Contacts of the helix formed by residues 132 - 157 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D LEU* 3.5 29.6 - - + -
64D ILE* 3.8 25.8 - - + +
65D LEU* 4.0 10.8 - - + -
112D VAL* 3.8 11.2 - - + -
117D ASP 3.5 24.7 - - - +
118D LEU* 3.3 8.6 + - + +
120D ARG* 2.9 18.5 + - + +
131D LYS* 1.3 70.9 - - - +
133D ARG* 1.3 59.9 + - - +
135D LEU* 3.1 5.6 + - - +
136D LEU* 2.9 49.8 + - + +
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Residues in contact with ARG 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C ASP* 4.5 4.9 + - - +
1D MSE 4.2 31.1 - - - +
3D PHE* 4.2 32.1 + - + +
115D GLU* 4.9 6.9 + - - +
118D LEU* 3.0 49.8 + - + +
119D GLU* 2.6 37.3 + - - -
131D LYS* 3.9 15.5 - - + -
132D VAL* 1.3 79.1 - - - +
134D GLU* 1.3 61.0 + - + +
136D LEU* 4.0 3.8 - - - +
137D SER* 2.5 39.5 + - - +
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Residues in contact with GLU 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C THR 5.5 0.2 - - - +
161C ASP 3.4 21.8 - - - +
162C VAL 4.0 6.2 - - - +
163C GLY* 3.8 13.6 - - - -
164C PRO* 3.9 14.8 - - - +
165C TRP* 3.8 14.5 - - + -
129D VAL 4.4 2.1 - - - +
130D VAL* 3.4 12.8 - - - +
131D LYS* 3.0 43.0 + - + +
133D ARG* 1.3 81.3 - - + +
135D LEU* 1.3 59.9 + - - +
137D SER* 3.8 1.0 - - - -
138D ALA* 2.9 30.7 + - - +
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Residues in contact with LEU 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C TRP* 3.7 32.3 - - + -
56D ASN* 5.0 0.2 - - - +
57D TRP* 3.5 32.1 - - + +
60D ARG* 3.8 24.0 - - + -
61D LEU* 3.3 46.2 - - + +
64D ILE* 4.0 11.9 - - + -
73D PHE* 5.1 2.2 - - + -
131D LYS 3.2 9.0 + - - +
132D VAL 3.1 9.0 + - - +
134D GLU* 1.3 78.6 - - - +
136D LEU* 1.3 64.3 + - + +
138D ALA* 3.3 4.3 + - - +
139D TRP* 2.9 27.0 + - - +
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Residues in contact with LEU 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D PHE* 3.8 22.2 - - + -
5D MSE 4.1 7.2 - - - -
8D ALA* 5.8 0.4 - - + -
12D LEU* 5.0 2.1 - - + +
57D TRP 5.9 0.7 - - - +
61D LEU* 4.4 15.3 - - + -
108D LEU* 3.8 33.7 - - + -
112D VAL* 4.6 1.1 - - + -
118D LEU* 3.9 18.8 - - + -
132D VAL* 2.9 37.1 + - + +
133D ARG 4.1 0.4 - - - +
135D LEU* 1.3 80.2 - - + +
137D SER* 1.3 65.7 + - - +
139D TRP* 3.2 29.4 + - + +
140D VAL* 3.1 27.0 + - - +
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Residues in contact with SER 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C TYR* 3.8 14.3 - - - -
161C ASP* 3.3 40.9 - - - +
162C VAL* 3.8 4.3 - - - -
3D PHE* 3.2 19.5 - - - +
133D ARG 2.5 24.9 + - - -
134D GLU 3.8 0.7 - - - -
136D LEU* 1.3 71.8 - - - +
138D ALA* 1.3 66.2 + - - +
140D VAL* 3.1 4.5 + - - +
141D VAL* 3.0 27.2 + - - +
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Residues in contact with ALA 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C VAL* 3.8 12.7 - - + +
165C TRP* 4.0 32.8 - - + -
169C LEU* 4.2 7.0 - - + +
57D TRP* 3.8 15.6 - - + -
134D GLU 2.9 19.3 + - - +
135D LEU 3.5 5.2 - - - +
