLU* 2.9 21.4 + - - -
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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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91A ASN* 3.0 9.4 + - - +
92A GLY* 1.3 74.2 - - - +
94A GLU* 1.3 57.5 + - - +
96A LEU* 3.2 5.2 + - + +
97A GLN* 2.9 48.7 + - - +
148A ILE* 4.1 26.2 - - + -
151A LEU* 3.7 31.6 - - + +
152A LYS* 4.1 19.5 - - + -
155A TRP* 4.2 42.3 - - + +
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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
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86A ARG* 3.1 36.5 + - - +
89A TRP 3.8 6.7 - - - +
90A ALA* 3.4 18.4 - - - +
91A ASN* 3.0 24.7 + - - +
93A LEU* 1.3 75.1 - - - +
95A ALA* 1.3 63.6 + - - +
97A GLN* 3.3 14.9 + - - +
98A THR* 2.9 30.9 + - - +
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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
----------------------------------------------------------
33A MET* 3.9 13.3 - - - +
37A PHE* 3.6 29.4 - - + -
51A PHE* 3.9 13.5 - - + -
89A TRP* 4.0 11.6 + - + -
91A ASN 2.9 18.0 + - - +
92A GLY 3.8 2.9 - - - +
94A GLU* 1.3 75.0 - - - +
96A LEU* 1.3 64.4 + - - +
98A THR* 3.2 8.5 + - - -
99A ALA* 3.0 22.5 + - - +
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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
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47A PHE* 4.4 7.9 - - + -
50A PHE* 4.1 11.2 - - + -
51A PHE* 3.8 22.0 - - + -
92A GLY 3.0 13.5 + - - +
93A LEU* 3.4 6.7 - - + +
95A ALA* 1.3 77.3 - - - +
97A GLN* 1.3 60.7 + - - +
99A ALA* 3.4 4.9 + - - +
100A LEU 3.2 16.3 + - - -
144A LEU* 4.1 22.7 - - + +
147A HIS* 4.1 29.4 - - + -
148A ILE* 3.9 23.4 - - + +
151A LEU* 3.8 27.4 - - + -
166A PHE* 4.2 11.0 - - + -
171A LEU* 5.8 1.1 - - + -
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Residues in contact with GLN 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A LEU* 2.9 33.8 + - - +
94A GLU* 3.8 15.5 - - - +
96A LEU* 1.3 72.9 - - - +
98A THR* 1.3 65.7 + - - +
100A LEU* 3.3 11.8 + - + +
101A LYS* 3.3 18.2 + - - +
148A ILE* 4.0 25.8 - - + -
152A LYS* 3.7 25.1 + - - -
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Residues in contact with THR 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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29A VAL* 5.4 2.9 - - + -
33A MET* 3.7 21.3 - - + -
85A GLU* 6.1 0.9 - - - +
86A ARG* 4.2 14.6 + - - -
89A TRP* 3.9 14.3 - - + -
94A GLU* 2.9 16.5 + - - +
95A ALA* 3.2 9.0 + - - -
97A GLN* 1.3 76.8 - - - +
99A ALA* 1.3 58.4 + - - +
101A LYS* 3.1 20.1 + - - +
102A LEU* 2.9 28.4 + - + +
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Residues in contact with ALA 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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30A TYR* 3.7 29.6 - - + +
33A MET* 4.4 2.6 - - + +
51A PHE* 4.2 11.9 - - + -
95A ALA 3.0 12.4 + - - +
96A LEU 3.6 9.4 - - - +
97A GLN 3.2 0.2 - - - -
98A THR* 1.3 78.4 - - - +
100A LEU* 1.3 56.3 + - - +
102A LEU* 3.4 8.1 - - - +
103A GLN* 2.8 34.1 + - - +
144A LEU* 3.9 13.7 - - + -
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Residues in contact with LEU 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 LEU 3.2 6.6 + - - +
97A GLN* 3.6 9.4 - - - +
98A THR 3.2 0.4 - - - -
99A ALA* 1.3 75.9 - - - +
101A LYS* 1.3 63.2 + - + +
103A GLN* 3.4 1.0 + - - +
104A LYS* 3.0 45.2 + - + +
141A ILE* 3.7 42.0 - - + +
144A LEU* 4.0 15.9 - - + +
145A GLY* 4.3 8.3 - - - +
148A ILE* 3.7 27.1 - - + -
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Residues in contact with LYS 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 GLN 3.3 12.8 + - - +
98A THR* 3.1 19.0 + - - +
100A LEU* 1.3 74.7 - - + +
102A LEU* 1.3 67.8 + - - +
104A LYS* 3.1 9.7 + - - +
105A SER* 3.0 24.8 + - - -
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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
