Contacts of the helix formed by residues 132 - 157 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 3.7 28.3 - - + -
64A ILE* 3.6 24.5 - - + -
65A LEU* 4.1 5.8 - - + -
112A VAL* 3.9 7.9 - - + -
117A ASP 3.3 26.0 - - - +
118A LEU* 3.4 8.4 + - - +
120A ARG* 2.8 24.7 + - + +
131A LYS* 1.3 70.4 - - - +
133A ARG* 1.3 58.7 + - - +
135A LEU* 3.1 9.6 + - - +
136A LEU* 2.9 43.6 + - + +
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Residues in contact with ARG 133 (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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1A MSE 4.1 36.7 - - - +
3A PHE* 4.2 27.4 - - + -
118A LEU* 3.1 33.0 + - + +
119A GLU* 2.9 33.1 + - - -
131A LYS* 3.1 37.2 - - + +
132A VAL* 1.3 77.2 - - - +
134A GLU* 1.3 72.0 + - - +
136A LEU* 4.0 3.9 - - - +
137A SER* 2.6 38.9 + - - +
161B ASP* 4.4 4.6 + - - +
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Residues in contact with GLU 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MSE 5.5 3.1 - - - +
129A VAL 4.4 1.9 - - - +
130A VAL* 3.5 10.2 - - - +
131A LYS* 3.0 42.6 + - + +
133A ARG* 1.3 95.7 + - - +
135A LEU* 1.3 59.2 + - - +
137A SER* 3.8 1.2 - - - -
138A ALA* 2.9 30.3 + - - +
160B THR 4.9 1.8 - - - +
161B ASP 3.3 20.6 - - - +
162B VAL* 4.0 9.8 - - - +
163B GLY* 3.5 22.4 - - - +
164B PRO* 4.1 6.4 - - - +
165B TRP* 3.8 10.7 - - + -
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Residues in contact with LEU 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ASN* 4.8 0.2 - - - +
57A TRP* 3.4 40.3 - - + +
60A ARG* 3.8 20.6 - - + -
61A LEU* 3.4 43.5 - - + +
64A ILE* 3.9 13.2 - - + -
131A LYS 3.1 9.4 + - - +
132A VAL* 3.1 9.9 + - - +
134A GLU* 1.3 72.4 - - - +
136A LEU* 1.3 66.6 + - + +
138A ALA* 3.4 3.4 + - - +
139A TRP* 3.0 26.2 + - - +
165B TRP* 3.7 31.2 - - + -
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Residues in contact with LEU 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A PHE* 3.8 18.2 - - + -
5A MSE 4.0 12.1 - - - -
8A ALA* 5.7 0.9 - - + -
12A LEU* 5.1 2.3 - - + +
57A TRP 6.0 0.4 - - - +
61A LEU* 4.5 14.1 - - + -
108A LEU* 3.7 36.3 - - + -
112A VAL* 4.5 0.9 - - + -
118A LEU* 3.7 29.6 - - + -
132A VAL* 2.9 26.4 + - + +
133A ARG 4.0 1.1 - - - +
135A LEU* 1.3 80.9 - - + +
137A SER* 1.3 62.8 + - - +
139A TRP* 3.2 39.0 - - + +
140A VAL* 3.2 14.2 + - - +
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Residues in contact with SER 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A PHE* 3.2 19.0 - - - +
133A ARG 2.6 25.5 + - - -
134A GLU 3.8 0.2 - - - -
136A LEU* 1.3 73.9 - - - +
138A ALA* 1.3 64.5 + - - +
140A VAL* 3.3 3.5 + - - +
141A VAL* 3.1 27.0 + - - +
158B TYR* 3.8 16.0 - - - -
161B ASP* 3.3 40.5 - - - +
162B VAL* 3.9 4.0 - - - -
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Residues in contact with ALA 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A TRP* 3.7 13.9 - - + -
134A GLU 2.9 19.0 + - - +
135A LEU 3.7 4.9 - - - +
