Contacts of the helix formed by residues 129 - 153 (chain P) in PDB entry 1OCR
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 129 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128P GLU* 1.3 79.7 - - + +
130P PRO* 1.4 68.7 - - + +
132P LEU* 2.8 18.4 + - + +
133P ASN* 2.8 27.3 + - - +
176P LEU* 4.5 20.9 - - + +
179P SER* 5.9 1.3 - - - +
180P GLU* 3.5 40.2 - - + +
35T SER* 3.5 15.0 + - - +
39T SER* 4.2 16.4 - - - +
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Residues in contact with PRO 130 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124P LEU* 4.7 5.2 - - + -
125P ASN 3.3 21.5 - - - +
126P PRO* 3.7 6.5 - - + +
128P GLU* 3.5 1.1 - - + -
129P VAL* 1.4 91.7 - - + +
131P LEU* 1.3 58.4 + - - +
133P ASN* 3.6 11.2 + - + +
134P THR* 2.8 28.1 + - - -
180P GLU* 4.0 12.3 - - + +
249P TRP* 3.9 3.1 - - + -
253P TYR* 3.5 21.9 - - + -
257P TYR* 3.6 37.0 - - + -
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Residues in contact with LEU 131 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126P PRO 3.3 11.4 + - - +
127P LEU* 3.9 26.2 - - + +
128P GLU 2.8 14.1 + - - +
130P PRO* 1.3 70.8 - - - +
132P LEU* 1.3 66.9 + - - +
134P THR* 3.1 13.7 + - + -
135P SER* 3.0 21.3 + - - +
253P TYR* 3.8 20.9 - - + +
31T CYS* 4.0 24.0 - - + -
34T ASN* 4.4 9.9 - - - +
35T SER* 5.3 0.7 - - - +
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Residues in contact with LEU 132 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128P GLU 3.2 1.4 + - - -
129P VAL* 2.8 13.8 + - + +
131P LEU* 1.3 80.2 - - - +
133P ASN* 1.3 63.0 + - - +
135P SER* 2.9 17.6 + - - +
136P VAL* 2.8 37.2 + - + +
172P TYR* 3.9 12.1 - - + +
176P LEU* 3.6 31.9 - - + -
28T VAL* 4.3 2.2 - - + +
31T CYS* 3.9 18.3 - - + +
32T THR* 3.8 21.1 - - + +
35T SER* 3.7 28.7 + - - +
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Residues in contact with ASN 133 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129P VAL* 2.8 26.0 + - - +
130P PRO* 3.8 6.3 - - - +
132P LEU* 1.3 72.5 - - - +
134P THR* 1.3 63.0 + - - +
136P VAL* 3.3 5.6 + - - +
137P LEU* 3.1 25.5 + - - +
173P PHE* 3.6 31.1 - - + -
176P LEU* 3.2 30.6 - - - +
177P GLN* 3.5 32.7 + - - +
180P GLU* 5.2 0.4 - - - +
249P TRP* 3.7 18.6 + - + -
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Residues in contact with THR 134 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130P PRO 2.8 14.1 + - - -
131P LEU* 3.1 18.7 + - + -
133P ASN* 1.3 80.9 - - - +
135P SER* 1.3 62.4 + - - +
137P LEU* 4.0 1.6 - - - +
138P LEU* 3.1 34.2 + - + +
249P TRP* 2.9 21.4 + - + +
250P LEU* 4.1 25.8 - - + -
253P TYR* 3.5 21.7 - - + -
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Residues in contact with SER 135 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131P LEU* 3.0 10.8 + - - -
132P LEU* 2.9 16.2 + - - +
134P THR* 1.3 76.7 - - - +
136P VAL* 1.3 61.7 + - - +
138P LEU* 4.2 8.1 - - - +
139P ALA* 3.0 25.8 + - - +
27T SER* 4.5 12.0 - - - -
28T VAL* 3.7 17.0 - - - +
31T CYS* 3.7 30.2 - - - +
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Residues in contact with VAL 136 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132P LEU* 2.8 28.0 + - + +
133P ASN* 3.7 9.2 - - - +
135P SER* 1.3 78.3 + - - +
