Contacts of the helix formed by residues 95 - 121 (chain A) in PDB entry 4ECB
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 CYS 95 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A GLY 3.4 1.0 - - - -
94A GLY* 1.3 79.5 - - - +
96A PRO* 1.3 79.3 - - + +
97A LYS* 3.2 14.7 + - - -
98A GLU* 3.2 23.4 + - - +
99A ARG* 3.0 31.4 + - - +
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Residues in contact with PRO 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A CYS* 1.3 87.4 - - + +
97A LYS* 1.3 62.4 + - - +
99A ARG* 3.7 11.6 - - - +
100A ALA* 3.1 24.9 + - - +
84B TYR* 3.7 12.4 - - + -
87B ASP* 3.3 34.5 - - + +
88B LYS* 3.8 35.7 - - + +
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Residues in contact with LYS 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A CYS* 3.2 13.1 - - - -
96A PRO* 1.3 79.9 - - - +
98A GLU* 1.3 58.9 + - - +
100A ALA* 3.5 3.7 + - - +
101A GLU* 3.0 40.3 + - - +
72B ASP* 3.6 47.7 + - - +
73B VAL* 3.8 25.6 - - + +
75B LEU* 5.3 1.4 - - + +
84B TYR* 4.2 8.6 - - + -
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Residues in contact with GLU 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A GLY* 3.3 9.9 - - - -
94A GLY* 2.7 32.7 + - - +
95A CYS* 3.2 18.5 + - - +
97A LYS* 1.3 81.0 - - - +
99A ARG* 1.3 57.1 + - - +
101A GLU* 3.3 7.7 - - + +
102A ILE* 3.1 27.7 + - + +
154A ASN* 3.2 29.7 + - - +
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Residues in contact with ARG 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ARG* 5.1 8.7 + - - +
92A LEU* 3.3 29.3 - - + +
93A GLY 2.8 44.0 + - - +
94A GLY* 3.5 6.3 + - - -
95A CYS* 3.0 27.1 + - - +
96A PRO* 3.7 18.0 - - - +
98A GLU* 1.3 75.4 - - - +
100A ALA* 1.3 58.4 + - - +
102A ILE* 3.4 3.1 + - - +
103A SER* 2.9 30.8 + - - -
87B ASP* 2.9 43.1 + - - +
92B LEU* 5.2 5.7 - - + +
99B ARG* 6.3 2.5 - - - +
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Residues in contact with ALA 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A PRO 3.1 18.6 + - - +
97A LYS* 3.7 3.6 - - - +
99A ARG* 1.3 74.1 - - - +
101A GLU* 1.3 55.1 + - - +
103A SER* 3.2 8.1 + - - -
104A MET* 2.8 35.9 + - - +
75B LEU* 3.6 35.0 - - + -
80B ALA* 3.7 7.7 - - - +
83B ARG* 6.5 0.4 - - - -
84B TYR* 3.9 17.5 - - + +
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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 LYS* 3.0 30.9 + - - +
98A GLU* 3.3 14.8 + - - +
100A ALA* 1.3 76.1 - - - +
102A ILE* 1.3 61.6 + - - +
104A MET* 3.4 30.3 + - - +
105A LEU* 3.1 28.1 + - + +
146A ARG* 3.1 40.9 + - - +
154A ASN* 3.9 12.3 - - - +
75B LEU* 4.4 1.7 - - - +
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Residues in contact with ILE 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ARG* 4.7 4.0 - - - +
91A MET 3.8 11.0 - - - +
92A LEU* 3.3 31.6 - - - +
93A GLY* 4.1 2.5 - - - +
98A GLU* 3.1 21.3 + - + +
99A ARG 3.8 4.0 - - - +
100A ALA 3.2 0.4 - - - -
101A GLU* 1.3 73.9 - - - +
103A SER* 1.3 63.8 + - - +
105A LEU* 3.3 11.0 + - + +
106A GLU* 3.0 21.4 + - - +
154A ASN* 3.7 34.5 - - + +
159A THR* 4.1 11.7 - - + +
160A HIS* 3.7 30.1 - - + +
161A PRO* 3.7 11.1 - - + +
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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
----------------------------------------------------------
83A ARG* 3.3 25.9 + - - +
99A ARG 2.9 17.7 + - - -
100A ALA* 3.2 7.8 + - - -
102A ILE* 1.3 75.9 - - - +
104A MET* 1.3 56.7 + - - +
106A GLU* 3.1 16.7 + - - +
107A GLY* 2.9 25.1 + - - -
77B GLN* 4.9 0.7 - - - +
79B MET* 5.3 1.2 - - - +
80B ALA* 3.8 23.5 + - - +
83B ARG* 3.9 16.2 + - - +
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Residues in contact with MET 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ALA 2.8 17.4 + - - +
101A GLU* 3.4 35.2 - - - +
103A SER* 1.3 75.5 - - - +
105A LEU* 1.3 62.8 + - + +
107A GLY 3.2 0.7 + - - -
