Contacts of the helix formed by residues 88 - 114 (chain A) in PDB entry 2E1B
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 ASP 88 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ASP* 5.6 0.3 - - - +
48A ARG* 2.6 33.7 + - + +
49A GLY* 3.7 6.7 - - - -
87A ILE* 1.3 66.0 - - - +
89A TRP* 1.3 67.0 + - - +
90A ASP* 3.7 8.8 + - - +
91A TYR* 3.0 31.8 + - + +
92A ARG* 2.9 20.3 + - - +
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Residues in contact with TRP 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ASP* 4.6 3.8 - - - -
14A TYR* 3.3 61.9 - + + -
15A LEU 4.7 2.0 - - - -
16A LYS* 3.2 49.1 - - + +
87A ILE* 2.4 17.2 + - + +
88A ASP* 1.3 68.1 + - - +
90A ASP* 1.3 63.6 + - - +
92A ARG* 2.7 29.8 + - + +
93A TYR* 2.5 63.7 + + + +
96A MET* 4.5 5.6 - - - -
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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
----------------------------------------------------------
88A ASP* 3.2 8.1 + - - +
89A TRP* 1.3 89.8 - - - +
91A TYR* 1.3 55.9 + - - +
93A TYR* 4.4 5.8 - - - +
94A LYS* 2.7 69.5 + - - +
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Residues in contact with TYR 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PRO* 4.2 15.2 - - - +
46A HIS* 3.9 8.5 + - - -
47A ASP* 3.7 30.7 - - - -
48A ARG* 3.1 52.9 + - + -
88A ASP* 3.0 27.9 + - - +
90A ASP* 1.3 78.3 - - - +
92A ARG* 1.3 61.7 + - - +
94A LYS* 4.2 5.6 - - - +
95A LEU* 3.5 30.7 + - + +
127A VAL* 3.2 41.5 - - + +
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Residues in contact with ARG 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A TYR* 3.4 11.0 - - - +
12A ASP* 3.3 35.0 + - - -
36A ILE* 2.5 46.1 + - - +
38A TYR* 4.3 1.8 - - - +
44A GLN* 5.4 2.0 - - - +
47A ASP* 2.6 33.6 + - + -
87A ILE* 3.5 12.8 - - + +
88A ASP 2.9 10.1 + - - +
89A TRP* 2.7 28.2 + - + +
91A TYR* 1.3 76.2 - - - +
93A TYR* 1.3 59.3 + - - +
95A LEU* 2.7 35.7 + - - +
96A MET* 3.1 11.4 + - - +
185A THR* 4.1 25.5 + - - +
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Residues in contact with TYR 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A TYR* 3.6 26.0 - + - -
89A TRP* 2.5 54.4 + + + +
90A ASP* 4.0 6.5 - - - +
92A ARG* 1.3 73.5 - - - +
94A LYS* 1.3 67.9 + - + +
95A LEU 3.1 0.7 + - - -
96A MET* 3.2 16.6 + - + +
97A ARG* 3.2 45.2 + - + +
187A VAL* 4.8 4.5 - - + -
192A GLU* 3.0 40.6 + - - +
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Residues in contact with LYS 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ASP* 2.7 62.8 + - - +
91A TYR* 4.7 4.9 - - - +
93A TYR* 1.3 78.8 - - + +
95A LEU* 1.3 58.8 + - - +
97A ARG* 4.2 29.3 + - - +
98A ILE* 3.0 31.3 + - - +
127A VAL 4.8 8.5 - - - +
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Residues in contact with LEU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A GLN* 4.2 23.1 - - + +
45A PRO* 3.8 31.6 - - + +
47A ASP* 5.0 5.2 - - + +
91A TYR* 3.5 29.8 + - + +
92A ARG* 2.7 20.6 + - - +
94A LYS* 1.3 80.5 - - - +
96A MET* 1.3 51.4 + - + +