137P LEU* 1.3 64.3 + - + +
139P ALA* 3.4 3.0 + - - +
140P SER* 3.1 20.1 + - - -
169P LEU* 3.1 41.4 - - + +
172P TYR* 3.5 33.4 - - + -
173P PHE* 4.1 12.1 - - + -
176P LEU* 4.3 5.4 - - + -
28T VAL* 4.1 13.2 - - + -
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Residues in contact with LEU 137 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133P ASN 3.1 9.0 + - - +
134P THR 4.0 2.7 - - - +
136P VAL* 1.3 79.7 - - + +
138P LEU* 1.3 66.6 + - - +
140P SER* 2.6 22.3 + - - +
141P GLY 3.1 4.7 + - - -
170P GLY* 4.9 2.0 - - - -
173P PHE* 3.5 54.1 - - + -
204P HIS* 4.1 9.9 - - + +
208P VAL* 5.1 2.5 - - + -
242P TRP* 4.5 22.4 - - + -
245P VAL* 4.5 9.6 - - + +
246P ASP* 3.7 22.3 - - - +
249P TRP* 3.7 28.9 - - + -
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Residues in contact with LEU 138 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134P THR* 3.1 38.0 + - + +
135P SER* 4.2 5.6 - - - +
137P LEU* 1.3 77.8 - - - +
139P ALA* 1.3 58.8 + - - +
141P GLY* 2.9 15.4 + - - -
142P VAL* 3.2 16.4 + - - +
246P ASP* 4.0 21.5 - - - +
250P LEU* 4.2 22.4 - - + -
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Residues in contact with ALA 139 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135P SER 3.0 20.7 + - - +
136P VAL 3.5 5.6 - - - +
138P LEU* 1.3 76.4 - - - +
140P SER* 1.3 57.4 + - - +
142P VAL* 3.2 6.4 + - - +
143P SER* 3.0 25.3 + - - -
169P LEU* 3.9 11.9 - - + +
20T THR* 5.6 0.5 - - - +
24T ALA* 3.9 28.3 - - + +
25T LEU* 4.9 1.6 - - + +
27T SER* 6.3 0.2 - - - -
28T VAL* 3.8 19.3 - - + -
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Residues in contact with SER 140 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136P VAL 3.1 11.2 + - - -
137P LEU* 2.6 23.4 + - - -
139P ALA* 1.3 74.4 - - - +
141P GLY* 1.3 64.7 + - - +
143P SER* 3.4 10.6 + - - -
144P ILE* 3.2 24.9 + - - +
166P THR* 3.9 11.9 - - - +
169P LEU* 3.7 21.0 - - - +
242P TRP* 2.9 31.8 + - - -
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Residues in contact with GLY 141 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137P LEU 3.1 7.5 + - - -
138P LEU 2.9 10.4 + - - -
140P SER* 1.3 78.8 - - - +
142P VAL* 1.3 59.3 + - - +
144P ILE* 3.3 9.9 - - - +
145P THR* 2.9 22.3 + - - -
242P TRP* 4.8 2.5 - - - -
243P HIS* 3.6 19.4 + - - -
246P ASP* 4.0 11.2 - - - -
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Residues in contact with VAL 142 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138P LEU 3.2 11.2 + - - +
139P ALA* 3.2 8.7 + - - +
140P SER 3.2 0.2 - - - -
141P GLY* 1.3 75.6 - - - +
143P SER* 1.3 65.0 + - - +
145P THR* 3.0 16.1 + - - -
146P TRP* 3.2 9.9 + - - +
16T TRP* 4.0 26.4 - - + +
19T LEU* 4.1 8.7 - - + -
20T THR* 3.4 36.0 + - - +
23T LEU* 6.1 4.7 - - + -
24T ALA* 4.2 11.4 - - + -
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Residues in contact with SER 143 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139P ALA 3.0 8.9 + - - -
140P SER* 3.4 16.8 - - - -
142P VAL* 1.3 76.4 - - - +
144P ILE* 1.3 63.5 + - - +
146P TRP* 3.0 8.0 + - - +
147P ALA 2.9 17.7 + - - -
162P ALA* 3.6 10.6 - - - +
165P ILE* 3.9 23.3 - - - +
166P THR* 2.7 26.9 + - - -
169P LEU* 4.3 0.2 - - - +
20T THR* 3.6 20.6 - - - -
