Contacts of the helix formed by residues 132 - 157 (chain B) in PDB entry 2RD9
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 VAL 132 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 3.8 24.9 - - + -
64B ILE* 3.7 29.6 - - + +
65B LEU* 4.2 10.5 - - + -
112B VAL* 4.1 8.3 - - + -
117B ASP 3.7 12.6 - - - +
118B LEU* 3.4 19.0 + - + +
120B ARG* 2.9 21.2 + - + +
131B LYS* 1.3 70.2 - - - +
133B ARG* 1.3 65.8 + - - +
135B LEU* 3.0 5.2 + - - +
136B LEU* 3.0 44.1 + - + +
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Residues in contact with ARG 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ASP* 4.5 5.5 + - - +
1B MSE 4.0 38.1 - - - +
3B PHE* 4.2 33.0 + - + +
115B GLU* 4.9 9.9 + - - +
118B LEU* 3.0 52.3 + - + +
119B GLU* 2.7 29.4 + - - -
131B LYS* 3.8 20.4 - - + -
132B VAL* 1.3 75.7 - - - +
134B GLU* 1.3 58.7 + - + +
136B LEU* 3.6 4.1 + - - +
137B SER* 2.6 38.9 + - - +
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Residues in contact with GLU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ASP 3.4 22.0 - - - +
162A VAL 4.0 6.0 - - - +
163A GLY* 3.8 8.5 - - - +
164A PRO* 3.7 22.7 - - - +
165A TRP* 3.6 14.0 - - + -
1B MSE 5.0 11.0 - - + +
129B VAL 4.4 2.1 - - - +
130B VAL* 3.4 9.9 - - - -
131B LYS* 2.9 44.2 + - + +
133B ARG* 1.3 80.0 - - + +
135B LEU* 1.3 65.2 + - - +
137B SER* 3.8 0.9 - - - -
138B ALA* 3.1 24.8 + - - +
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Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A TRP* 3.6 34.3 - - + -
57B TRP* 3.6 31.8 - - + +
60B ARG* 3.9 23.3 - - + -
61B LEU* 3.4 46.0 - - + +
64B ILE* 4.1 11.0 - - + -
73B PHE* 5.0 2.9 - - + -
131B LYS 3.2 9.7 + - - +
132B VAL 3.0 8.7 + - - +
134B GLU* 1.3 74.1 - - - +
136B LEU* 1.3 63.7 + - + +
138B ALA* 3.2 4.9 + - - +
139B TRP* 2.9 25.6 + - - +
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Residues in contact with LEU 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B PHE* 3.8 22.4 - - + -
5B MSE 4.2 6.7 - - - -
8B ALA* 5.8 0.4 - - + -
12B LEU* 5.0 1.9 - - + +
57B TRP 6.5 0.7 - - - -
61B LEU* 4.4 14.1 - - + -
108B LEU* 3.6 36.3 - - + -
112B VAL* 4.6 1.3 - - + -
118B LEU* 3.8 18.2 - - + -
132B VAL* 3.0 36.8 + - + +
133B ARG 4.0 1.3 - - - +
135B LEU* 1.3 80.3 - - + +
137B SER* 1.3 60.7 + - - +
139B TRP* 3.3 28.2 - - + +
140B VAL* 3.1 31.0 + - - +
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Residues in contact with SER 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A TYR* 3.8 12.8 - - - -
161A ASP* 3.3 41.1 - - - +
162A VAL* 3.8 4.3 - - - -
3B PHE* 3.2 18.5 - - - +
133B ARG* 2.6 22.8 + - - +
134B GLU 3.8 1.6 - - - -
136B LEU* 1.3 74.7 - - - +
138B ALA* 1.3 60.4 + - - +
140B VAL* 3.2 3.1 + - - +
141B VAL* 2.9 33.4 + - - +
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Residues in contact with ALA 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A VAL* 3.8 11.1 - - + +
165A TRP* 3.8 37.0 - - + -
169A LEU* 4.2 8.1 - - + +
57B TRP* 3.8 13.2 - - + -