97A ARG 3.3 0.4 - - - -
98A ILE* 3.1 5.0 + - + +
99A HIS* 2.6 38.9 + - - +
125A MET* 4.4 6.2 - - + +
126A SER 3.6 24.2 - - - +
127A VAL* 3.7 21.5 - - + +
185A THR* 4.9 0.7 - - - +
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Residues in contact with MET 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ASP* 3.5 24.7 - - - +
14A TYR* 3.9 18.8 - - + -
89A TRP* 4.5 4.5 - - - -
92A ARG* 3.1 20.1 + - - +
93A TYR* 3.5 27.4 - - - +
95A LEU* 1.3 74.2 - - - +
97A ARG* 1.3 56.6 + - - +
99A HIS* 4.0 0.2 - - - +
100A THR* 2.7 39.7 + - - -
185A THR* 3.2 33.4 - - - +
186A HIS 3.0 28.5 - - - +
187A VAL* 3.4 18.8 - - + +
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Residues in contact with ARG 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A TYR* 3.2 39.6 + - + +
94A LYS* 4.3 29.8 + - - +
96A MET* 1.3 78.6 - - - +
98A ILE* 1.3 56.7 + - - +
101A GLY* 2.8 21.8 + - - -
187A VAL* 3.5 9.4 - - + +
192A GLU 2.9 22.6 + - - +
193A ILE* 2.7 46.1 + - - +
194A GLY* 4.7 2.2 - - - -
215A LEU* 3.6 24.5 - - + +
216A GLU 3.0 28.1 + - - +
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Residues in contact with ILE 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A LYS 3.0 23.6 - - - +
95A LEU* 3.1 9.8 + - - +
96A MET 3.1 0.4 - - - -
97A ARG* 1.3 74.9 - - - +
99A HIS* 1.3 61.8 - - - +
101A GLY* 2.8 17.1 + - - -
102A LEU* 3.0 15.3 + - + +
125A MET* 3.9 27.1 - - + -
126A SER 4.0 5.6 - - - +
127A VAL 3.4 19.7 - - - +
128A GLU 3.2 31.0 - - - +
129A LYS 4.3 0.4 - - - +
130A GLY* 4.2 15.5 - - - +
213A MET* 5.4 5.2 - - + +
215A LEU* 4.2 19.5 - - + -
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Residues in contact with HIS 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A TYR* 5.5 0.2 - - - -
42A GLY* 4.1 7.4 - - - -
44A GLN* 2.8 38.4 + - + +
95A LEU 2.6 20.4 + - - +
96A MET 4.0 2.2 - - - +
98A ILE* 1.3 74.7 - - - +
100A THR* 1.3 63.7 + - - +
101A GLY 3.2 0.7 + - - -
102A LEU* 3.3 12.4 + - + +
103A HIS* 3.5 8.6 + + - -
125A MET* 3.3 34.1 - - + +
182A CYS* 3.0 15.4 - - - -
183A GLY 5.2 0.4 - - - -
184A GLY* 4.1 6.1 - - - -
185A THR 4.3 2.7 - - - +
186A HIS* 3.3 21.9 - + + +
300A ZN 2.7 30.8 - - - -
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Residues in contact with THR 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A MET 2.7 27.5 + - - -
97A ARG 3.9 0.2 - - - -
99A HIS* 1.3 73.1 - - - +
101A GLY* 1.3 63.2 + - - +
103A HIS* 3.5 5.5 + - + +
104A LEU* 3.3 15.6 + - - +
161A VAL* 4.2 8.5 - - + -
174A ILE* 4.1 8.2 - - + +
186A HIS* 3.0 22.1 + - - +
187A VAL* 3.1 29.1 + - + -
190A ILE* 3.9 17.7 - - + -
193A ILE* 3.5 23.7 - - + +
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Residues in contact with GLY 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ARG 2.8 12.9 + - - -
98A ILE* 2.8 12.2 + - - -
100A THR* 1.3 78.4 - - - +
102A LEU* 1.3 55.8 + - - -
104A LEU* 2.9 7.3 + - - +
105A LEU* 2.8 26.0 + - - +
151A PHE* 3.8 16.0 - - - -
193A ILE* 3.9 10.3 - - - -
213A MET* 4.0 11.4 - - - -
215A LEU* 5.7 0.4 - - - -