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22A LEU* 6.5 1.1 - - + -
25A HIS* 5.2 7.4 - - + -
26A SER* 3.9 27.6 - - - -
29A VAL* 4.0 31.2 - - + -
30A TYR* 3.7 35.2 - - + +
33A MET* 5.6 0.9 - - + -
98A THR* 2.9 16.1 + - + +
99A ALA* 3.4 8.7 - - - +
101A LYS* 1.3 76.4 - - - +
103A GLN* 1.3 65.4 + - - +
105A SER* 2.9 22.8 + - - +
106A VAL* 3.0 21.1 + - + +
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Residues in contact with GLN 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LYS* 5.4 3.5 + - - +
26A SER* 5.6 1.4 + - - -
30A TYR* 2.8 36.1 + - - +
54A ARG* 5.1 1.2 - - - +
58A ALA* 6.0 1.0 - - - +
99A ALA 2.8 18.3 + - - +
100A LEU 3.8 3.6 - - - +
102A LEU* 1.3 74.1 - - - +
104A LYS* 1.3 57.9 + - - +
106A VAL* 3.5 12.8 + - - +
107A ASN* 2.9 29.1 + - - +
136A GLU* 3.8 18.8 + - - +
137A SER* 4.8 10.3 + - - +
140A THR* 4.1 18.6 - - + +
141A ILE* 4.0 16.7 - - + +
144A LEU* 3.7 17.0 - - + -
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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
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100A LEU* 3.0 40.6 + - + +
101A LYS* 3.1 7.4 + - - +
103A GLN* 1.3 74.5 - - - +
105A SER* 1.3 60.7 + - - +
107A ASN* 3.3 9.0 + - - +
108A GLN* 2.9 28.5 + - - +
141A ILE* 3.9 26.0 - - + -
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Residues in contact with SER 105 (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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22A LEU* 4.7 3.8 - - - +
101A LYS 3.0 11.8 + - - -
102A LEU* 2.9 22.3 + - - +
104A LYS* 1.3 74.1 - - - +
106A VAL* 1.3 63.7 + - - +
108A GLN* 3.4 8.2 + - - +
109A ALA* 3.1 21.7 + - - +
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Residues in contact with VAL 106 (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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19A THR* 5.9 1.1 - - + -
22A LEU* 4.2 28.9 - - + +
23A LYS* 3.8 35.7 - - + +
26A SER* 4.4 22.2 - - - +
102A LEU* 3.0 28.4 + - + +
103A GLN* 3.8 14.1 - - - +
105A SER* 1.3 74.2 - - - +
107A ASN* 1.3 67.2 + - - +
109A ALA* 3.3 2.8 + - - +
110A LEU* 3.1 29.5 + - + +
137A SER* 5.5 1.1 - - - +
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Residues in contact with ASN 107 (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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103A GLN 2.9 18.6 + - - +
104A LYS* 3.5 6.3 + - - +
105A SER 3.3 0.2 - - - -
106A VAL* 1.3 78.6 - - - +
108A GLN* 1.3 60.9 + - - +
110A LEU* 3.4 4.8 + - - +
111A LEU* 3.1 39.2 + - - +
134A LEU* 4.3 14.2 - - - +
137A SER* 3.1 34.2 + - - -
138A VAL* 4.8 8.2 - - - +
141A ILE* 4.0 17.3 - - + +
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Residues in contact with GLN 108 (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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104A LYS 2.9 16.5 + - - +
105A SER* 3.6 10.3 - - - +
106A VAL 3.2 0.2 - - - -
107A ASN* 1.3 77.7 - - - +
109A ALA* 1.3 61.3 + - - +
111A LEU* 3.2 21.3 + - - +
112A ASP* 3.0 43.5 + - - +
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Residues in contact with ALA 109 (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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19A THR* 5.0 9.4 + - + +
22A LEU* 3.4 33.0 - - + -
105A SER 3.1 10.9 + - - +
106A VAL 3.3 4.4 + - - +
108A GLN* 1.3 77.4 - - - +
110A LEU* 1.3 56.6 + - - +
112A ASP* 3.1 11.1 + - - +
113A LEU* 2.9 28.1 + - - +
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Residues in contact with LEU 110 (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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19A THR* 3.9 26.0 - - + -
23A LYS* 4.8 13.5 - - - +
65A LEU* 5.6 3.4 - - + -
106A VAL* 3.1 27.1 + - + +
107A ASN* 3.7 5.4 - - - +
108A GLN 3.3 0.2 - - - -
109A ALA* 1.3 72.9 - - - +
111A LEU* 1.3 59.6 + - - +