137A SER* 1.3 76.2 - - - +
139A TRP* 1.3 51.4 + - - +
141A VAL* 3.4 1.4 + - - +
142A HIS* 2.7 35.2 + - - +
162B VAL* 3.9 12.5 - - + +
165B TRP* 3.9 37.7 - - + -
169B LEU* 4.0 7.2 - - + +
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Residues in contact with TRP 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 3.7 22.4 - - + -
53A GLU* 3.3 29.1 + - - -
57A TRP* 3.2 56.5 - + + -
58A ILE* 4.1 31.9 - - + -
101A ARG* 3.5 21.9 - - - +
104A ASN* 4.2 14.1 - - + -
105A LEU* 4.4 8.5 - - + -
108A LEU* 4.0 20.2 - - + -
135A LEU 3.0 12.6 + - - +
136A LEU* 3.2 32.5 - - + +
138A ALA* 1.3 76.5 - - - +
140A VAL* 1.3 61.5 + - - +
142A HIS* 3.3 2.9 + - - +
143A ASP* 3.2 20.8 + - - +
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Residues in contact with VAL 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ALA* 3.8 31.4 - - + +
11A LEU* 3.5 33.2 - - + -
12A LEU* 3.8 24.0 - - + -
136A LEU 3.2 12.4 + - - +
137A SER 3.3 6.7 + - - +
139A TRP* 1.3 74.3 - - - +
141A VAL* 1.3 63.7 + - - +
143A ASP* 3.3 8.5 + - - +
144A LEU* 3.1 26.7 + - + +
30B TRP* 4.5 1.3 - - + -
158B TYR* 3.8 22.2 - - + -
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Residues in contact with VAL 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A SER 3.1 16.5 + - - +
138A ALA 3.8 4.0 - - - +
140A VAL* 1.3 73.6 - - + +
142A HIS* 1.3 57.9 + - - +
144A LEU* 3.7 6.9 - - - +
145A THR* 2.6 49.4 + - - +
155B ALA* 4.0 24.7 - - + +
158B TYR* 3.7 21.3 - - + -
162B VAL* 3.4 18.2 - - + -
169B LEU* 3.7 25.4 - - + -
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Residues in contact with HIS 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A HIS* 3.3 10.1 - + - -
49A LEU* 3.8 12.9 - - + +
52A ALA* 4.0 13.9 - - + +
57A TRP* 3.4 24.4 + + + -
138A ALA 2.7 18.6 + - - +
139A TRP 3.3 10.1 - - - +
141A VAL* 1.3 73.5 - - - +
143A ASP* 1.3 63.8 + - - +
145A THR* 3.7 1.9 - - - -
146A HIS* 3.0 40.8 + + - -
300A NI 2.1 44.4 - - + +
301A IMD 3.1 13.2 - + - -
169B LEU* 4.0 11.2 - - + +
-9D HIS* 3.0 15.6 + + - -
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Residues in contact with ASP 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 3.9 7.1 - - + +
15A THR* 2.7 36.6 + - + +
49A LEU* 4.0 17.4 - - - +
57A TRP* 5.6 0.2 + - - -
101A ARG* 2.8 40.8 + - - -
139A TRP* 3.2 12.7 + - - +
140A VAL* 3.3 11.7 - - - +
142A HIS* 1.3 80.7 + - - +
144A LEU* 1.3 66.7 + - + +
146A HIS* 3.3 1.7 + - - +
147A ILE* 3.0 28.8 + - + +
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Residues in contact with LEU 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 3.9 26.2 - - + -
140A VAL* 3.1 21.3 + - + +
141A VAL* 3.3 6.3 + - + +
143A ASP* 1.3 80.8 - - + +
145A THR* 1.3 58.6 + - - +
147A ILE* 3.4 6.1 + - + +
148A ALA* 3.0 15.6 + - - +
22B PHE* 3.6 33.4 - - + -
151B VAL* 2.9 39.1 - - + +
154B MSE 3.8 13.5 - - + +
155B ALA* 3.5 38.8 - - + +