108A ALA* 2.9 30.2 + - + +
142A MET* 5.9 3.6 - - + -
146A ARG* 5.3 2.7 - - - +
74B LYS 4.2 9.6 - - - +
75B LEU* 4.0 18.4 - - + -
76B THR* 3.4 50.3 - - - +
77B GLN* 3.5 8.8 - - + +
80B ALA* 3.7 7.6 - - + +
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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
----------------------------------------------------------
101A GLU 3.1 20.3 + - - +
102A ILE* 3.6 13.7 - - + +
104A MET* 1.3 74.8 - - + +
106A GLU* 1.3 65.8 + - - +
108A ALA* 3.3 5.3 + - - +
109A VAL* 2.9 30.4 + - - +
142A MET* 4.6 7.9 - - + -
143A PHE* 4.3 15.2 - - + -
146A ARG* 3.6 40.8 - - - +
153A LEU* 3.9 38.4 - - + +
154A ASN* 4.5 9.9 - - + +
159A THR* 5.3 0.7 - - - +
161A PRO* 3.9 15.7 - - + -
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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
----------------------------------------------------------
79A MET* 3.3 31.0 - - + +
83A ARG* 2.7 35.1 + - - +
102A ILE 3.0 10.0 + - - +
103A SER* 3.1 18.4 + - - +
105A LEU* 1.3 78.1 - - - +
107A GLY* 1.3 56.6 + - - +
109A VAL* 3.3 0.8 + - - -
110A LEU* 3.0 35.9 + - + +
160A HIS* 2.6 26.3 + - - +
161A PRO* 4.2 3.8 - - + +
164A MET* 3.7 21.7 - - + +
83B ARG* 6.0 1.0 - - - -
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Residues in contact with GLY 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A SER 2.9 10.9 + - - -
104A MET 3.2 0.9 + - - -
106A GLU* 1.3 79.3 + - - +
108A ALA* 1.3 57.1 + - - +
110A LEU* 3.3 13.2 + - - +
111A ASP* 3.0 31.9 + - - +
77B GLN* 3.4 24.0 - - - +
79B MET* 6.6 0.2 - - - -
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Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A MET* 2.9 16.6 + - + +
105A LEU 3.7 3.6 - - - +
107A GLY* 1.3 77.7 - - - +
109A VAL* 1.3 61.1 + - - +
111A ASP* 3.6 12.2 + - - +
112A ILE* 3.8 12.0 + - - +
139A MET* 5.1 1.4 - - - +
142A MET* 3.2 35.2 - - + -
143A PHE* 3.7 10.6 - - + -
77B GLN* 3.6 14.8 - - + +
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Residues in contact with VAL 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LEU 2.9 23.9 + - - +
106A GLU* 3.7 4.3 - - - +
108A ALA* 1.3 73.5 - - - +
110A LEU* 1.3 65.6 + - - +
112A ILE* 3.0 8.6 + - - +
113A ARG* 3.0 22.5 + - + +
143A PHE* 3.7 23.1 - - + -
153A LEU* 4.9 2.2 - - + -
161A PRO* 4.1 7.4 - - + +
164A MET* 3.4 42.8 - - + +
165A LEU* 3.7 22.2 - - + +
168A ALA* 4.0 10.8 - - + -
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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
----------------------------------------------------------
13A LEU* 6.3 0.2 - - + -
79A MET* 4.0 33.0 - - + -
106A GLU* 3.0 24.4 + - + +
107A GLY* 3.3 8.7 + - - +
109A VAL* 1.3 77.2 - - + +
111A ASP* 1.3 56.2 + - - +
113A ARG* 4.3 10.8 - - + +
114A TYR* 2.7 77.3 + - + +
164A MET* 3.7 19.1 - - + -
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Residues in contact with ASP 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A GLY 3.0 15.4 + - - +
108A ALA* 3.8 8.0 - - - +
109A VAL 3.3 0.6 - - - -
110A LEU* 1.3 74.4 - - - +
112A ILE* 1.3 57.1 + - - +
114A TYR* 5.1 1.3 - - - -
115A GLY* 3.1 23.3 + - - +
132A PHE* 4.7 0.3 - - - -
139A MET* 3.3 28.6 - - + +
77B GLN* 2.9 29.2 + - - +
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Residues in contact with ILE 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ALA 3.9 7.6 - - - +
109A VAL* 3.0 9.2 + - - +
111A ASP* 1.3 74.7 - - - +
113A ARG* 1.3 60.7 + - - +
115A GLY* 3.0 2.8 + - - -
116A VAL* 3.0 28.9 + - + +
132A PHE* 3.7 4.8 - - + -
136A LEU* 3.9 9.0 - - + -
139A MET* 4.0 29.8 - - + -
140A LEU* 3.9 22.9 - - + -
143A PHE* 3.6 30.3 - - + -
165A LEU* 5.1 6.1 - - + -
168A ALA* 4.1 16.6 - - + -
169A LEU* 6.2 0.2 - - + -
172A VAL* 3.9 28.0 - - + -
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Residues in contact with ARG 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LYS* 5.4 0.6 - - - +