136D LEU 3.3 0.2 - - - -
137D SER* 1.3 74.3 - - - +
139D TRP* 1.3 52.9 + - - +
141D VAL* 3.3 1.6 + - - +
142D HIS* 2.7 36.7 + - - +
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Residues in contact with TRP 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LEU* 3.7 24.1 - - + +
53D GLU* 3.3 28.4 + - - -
57D TRP* 3.3 56.5 - + + -
58D ILE* 4.0 31.9 - - + -
101D ARG* 3.4 21.2 - - - +
104D ASN* 4.1 15.0 - - + -
105D LEU* 4.2 9.4 - - + -
108D LEU* 4.2 17.5 - - + -
135D LEU 2.9 13.7 + - - +
136D LEU* 3.3 32.1 - - + +
137D SER 3.2 0.2 - - - -
138D ALA* 1.3 76.5 - - - +
140D VAL* 1.3 62.4 + - - +
142D HIS* 3.3 3.0 + - + +
143D ASP* 3.2 20.2 + - - +
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Residues in contact with VAL 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C TRP* 4.4 1.8 - - + -
158C TYR* 3.8 21.1 - - + -
8D ALA* 3.6 30.7 - - + +
11D LEU* 3.7 32.3 - - + -
12D LEU* 3.9 25.1 - - + -
136D LEU 3.1 15.4 + - - +
137D SER 3.1 6.7 + - - +
139D TRP* 1.3 74.4 - - - +
141D VAL* 1.3 61.1 + - - +
143D ASP* 3.2 8.2 + - + +
144D LEU* 3.2 27.0 + - + +
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Residues in contact with VAL 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C ALA* 3.9 26.7 - - + +
158C TYR* 3.6 22.2 - - + +
162C VAL* 3.5 16.6 - - + -
169C LEU* 3.8 24.7 - - + -
137D SER 3.0 16.6 + - - +
138D ALA 3.9 3.1 - - - +
140D VAL* 1.3 73.5 - - + +
142D HIS* 1.3 57.7 + - - +
144D LEU* 3.4 7.9 + - + +
145D THR* 2.6 50.0 + - - +
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Residues in contact with HIS 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-9A HIS* 3.2 14.1 + + - -
169C LEU* 4.0 10.7 - - + +
301C IMD 3.2 13.5 - + - -
48D HIS* 3.3 12.6 - + - -
49D LEU* 4.0 13.3 - - + +
52D ALA* 4.0 14.8 - - + +
57D TRP* 3.4 25.2 + + + -
138D ALA 2.7 22.5 + - - +
139D TRP 3.4 6.3 - - - +
141D VAL* 1.3 70.8 - - - +
143D ASP* 1.3 68.8 + - - +
145D THR* 3.8 1.6 - - - -
146D HIS* 3.2 37.9 + + - -
300D NI 2.1 44.5 - - + +
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Residues in contact with ASP 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D LEU* 6.2 1.8 - - + -
12D LEU* 3.7 7.9 - - + +
15D THR* 2.6 38.4 + - + +
49D LEU* 4.2 17.1 - - - +
101D ARG* 2.7 38.8 + - - -
139D TRP* 3.2 14.4 + - - +
140D VAL* 3.4 10.8 - - - +
142D HIS* 1.3 81.0 + - - +
144D LEU* 1.3 60.5 + - + +
146D HIS* 3.4 2.6 + - - +
147D ILE* 2.9 33.9 + - + +
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Residues in contact with LEU 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C PHE* 3.9 19.3 - - + -
151C VAL* 2.8 39.7 - - + +
154C MSE 3.8 13.9 - - + +
155C ALA* 3.5 39.9 - - + +
158C TYR* 6.3 0.2 - - + -
11D LEU* 3.8 27.1 - - + -
140D VAL* 3.2 30.8 + - + +
141D VAL* 3.8 8.5 - - + +
143D ASP* 1.3 80.4 - - + +
145D THR* 1.3 58.4 + - - +
147D ILE* 3.3 5.8 + - + -
148D ALA* 3.0 14.9 + - - +
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Residues in contact with THR 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C ALA* 5.1 3.8 - - - +