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Residues in contact with THR 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A VAL* 2.6 42.4 + - - +
142A HIS* 3.7 6.7 - - - -
144A LEU* 1.3 72.2 - - - +
146A HIS* 1.3 57.9 + - - +
148A ALA* 3.4 7.5 + - - +
149A GLN* 3.0 24.6 + - - +
152A ARG* 5.0 1.6 + - - -
301A IMD 4.0 8.5 - - + -
155B ALA* 5.0 3.7 - - - +
169B LEU* 3.6 24.8 + - - +
172B LEU* 3.7 23.6 - - + +
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Residues in contact with HIS 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TRP* 4.3 9.2 - + - -
45A VAL* 3.7 18.9 - - + +
48A HIS* 3.1 12.8 + + - -
49A LEU* 4.0 14.8 - - + -
142A HIS* 3.0 46.4 + + - +
143A ASP 3.9 2.5 - - - +
145A THR* 1.3 77.2 - - - +
147A ILE* 1.3 63.8 + - - +
149A GLN* 2.8 32.2 + - - +
150A ILE* 3.0 27.7 + - - +
300A NI 2.2 34.9 - - + +
301A IMD 3.1 13.5 + + - -
172B LEU* 4.5 4.9 - - + +
173B ASN 5.5 2.9 - - - -
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Residues in contact with ILE 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A THR* 4.1 23.1 - - + +
18A THR* 5.5 7.6 - - + -
19A LEU* 4.0 27.1 - - + -
22A PHE* 6.2 1.6 - - + -
49A LEU* 5.5 0.8 - - + +
143A ASP 3.0 25.2 + - - +
144A LEU* 3.5 13.9 - - + +
146A HIS* 1.3 74.7 - - - +
148A ALA* 1.3 56.4 + - - +
150A ILE* 3.1 8.2 + - - +
151A VAL* 3.0 42.0 + - + +
22B PHE* 4.1 27.1 - - + -
147B ILE* 5.0 3.4 - - + -
151B VAL* 3.6 24.2 - - + -
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Residues in contact with ALA 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A LEU 3.0 17.4 + - - +
145A THR* 3.6 8.3 - - - +
147A ILE* 1.3 73.1 - - - +
149A GLN* 1.3 61.5 + - - +
151A VAL* 3.8 7.5 - - - +
152A ARG* 2.9 50.1 + - - +
148B ALA* 5.0 7.1 - - + +
151B VAL* 4.0 15.5 - - + -
152B ARG* 4.8 13.9 - - + -
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Residues in contact with GLN 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLU* 4.0 14.8 + - + +
39A THR* 5.2 1.4 - - - -
40A TRP* 4.2 8.7 + - - +
45A VAL* 3.6 22.6 - - + +
145A THR 3.0 13.2 + - - +
146A HIS* 2.8 44.2 + - - +
148A ALA* 1.3 75.1 - - - +
150A ILE* 1.3 59.7 + - - +
152A ARG* 3.5 15.3 + - - +
153A SER* 2.7 38.4 + - - +
172B LEU* 4.0 15.6 - - + +
173B ASN* 2.8 37.0 + - - +
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Residues in contact with ILE 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 3.9 28.7 - - + -
22A PHE* 4.3 7.9 - - + -
23A LEU* 4.2 11.2 - - + -
42A VAL* 3.9 31.3 - - + +
45A VAL* 3.8 31.0 - - + -
46A VAL* 4.0 21.5 - - + -
49A LEU* 5.2 0.2 - - + -
146A HIS 3.0 14.7 + - - +
147A ILE* 3.1 8.3 + - - +
149A GLN* 1.3 79.1 - - - +
151A VAL* 1.3 63.3 + - + +
153A SER* 3.3 3.5 + - - -
154A MSE 3.1 34.3 + - - +
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Residues in contact with VAL 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PHE* 4.0 20.0 - - + -
147A ILE* 3.0 24.5 + - + +
148A ALA* 3.8 7.0 - - - +
150A ILE* 1.3 75.5 - - + +
152A ARG* 1.3 56.2 + - - +