113A LEU* 3.3 7.9 + - + +
114A HIS* 2.8 28.9 + - - +
129A LEU* 4.6 17.6 - - + +
133A TYR* 4.1 31.6 - - + +
134A LEU* 3.6 19.9 - - + +
136A GLU* 5.0 0.4 - - - +
137A SER* 3.5 25.1 - - - +
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Residues in contact with LEU 111 (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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107A ASN* 3.1 34.9 + - - +
108A GLN* 3.2 29.4 + - - +
110A LEU* 1.3 75.8 - - - +
112A ASP* 1.3 57.8 + - - +
114A HIS* 3.2 8.3 + - + +
115A ALA* 2.9 28.3 + - - +
134A LEU* 4.2 24.9 - - + -
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Residues in contact with ASP 112 (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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108A GLN* 3.0 39.8 + - - +
109A ALA* 3.3 11.7 - - - +
111A LEU* 1.3 74.4 - - - +
113A LEU* 1.3 64.9 + - - +
115A ALA* 3.2 8.5 + - - +
116A VAL* 3.1 26.9 + - - +
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Residues in contact with LEU 113 (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 ASP 4.8 1.3 - - - +
12A CYS* 4.3 7.6 - - - +
15A GLY* 3.6 32.1 - - - +
16A LEU* 4.1 14.6 - - + -
18A ARG* 5.7 0.2 - - - +
19A THR* 3.5 28.0 - - + +
65A LEU* 5.8 0.4 - - + -
109A ALA 2.9 16.1 + - - +
110A LEU* 3.7 8.1 - - + +
112A ASP* 1.3 74.1 - - - +
114A HIS* 1.3 63.9 + - - +
116A VAL* 3.1 12.3 + - + +
117A ALA* 3.0 21.0 + - - +
125A MET* 3.7 28.7 - - + +
129A LEU* 3.9 15.9 - - + -
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Residues in contact with HIS 114 (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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110A LEU 2.8 14.1 + - - +
111A LEU* 3.3 15.5 - - + +
112A ASP 3.2 0.2 - - - -
113A LEU* 1.3 77.6 - - - +
115A ALA* 1.3 58.1 + - - +
117A ALA* 3.2 4.9 + - - +
118A ALA* 2.9 32.7 + - + +
126A THR* 3.3 41.3 + - + +
129A LEU* 3.9 20.1 - - + +
130A GLU* 2.8 35.7 + - + -
134A LEU* 4.1 11.7 - - + -
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Residues in contact with ALA 115 (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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111A LEU 2.9 13.6 + - - +
112A ASP* 3.2 13.4 + - - +
114A HIS* 1.3 78.7 + - - +
116A VAL* 1.3 57.8 + - + +
118A ALA* 3.7 6.1 - - - +
119A ASP* 2.9 30.7 + - - +
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Residues in contact with VAL 116 (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 ASP* 3.9 29.2 - - + +
12A CYS* 3.7 19.7 - - - -
18A ARG* 6.1 2.5 - - - +
112A ASP 3.1 14.2 + - - +
113A LEU* 3.1 14.1 + - + +
115A ALA* 1.3 77.0 - - + +
117A ALA* 1.3 59.0 + - - +
119A ASP* 3.2 8.9 + - - +
120A LYS* 2.8 43.5 + - + +
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Residues in contact with ALA 117 (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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12A CYS* 3.8 12.3 - - - -
113A LEU 3.0 13.0 + - - +
114A HIS* 3.2 10.1 + - - +
116A VAL* 1.3 75.6 - - - +
118A ALA* 1.3 60.2 + - - +
120A LYS 3.3 1.9 + - - -
121A SER 3.1 4.7 + - - -
122A ASP* 2.9 28.4 + - + +
125A MET* 4.0 33.4 - - + -
126A THR* 3.7 17.3 - - + +
129A LEU* 4.8 0.2 - - + -
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Residues in contact with ALA 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A HIS* 2.9 23.5 + - + +
115A ALA* 3.7 7.6 - - - +
117A ALA* 1.3 75.4 - - - +
119A ASP* 1.3 57.8 + - - +
121A SER* 2.9 21.9 + - - +
122A ASP 4.8 1.1 - - - +
126A THR* 3.7 13.8 - - + +
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Residues in contact with ASP 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ALA 2.9 19.0 + - - +
116A VAL* 3.5 7.6 - - - +
118A ALA* 1.3 77.1 - - - +
120A LYS* 1.3 82.5 + - - +
121A SER* 3.2 3.4 + - - -
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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