134B GLU 3.1 19.4 + - - +
135B LEU 3.5 4.5 - - - +
137B SER* 1.3 72.0 - - - +
139B TRP* 1.3 55.8 + - - +
141B VAL* 4.0 0.4 - - - +
142B HIS* 2.7 37.2 + - - +
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Residues in contact with TRP 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU* 3.7 24.8 - - + +
53B GLU* 3.3 28.1 + - - -
57B TRP* 3.1 56.7 - + + -
58B ILE* 3.9 31.2 - - + -
101B ARG* 3.5 20.5 - - - +
104B ASN* 4.1 16.4 - - + -
105B LEU* 4.3 9.2 - - + -
108B LEU* 4.0 18.6 - - + -
135B LEU 2.9 13.1 + - - +
136B LEU* 3.3 29.6 - - + +
138B ALA* 1.3 76.8 - - - +
140B VAL* 1.3 61.2 + - - +
142B HIS* 3.3 6.8 + - + +
143B ASP* 3.3 11.6 + - - +
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Residues in contact with VAL 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A TRP* 4.3 2.2 - - + -
158A TYR* 3.8 21.1 - - + -
8B ALA* 3.6 40.2 - - + +
11B LEU* 3.6 32.3 - - + -
12B LEU* 3.8 17.0 - - + -
136B LEU 3.1 17.8 + - - +
137B SER 3.2 6.5 + - - +
139B TRP* 1.3 75.5 - - - +
141B VAL* 1.3 64.4 + - - +
142B HIS 3.3 0.5 + - - -
143B ASP* 3.3 5.2 + - - +
144B LEU* 3.2 25.9 + - + +
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Residues in contact with VAL 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ALA* 3.7 26.9 - - + +
158A TYR* 3.5 30.5 - - + -
162A VAL* 3.6 12.1 - - + -
169A LEU* 3.7 23.3 - - + -
137B SER 2.9 21.0 + - - +
138B ALA 4.0 2.2 - - - +
140B VAL* 1.3 77.6 - - + +
142B HIS* 1.3 57.1 + - - +
144B LEU* 3.7 5.9 - - - +
145B THR* 2.8 45.9 + - - +
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Residues in contact with HIS 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A LEU* 4.1 12.7 - - + +
303A IMD 3.2 14.6 - + - -
48B HIS* 3.4 9.9 - + - -
49B LEU* 4.0 12.2 - - + +
52B ALA* 4.3 13.2 - - + +
57B TRP* 3.5 25.7 + + + -
138B ALA 2.7 22.2 + - - +
139B TRP 3.5 3.1 - - - +
140B VAL 3.2 0.2 - - - -
141B VAL* 1.3 71.9 - - - +
143B ASP* 1.3 67.0 + - - +
145B THR* 3.5 2.0 + - - -
146B HIS* 3.1 42.4 + + - -
300B NI 2.1 45.1 - - + +
-9C HIS* 3.0 14.4 + + - -
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Residues in contact with ASP 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 5.2 0.6 - - + -
12B LEU* 3.7 8.1 - - + +
15B THR* 2.7 36.5 + - + +
49B LEU* 4.0 19.5 - - - +
57B TRP* 5.7 0.2 + - - -
97B PHE* 4.5 0.2 - - - -
101B ARG* 2.7 38.1 + - - -
139B TRP* 3.3 13.0 + - - +
140B VAL* 3.4 11.0 - - - +
142B HIS* 1.3 79.5 + - - +
144B LEU* 1.3 65.2 + - + +
146B HIS* 3.2 4.3 + - - +
147B ILE* 3.0 29.3 + - + +
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Residues in contact with LEU 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PHE* 3.8 29.6 - - + -
151A VAL* 2.9 38.9 - - + +
154A MSE 3.8 7.9 - - + +
155A ALA* 3.5 39.5 - - + +
11B LEU* 3.8 34.3 - - + -
15B THR* 6.1 0.2 - - - +
140B VAL* 3.2 20.7 + - + +
141B VAL* 3.8 6.1 - - + +
143B ASP* 1.3 81.7 - - + +
145B THR* 1.3 61.6 + - - +
147B ILE* 3.3 7.3 + - + +
148B ALA* 3.1 10.6 + - - +