154A MSE 3.4 8.2 + - - +
155A ALA* 3.0 26.6 + - + +
144B LEU* 2.9 46.7 - - + +
147B ILE* 3.7 23.3 - - + -
148B ALA* 4.0 13.9 - - + +
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Residues in contact with ARG 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLU* 2.7 46.3 + - - +
145A THR 5.0 1.2 + - - -
148A ALA* 2.9 39.2 + - - +
149A GLN* 3.7 9.0 - - - +
151A VAL* 1.3 73.0 - - - +
153A SER* 1.3 60.3 + - - +
155A ALA* 3.4 7.1 + - - +
156A LYS* 3.0 30.1 + - - +
148B ALA* 4.9 13.2 - - + +
152B ARG* 5.8 9.4 - - - +
172B LEU* 3.2 26.7 - - - +
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Residues in contact with SER 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A CYS* 3.2 27.4 - - - +
34A ASN* 3.5 33.0 - - - +
35A GLU* 3.6 14.6 + - - +
40A TRP 4.3 6.2 + - - -
41A THR 5.6 0.2 - - - -
42A VAL* 4.2 5.0 - - - +
149A GLN* 2.7 26.8 + - - +
150A ILE* 3.5 5.1 - - - -
152A ARG* 1.3 75.8 - - - +
154A MSE 1.3 64.0 + - - +
156A LYS* 3.4 7.3 + - - +
157A ARG 3.5 6.6 + - - -
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Residues in contact with MSE 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PHE* 3.8 27.6 - - + -
23A LEU* 3.8 14.4 - - - -
26A LEU* 3.7 20.0 - - + -
30A TRP* 3.5 24.1 - - + +
33A CYS* 3.4 20.0 - - - -
42A VAL* 4.0 6.1 - - + -
150A ILE* 3.1 17.3 + - - +
151A VAL* 3.7 6.7 - - - +
153A SER* 1.3 74.0 - - - +
155A ALA* 1.3 65.1 + - - +
157A ARG* 3.1 20.3 - - - +
158A TYR* 4.4 1.2 + - - -
11B LEU* 3.3 42.0 - - + -
144B LEU* 3.8 10.6 - - + +
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Residues in contact with ALA 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A VAL* 3.0 17.3 + - + +
152A ARG* 3.7 9.4 - - - +
153A SER 3.4 0.2 - - - -
154A MSE 1.3 75.4 - - - +
156A LYS* 1.3 62.6 + - - +
158A TYR* 3.1 13.3 + - - +
159A ASP* 4.0 4.9 + - - +
141B VAL* 3.7 31.6 - - + +
144B LEU* 3.5 25.4 - - + +
145B THR* 5.2 4.3 - - - +
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Residues in contact with LYS 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASN 4.1 7.2 - - - +
35A GLU* 3.6 39.8 + - + +
36A GLY* 4.5 4.4 - - - +
152A ARG 3.0 17.6 + - - +
153A SER 3.6 7.4 - - - +
154A MSE 3.2 0.4 - - - -
155A ALA* 1.3 73.7 - - - +
157A ARG* 1.3 67.7 + - - +
158A TYR 2.9 1.9 + - - -
159A ASP* 3.0 30.6 + - - +
-1B GLN* 2.8 38.4 + - - +
167D GLU* 2.9 29.0 + - - -
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Residues in contact with ARG 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A SER* 3.5 32.2 + - - -
30A TRP* 3.8 36.0 - - + -
33A CYS* 4.2 17.9 - - + -
34A ASN 5.4 0.2 + - - -
153A SER 3.5 5.7 + - - +
154A MSE 3.1 16.7 + - - +
156A LYS* 1.3 78.9 - - - +
158A TYR* 1.3 64.1 + - + +
161A ASP* 3.3 6.4 - - - +
-1B GLN* 3.4 7.2 + - - +
2B ASN* 2.7 61.9 + - + +
4B GLN* 5.5 1.2 - - - +
7B GLU* 2.9 29.6 + - - -
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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