12A GLY* 4.1 18.4 + - - +
13A LEU* 5.9 5.8 - - + -
109A VAL* 3.0 16.6 + - + +
110A LEU* 4.2 13.2 - - + +
112A ILE* 1.3 78.0 - - - +
114A TYR* 1.3 68.4 + - + +
116A VAL* 3.3 14.1 + - - +
117A SER* 3.2 21.3 + - - +
164A MET 5.8 0.2 - - - +
167A ASP* 3.2 28.5 + - - +
168A ALA* 4.3 19.3 - - + +
171A VAL* 3.7 24.3 - - - +
213A LEU 3.1 19.6 + - - -
214A GLN* 2.9 31.8 + - - +
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Residues in contact with TYR 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 3.6 33.1 - - + +
78A SER* 4.4 9.0 + - - -
79A MET* 4.5 8.0 - - - +
110A LEU* 2.7 60.4 + - + +
111A ASP* 4.9 1.3 - - - +
113A ARG* 1.3 77.0 - - + +
115A GLY* 1.3 56.9 + - - +
117A SER* 4.0 10.0 - - - +
118A ARG* 2.8 36.0 + - - +
114B TYR* 6.0 7.9 - + - -
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Residues in contact with GLY 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ASP 3.1 15.5 + - - -
112A ILE 3.0 9.8 + - - -
114A TYR* 1.3 78.6 - - - +
116A VAL* 1.3 61.9 + - - +
118A ARG* 3.8 16.0 + - - +
119A ILE* 3.8 14.6 - - - +
132A PHE* 3.7 21.4 - - - -
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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
----------------------------------------------------------
112A ILE 3.0 15.0 + - - +
113A ARG* 3.5 12.1 - - - +
114A TYR 3.2 0.2 - - - -
115A GLY* 1.3 75.8 - - - +
117A SER* 1.3 63.5 + - - +
119A ILE* 3.2 11.3 + - - +
120A ALA* 3.1 18.6 + - + +
132A PHE* 3.7 21.3 - - + -
171A VAL* 3.8 17.3 - - + -
172A VAL* 4.0 15.3 - - + -
175A MET* 3.8 10.5 - - + -
214A GLN* 3.8 11.2 - - - +
220A PHE* 3.7 31.6 - - + -
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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
----------------------------------------------------------
13A LEU* 5.6 5.4 - - - +
113A ARG* 3.2 21.9 + - - +
114A TYR* 3.2 13.4 + - - -
116A VAL* 1.3 78.0 - - - +
118A ARG* 1.3 63.0 + - - +
119A ILE 3.2 0.9 + - - -
120A ALA* 3.6 2.3 + - - -
121A TYR* 3.5 26.5 - - - -
214A GLN* 2.8 30.7 + - - +
118B ARG* 5.2 1.6 + - - -
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Residues in contact with ARG 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A TYR 2.8 18.3 + - - +
115A GLY* 3.8 11.7 - - - +
116A VAL 3.2 0.2 - - - -
117A SER* 1.3 77.8 - - - +
119A ILE* 1.3 64.3 + - + +
121A TYR* 5.2 0.9 + - - +
122A SER* 4.6 4.0 + - - -
128A LEU* 5.8 0.2 - - - +
117B SER* 4.4 6.1 + - - -
118B ARG* 3.7 76.9 + - + +
121B TYR* 5.5 4.8 - - - +
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Residues in contact with ILE 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A GLY 3.8 11.0 - - - +
116A VAL* 3.3 13.5 - - - +
118A ARG* 1.3 84.8 - - + +
120A ALA* 1.3 64.2 + - - +
121A TYR 3.2 3.4 - - - -
122A SER* 3.2 24.9 + - - -
125A PHE* 3.7 30.3 - - + +
128A LEU* 3.7 31.2 - - + +
129A LYS* 3.7 31.6 - - + +
132A PHE* 4.0 17.9 - - + -
175A MET* 4.4 7.4 - - + -
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Residues in contact with ALA 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A VAL 3.1 16.5 + - - +
117A SER 3.6 6.7 + - - +
119A ILE* 1.3 77.2 - - + +
121A TYR* 1.3 53.9 + - + +
122A SER 3.5 0.7 - - - -
125A PHE* 4.3 9.6 - - - -
214A GLN* 3.9 21.5 - - + +
218A ALA* 3.6 1.2 - - - +
219A THR* 2.8 34.8 + - - -
220A PHE* 3.2 32.4 + - + +
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Residues in contact with TYR 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A SER* 3.5 23.5 + - - -
118A ARG 5.2 1.5 + - - +
119A ILE 3.2 1.0 - - - -
120A ALA* 1.3 78.1 - - + +
122A SER* 1.3 58.4 + - - +
123A LYS 4.0 0.9 + - - -
214A GLN* 3.5 24.2 + - + +
215A GLY* 2.9 24.8 + - - -
217A GLN* 3.8 34.5 - - + +
218A ALA* 3.6 26.5 - - + +
219A THR* 4.4 6.6 + - - +
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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