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Residues in contact with THR 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ALA* 5.2 3.5 - - - +
169A LEU* 3.5 26.0 + - - +
172A LEU* 3.7 24.1 - - + +
303A IMD 3.9 9.6 - - + -
141B VAL* 2.8 40.0 + - - +
142B HIS* 3.8 7.2 - - - -
144B LEU* 1.3 72.6 - - - +
146B HIS* 1.3 58.0 + - - +
148B ALA* 3.5 7.0 + - - +
149B GLN* 2.9 24.6 + - - +
152B ARG* 4.9 1.7 + - - -
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Residues in contact with HIS 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A LEU* 4.5 4.9 - - + +
173A ASN 5.6 3.1 - - - -
303A IMD 3.2 12.4 + + - -
40B TRP* 4.4 8.1 - + - -
45B VAL* 3.6 17.3 - - + +
48B HIS* 3.0 14.5 + + - -
49B LEU* 4.0 13.7 - - + -
142B HIS* 3.1 42.7 + + - +
143B ASP 3.9 2.5 - - - +
145B THR* 1.3 74.1 - - - +
147B ILE* 1.3 61.2 + - - +
149B GLN* 2.7 30.1 + - - +
150B ILE* 2.8 34.5 + - - +
300B NI 2.2 36.2 - - + +
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Residues in contact with ILE 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PHE* 4.0 29.6 - - + -
147A ILE* 5.0 2.9 - - + -
151A VAL* 3.7 20.2 - - + -
15B THR* 4.0 24.2 - - + +
18B THR* 5.3 7.0 - - + -
19B LEU* 4.0 23.8 - - + -
22B PHE* 6.0 2.7 - - + -
49B LEU* 5.8 0.4 - - + -
143B ASP 3.0 24.6 + - - +
144B LEU* 3.3 13.0 + - + +
146B HIS* 1.3 75.7 - - - +
148B ALA* 1.3 56.7 + - - +
150B ILE* 3.1 12.1 + - + +
151B VAL* 2.8 38.0 + - + +
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Residues in contact with ALA 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ALA* 5.0 9.2 - - + -
151A VAL* 4.0 16.1 - - + +
152A ARG* 4.9 14.6 - - + +
144B LEU 3.1 13.2 + - - +
145B THR* 3.6 11.4 - - - +
147B ILE* 1.3 73.5 - - - +
149B GLN* 1.3 58.9 + - - +
151B VAL* 3.7 6.8 - - - +
152B ARG* 2.9 50.9 + - - +
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Residues in contact with GLN 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A LEU* 4.1 15.7 - - + +
173A ASN* 3.0 36.6 + - - +
35B GLU* 4.0 14.3 + - + +
39B THR* 5.5 1.2 - - - -
40B TRP* 4.4 7.5 + - - +
45B VAL* 3.5 23.9 - - + +
145B THR 2.9 15.0 + - - +
146B HIS* 2.7 43.3 + - - +
147B ILE 3.2 0.2 - - - -
148B ALA* 1.3 76.9 - - - +
150B ILE* 1.3 62.8 + - - +
152B ARG* 3.7 15.9 - - - +
153B SER* 3.0 31.4 + - - +
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Residues in contact with ILE 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU* 4.1 24.7 - - + -
22B PHE* 4.4 8.7 - - + -
23B LEU* 4.2 8.5 - - + -
42B VAL* 3.7 31.5 - - + +
45B VAL* 3.7 29.8 - - + -
46B VAL* 4.0 23.1 - - + +
49B LEU* 5.1 0.7 - - + -
146B HIS 2.8 16.1 + - - +
147B ILE* 3.4 8.3 - - - +
149B GLN* 1.3 77.3 - - - +
151B VAL* 1.3 62.7 + - - +
153B SER* 3.3 6.5 + - - -
154B MSE 3.2 36.7 + - - +
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Residues in contact with VAL 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A LEU* 2.9 43.1 - - + +
147A ILE* 3.6 24.5 - - + -
148A ALA* 4.0 15.0 - - + +
22B PHE* 3.8 23.3 - - + -