169C LEU* 3.4 26.7 + - - +
172C LEU* 3.7 22.1 - - + +
301C IMD 4.0 8.3 - - + -
141D VAL* 2.6 42.1 + - - +
142D HIS* 3.8 6.1 - - - -
144D LEU* 1.3 71.7 - - - +
146D HIS* 1.3 58.2 + - - +
148D ALA* 3.4 8.3 - - - +
149D GLN* 3.0 25.0 + - - +
152D ARG* 4.9 1.7 + - - -
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Residues in contact with HIS 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C LEU* 4.5 4.5 - - + +
173C ASN 5.6 3.1 - - - -
301C IMD 3.2 12.4 - + - -
40D TRP* 4.3 9.6 - + - -
45D VAL* 3.6 18.2 - - + +
48D HIS* 3.1 12.1 + + - -
49D LEU* 4.0 13.7 - - + -
142D HIS* 3.2 41.7 + + - +
143D ASP 3.9 2.5 - - - +
145D THR* 1.3 77.3 - - - +
147D ILE* 1.3 65.4 + - - +
149D GLN* 2.9 28.7 + - - +
150D ILE* 3.0 28.7 + - - +
300D NI 2.3 37.1 - - + +
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Residues in contact with ILE 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C PHE* 4.2 26.5 - - + -
147C ILE* 5.2 2.2 - - + -
151C VAL* 3.6 22.0 - - + -
15D THR* 4.0 25.6 - - + +
18D THR* 5.5 7.9 - - + -
19D LEU* 4.1 24.0 - - + -
22D PHE* 6.0 2.0 - - + -
49D LEU* 5.7 0.9 - - + -
143D ASP* 2.9 25.3 + - + +
144D LEU* 3.3 12.1 + - + +
146D HIS* 1.3 75.5 - - - +
148D ALA* 1.3 57.2 + - - +
150D ILE* 3.3 9.2 + - - +
151D VAL* 3.0 37.8 + - + +
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Residues in contact with ALA 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C ALA* 5.1 8.2 - - + +
151C VAL* 3.9 14.6 - - + +
152C ARG* 4.8 13.5 - - + -
144D LEU 3.0 13.1 + - - +
145D THR* 3.4 13.0 - - - +
147D ILE* 1.3 73.9 - - - +
149D GLN* 1.3 60.4 + - - +
151D VAL* 3.3 6.8 + - - +
152D ARG* 2.8 50.8 + - - +
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Residues in contact with GLN 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C LEU* 4.0 15.3 - - + +
173C ASN* 2.8 36.6 + - - +
35D GLU* 4.1 12.7 + - + +
39D THR* 5.3 1.4 - - - -
40D TRP* 4.3 8.6 + - - +
45D VAL* 3.7 22.8 - - + +
145D THR 3.0 14.6 + - - +
146D HIS* 2.9 37.9 + - - +
148D ALA* 1.3 76.9 - - - +
150D ILE* 1.3 60.5 + - - +
152D ARG* 3.6 15.7 - - - +
153D SER* 2.8 34.8 + - - +
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Residues in contact with ILE 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D LEU* 3.9 34.1 - - + -
22D PHE* 4.2 9.2 - - + -
23D LEU* 4.2 9.6 - - + -
42D VAL* 3.9 26.1 - - + +
45D VAL* 3.7 29.6 - - + -
46D VAL* 4.3 13.0 - - + -
49D LEU* 5.2 0.7 - - + -
146D HIS 3.0 21.0 + - - +
147D ILE* 3.5 7.4 - - - +
148D ALA 3.3 0.2 - - - -
149D GLN* 1.3 76.5 - - - +
151D VAL* 1.3 63.3 + - - +
153D SER* 3.2 5.2 + - - -
154D MSE 3.2 40.2 + - - +
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Residues in contact with VAL 151 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C LEU* 3.0 44.1 - - + +
147C ILE* 3.8 21.8 - - + -
148C ALA* 4.0 14.4 - - + +
151C VAL* 5.8 0.2 - - + -
22D PHE* 3.8 21.5 - - + -
147D ILE* 3.0 24.9 + - + +
148D ALA* 3.7 6.7 - - - +
150D ILE* 1.3 75.3 - - - +