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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
----------------------------------------------------------
98A ILE* 3.0 12.7 + - + +
99A HIS* 3.3 8.9 + - + +
101A GLY* 1.3 75.9 - - - +
103A HIS* 1.3 66.1 + - + +
105A LEU* 3.1 4.0 + - + +
106A GLU 3.0 17.7 + - - -
123A SER* 4.0 18.8 - - - +
124A GLY 4.0 16.6 - - - +
125A MET* 4.1 25.8 - - + -
130A GLY* 4.5 5.2 - - - -
131A ARG 4.2 15.3 - - - +
132A TYR* 3.7 35.4 + - + -
213A MET* 3.4 25.4 - - + -
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Residues in contact with HIS 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A HIS* 3.5 12.3 + + - -
100A THR* 3.5 9.3 + - - +
101A GLY 3.2 0.8 - - - -
102A LEU* 1.3 78.8 - - + +
104A LEU* 1.3 64.7 + - - +
106A GLU* 3.0 20.8 + - - +
107A HIS* 3.3 7.3 + - - +
132A TYR* 4.9 1.6 - - - -
161A VAL* 5.9 2.6 - - - +
172A THR* 3.3 19.6 + - - -
173A GLN* 5.7 1.4 + - - -
174A ILE* 4.2 16.2 - - + +
178A GLU* 4.7 1.0 - - - +
180A ILE* 3.8 32.9 - - + +
182A CYS* 3.2 29.9 - - + +
186A HIS* 3.2 32.7 - + - -
300A ZN 3.4 16.9 - - - -
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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
----------------------------------------------------------
100A THR 3.3 9.1 + - - +
101A GLY* 2.9 9.9 + - - +
103A HIS* 1.3 76.0 - - - +
105A LEU* 1.3 67.2 + - - +
107A HIS* 3.1 4.6 + - + +
108A VAL* 2.8 31.5 + - + +
151A PHE* 3.3 45.1 - - + +
154A TYR* 4.0 12.6 - - + -
155A VAL* 4.4 4.9 - - + -
174A ILE* 3.8 19.2 - - + +
177A PHE* 3.7 31.2 - - + -
190A ILE* 4.1 22.2 - - + -
193A ILE* 4.9 3.1 - - + -
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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 GLY 2.8 6.1 + - - -
102A LEU* 3.4 9.4 - - + +
104A LEU* 1.3 77.3 - - - +
106A GLU* 1.3 57.6 + - - +
108A VAL* 4.2 5.6 - - + -
109A LEU* 2.8 50.1 + - + +
132A TYR* 4.2 20.2 - - + -
147A ILE* 3.8 29.2 - - + -
151A PHE* 4.5 9.6 - - + -
196A ILE* 6.0 1.6 - - + -
199A LEU* 4.9 9.4 - - + -
211A LEU* 3.9 25.1 - - + +
213A MET* 3.3 34.1 - - + -
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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
----------------------------------------------------------
102A LEU 3.0 6.9 + - - +
103A HIS* 3.1 13.4 - - - +
105A LEU* 1.3 77.1 - - - +
107A HIS* 1.3 61.1 + - - +
109A LEU* 3.4 3.3 + - - +
110A ASN* 3.1 28.5 + - - +
118A TRP* 3.6 16.7 - - + -
120A LEU* 5.0 5.9 - - - +
132A TYR* 3.1 33.1 + - - +
178A GLU* 4.0 13.9 - - + +
180A ILE* 2.9 38.5 - - + +
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Residues in contact with HIS 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A HIS 3.3 4.5 + - - +
104A LEU* 3.1 9.0 + - + +
106A GLU* 1.3 76.0 - - - +
108A VAL* 1.3 60.4 + - - +
110A ASN* 2.6 25.3 + - - +
111A GLU* 2.9 42.2 + - + +
115A GLU* 5.8 0.7 - - - -
154A TYR* 3.8 18.6 + + - -
177A PHE* 3.4 61.2 - + + +
178A GLU* 2.5 49.1 + - - +