147B ILE* 2.8 26.0 + - + +
148B ALA* 3.8 6.7 - - - +
150B ILE* 1.3 76.6 - - - +
152B ARG* 1.3 56.8 + - - +
154B MSE 3.3 8.6 + - - +
155B ALA* 3.0 26.0 + - + +
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Residues in contact with ARG 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ALA* 4.8 13.7 - - + -
152A ARG* 5.8 9.4 - - - +
172A LEU* 3.2 25.9 - - - +
35B GLU* 2.8 47.2 + - - +
145B THR 4.9 1.0 + - - -
148B ALA* 2.9 41.3 + - - +
149B GLN* 3.7 9.1 - - - +
151B VAL* 1.3 73.1 - - - +
153B SER* 1.3 61.3 + - - +
155B ALA* 3.4 8.1 + - - +
156B LYS* 2.9 29.1 + - - +
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Residues in contact with SER 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B CYS* 3.3 21.8 + - - +
34B ASN* 3.4 44.1 - - - +
35B GLU* 3.6 10.5 + - - +
40B TRP 4.5 5.0 + - - -
41B THR 5.6 0.2 - - - -
42B VAL* 4.2 4.5 + - - +
149B GLN* 3.0 19.1 + - - +
150B ILE* 3.4 9.7 - - - -
152B ARG* 1.3 74.7 - - - +
154B MSE 1.3 62.8 + - - +
156B LYS* 3.4 7.5 + - - -
157B ARG 3.5 6.8 + - - -
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Residues in contact with MSE 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 3.0 40.8 - - + -
144A LEU* 3.8 13.0 - - + +
22B PHE* 3.8 24.2 - - + -
23B LEU* 3.8 22.0 - - + -
26B LEU* 3.6 17.0 - - + -
30B TRP* 3.5 24.3 - - + +
33B CYS* 3.5 19.1 - - - -
42B VAL* 4.1 5.4 - - + -
150B ILE* 3.2 18.7 + - - +
151B VAL 3.6 7.2 - - - +
153B SER* 1.3 77.0 - - - +
155B ALA* 1.3 61.3 + - - +
157B ARG* 3.2 19.4 - - - +
158B TYR* 4.3 2.1 + - - -
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Residues in contact with ALA 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A VAL* 4.0 24.4 - - + +
144A LEU* 3.5 25.0 - - + +
145A THR* 5.0 4.7 - - - +
151B VAL 3.0 16.9 + - - +
152B ARG* 3.8 9.0 - - - +
153B SER 3.3 0.2 - - - -
154B MSE 1.3 75.0 - - - +
156B LYS* 1.3 62.8 + - - +
158B TYR* 3.1 20.1 + - - +
159B ASP* 3.8 6.5 + - - +
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Residues in contact with LYS 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-1A GLN* 2.7 41.4 + - - +
305A GOL 2.7 40.6 + - - -
34B ASN 4.1 5.2 - - - +
35B GLU* 3.5 36.3 - - + +
36B GLY* 4.1 4.2 - - - +
152B ARG 2.9 17.7 + - - +
153B SER* 3.6 7.9 - - - +
154B MSE 3.3 0.2 - - - -
155B ALA* 1.3 73.1 - - - +
157B ARG* 1.3 53.0 + - - +
158B TYR 3.1 3.1 + - - -
159B ASP* 3.2 28.5 + - - +
167C GLU* 3.4 12.7 + - - -
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Residues in contact with ARG 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-1A GLN* 3.3 7.1 + - - +
2A ASN* 2.8 67.9 + - + +
4A GLN* 5.4 1.2 - - - +
7A GLU* 3.1 28.7 + - - -
29B SER* 3.5 32.3 + - - -
30B TRP* 4.0 29.5 - - + -
33B CYS* 4.0 23.1 - - + -
153B SER 3.5 6.3 + - - +
154B MSE 3.2 18.8 + - - +
156B LYS* 1.3 77.3 - - - +
158B TYR* 1.3 61.5 + - + +
161B ASP* 3.4 2.8 - - - +
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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