152D ARG* 1.3 56.9 + - - +
154D MSE 3.3 9.2 + - - +
155D ALA* 2.9 27.8 + - + +
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Residues in contact with ARG 152 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C ALA* 5.0 12.8 - - + +
152C ARG* 5.6 9.8 - - - +
172C LEU* 3.2 25.7 - - - +
35D GLU* 2.8 43.5 + - - +
145D THR 4.9 1.2 + - - -
148D ALA* 2.8 42.6 + - - +
149D GLN* 3.6 12.2 - - - +
151D VAL* 1.3 71.5 - - - +
153D SER* 1.3 59.1 - - - +
155D ALA* 3.8 8.2 - - - +
156D LYS* 3.1 28.8 + - - +
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Residues in contact with SER 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D CYS* 3.4 20.2 + - - +
34D ASN* 3.3 39.7 - - - +
35D GLU* 3.5 15.6 + - - +
40D TRP 4.5 4.0 + - - -
41D THR 5.7 0.2 - - - -
42D VAL* 4.2 5.3 + - - -
149D GLN* 2.8 27.7 + - - +
150D ILE* 3.5 5.3 - - - -
152D ARG* 1.3 75.8 - - - +
154D MSE 1.3 62.6 + - - +
156D LYS* 3.4 7.8 + - - +
157D ARG* 3.6 7.3 + - - -
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Residues in contact with MSE 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LEU* 3.1 41.5 - - + -
144C LEU* 3.9 9.2 - - + +
22D PHE* 3.7 32.8 - - + -
23D LEU* 3.8 14.1 - - + -
26D LEU* 3.5 17.5 - - + -
30D TRP* 3.4 25.4 - - + +
33D CYS* 3.6 20.6 - - - -
42D VAL* 4.0 5.4 - - + -
150D ILE* 3.2 16.9 + - - +
151D VAL* 3.6 6.7 - - - +
153D SER* 1.3 73.8 - - - +
155D ALA* 1.3 65.5 + - - +
157D ARG* 3.2 18.4 - - - +
158D TYR* 4.3 1.7 + - - -
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Residues in contact with ALA 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C VAL* 3.7 32.0 - - + +
144C LEU* 3.6 25.2 - - + +
145C THR* 5.1 4.3 - - - +
151D VAL* 2.9 19.8 + - + +
152D ARG* 3.8 9.4 - - - +
153D SER 3.5 0.2 - - - -
154D MSE 1.3 72.6 - - - +
156D LYS* 1.3 62.1 + - - +
158D TYR* 3.1 12.1 + - - -
159D ASP* 4.0 5.6 + - - +
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Residues in contact with LYS 156 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A GLU* 3.9 21.1 + - - -
-3C TYR* 6.3 0.4 - - - -
-1C GLN* 2.6 60.4 + - - -
34D ASN* 3.9 5.5 + - - +
35D GLU* 3.6 39.7 - - + +
36D GLY* 4.2 11.1 - - - +
152D ARG 3.1 17.8 + - - +
153D SER 3.6 7.6 - - - +
154D MSE 3.2 0.4 - - - -
155D ALA* 1.3 72.1 - - - +
157D ARG* 1.3 55.4 + - - +
158D TYR 3.0 3.7 + - - -
159D ASP* 3.1 29.8 + - - +
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Residues in contact with ARG 157 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-1C GLN* 3.4 6.1 + - - +
2C ASN* 2.7 69.1 + - + +
4C GLN* 6.1 0.2 - - - +
7C GLU* 3.3 26.9 + - - -
29D SER* 3.3 28.4 + - - -
30D TRP* 3.8 40.7 - - + -
33D CYS* 4.1 19.1 - - + -
153D SER 3.6 7.1 + - - +
154D MSE 3.2 18.1 + - - +
156D LYS* 1.3 79.3 - - - +
158D TYR* 1.3 59.7 + - + +
159D ASP 3.6 0.2 - - - -
161D ASP* 3.5 1.7 - - - +
----------------------------------------------------------
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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