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Residues in contact with VAL 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LEU* 2.8 26.7 + - + +
105A LEU* 3.7 6.5 - - + +
107A HIS* 1.3 74.4 - - - +
109A LEU* 1.3 57.7 + - - +
111A GLU* 3.2 6.2 + - - +
112A VAL* 2.9 28.3 + - + +
147A ILE* 3.6 42.2 - - + +
150A LEU* 3.7 15.3 - - + -
151A PHE* 3.9 17.7 - - + +
154A TYR* 3.5 32.8 - - + -
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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
----------------------------------------------------------
105A LEU* 2.8 44.2 + - + +
106A GLU 3.6 4.7 - - - +
108A VAL* 1.3 71.9 - - - +
110A ASN* 1.3 60.7 + - - +
112A VAL* 4.5 1.3 - - - +
113A LEU* 2.7 55.1 + - + +
118A TRP* 3.8 27.1 - - + +
132A TYR* 4.0 20.2 - - + -
134A ILE* 4.6 7.9 - - + -
140A LEU* 5.5 0.7 - - + -
147A ILE* 3.8 31.2 - - + -
211A LEU* 4.0 17.5 - - + -
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Residues in contact with ASN 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A GLU* 3.1 14.0 + - - +
107A HIS* 2.6 18.6 + - - +
109A LEU* 1.3 70.9 - - - +
111A GLU* 1.3 56.1 + - - +
114A GLY* 2.6 32.4 + - - -
115A GLU* 3.1 41.6 + - + +
116A GLY 4.7 0.8 - - - +
118A TRP* 2.8 32.8 - - - +
178A GLU* 3.0 33.7 - - - +
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Residues in contact with GLU 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A HIS* 2.9 41.8 + - + +
108A VAL 3.5 7.2 - - - +
110A ASN* 1.3 79.6 - - - +
112A VAL* 1.3 61.0 + - - +
114A GLY* 4.2 2.4 + - - -
115A GLU* 4.4 11.4 - - - +
146A GLN* 5.5 0.4 + - - -
150A LEU* 3.9 13.9 - - + -
154A TYR* 3.6 20.9 + - - +
----------------------------------------------------------
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Residues in contact with VAL 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A VAL* 2.9 22.6 + - + +
109A LEU* 4.2 2.0 - - - +
111A GLU* 1.3 77.0 - - - +
113A LEU* 1.3 68.0 + - + +
114A GLY 3.6 0.2 + - - -
143A TYR* 3.7 40.4 - - + -
146A GLN* 3.5 43.1 + - - +
147A ILE* 4.4 11.7 - - + -
150A LEU* 3.5 20.2 - - + -
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Residues in contact with LEU 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A LEU* 2.7 39.8 + - + +
112A VAL* 1.3 79.1 - - + +
114A GLY* 1.3 56.1 + - - +
117A ASN* 3.1 20.5 + - + +
118A TRP* 4.1 22.7 - - + -
134A ILE* 4.3 3.8 - - + -
136A TYR* 3.3 53.0 + - + +
140A LEU* 3.9 21.5 - - + -
143A TYR* 3.8 30.1 - - + -
147A ILE* 5.8 0.4 - - + -
----------------------------------------------------------
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Residues in contact with GLY 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A LEU 3.4 0.4 + - - -
110A ASN* 2.6 21.4 + - - -
111A GLU 4.6 2.0 - - - -
112A VAL 3.3 1.6 - - - -
113A LEU* 1.3 74.2 - - - +
115A GLU* 1.3 69.2 + - - -
116A GLY 3.0 0.5 + - - -
117A ASN* 2.9 29.2 + - - +
118A TRP* 3.8 6.1 - - - -
----------------------------------------------------------
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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