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Residues in contact with ILE 144 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140P SER 3.2 17.8 + - - +
141P GLY* 3.3 15.3 - - - +
143P SER* 1.3 77.5 + - - +
145P THR* 1.3 60.8 + - - +
147P ALA* 3.2 5.2 + - + +
148P HIS* 2.9 27.4 + - - +
163P LEU* 5.4 2.0 - - + -
166P THR* 3.6 14.4 - - + +
215P LEU* 3.6 30.7 - - + -
235P PHE* 4.2 16.8 - - + -
239P ALA* 3.8 25.8 - - + -
242P TRP* 4.1 15.9 - - + -
243P HIS* 3.8 22.4 - - + +
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Residues in contact with THR 145 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141P GLY 2.9 14.7 + - - -
142P VAL 3.0 10.6 + - - -
144P ILE* 1.3 77.9 - - - +
146P TRP* 1.3 63.4 + - - +
148P HIS* 3.3 7.9 + - + +
149P HIS* 2.9 42.5 + - + +
243P HIS* 4.1 13.0 + - - -
16T TRP* 3.5 41.4 - - + -
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Residues in contact with TRP 146 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142P VAL 3.2 4.8 + - - +
143P SER* 3.0 7.0 + - - +
145P THR* 1.3 76.0 - - - +
147P ALA* 1.3 63.5 + - - +
149P HIS* 3.2 3.1 + - - +
150P SER* 2.9 36.3 + - - -
158P HIS* 4.0 24.9 + + + +
161P GLN* 3.6 33.0 - - + -
162P ALA* 3.4 26.9 - - + -
165P ILE* 3.9 9.6 - - + -
13T ALA* 3.5 22.6 + - + +
16T TRP* 3.6 24.6 - - + +
17T ARG* 3.0 34.0 - - + +
20T THR* 3.6 24.5 - - + +
21T PHE* 3.6 20.2 - + - -
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Residues in contact with ALA 147 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143P SER 2.9 8.9 + - - +
144P ILE* 3.2 13.9 - - + +
146P TRP* 1.3 75.6 - - - +
148P HIS* 1.3 64.4 + - - +
150P SER* 3.1 4.0 + - - -
151P LEU* 2.9 18.4 + - - +
159P MET* 3.5 20.2 - - + +
162P ALA* 3.5 21.5 - - + +
163P LEU* 4.0 15.0 - - + +
235P PHE* 3.9 15.5 - - + -
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Residues in contact with HIS 148 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144P ILE 2.9 12.7 + - - +
145P THR* 3.5 12.3 - - + +
147P ALA* 1.3 76.9 - - - +
149P HIS* 1.3 64.9 + + - +
151P LEU* 3.2 6.3 + - - +
152P MET* 3.0 56.1 + - + +
232P HIS* 3.6 27.4 + + - -
235P PHE* 3.4 26.6 - + + -
236P GLU* 4.1 25.4 + - + +
239P ALA* 6.0 4.3 - - + -
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Residues in contact with HIS 149 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145P THR* 2.9 33.5 + - + +
146P TRP* 3.7 5.6 - - - +
148P HIS* 1.3 84.4 - + - +
150P SER* 1.3 67.6 + - - +
151P LEU 3.0 1.6 - - - -
152P MET* 3.3 15.3 + - + +
153P GLU* 3.0 34.0 + - + +
11T THR* 4.9 5.8 - - - +
12T GLY 4.3 18.3 + - - -
13T ALA* 3.7 22.4 - - + +
16T TRP* 3.8 26.4 + + - -
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Residues in contact with SER 150 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146P TRP* 2.9 37.9 + - - -
147P ALA 3.5 7.6 - - - -
149P HIS* 1.3 74.9 - - - +
151P LEU* 1.3 63.0 + - - +
153P GLU* 3.1 4.4 + - - -
154P GLY 3.0 4.5 + - - -
155P ASP* 2.8 37.1 + - - +
158P HIS* 3.5 9.1 + - - +
159P MET* 3.5 25.1 - - - -
13T ALA* 3.9 9.2 - - - +
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Residues in contact with LEU 151 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147P ALA 2.9 12.6 + - - +
148P HIS* 3.3 10.1 - - - +
150P SER* 1.3 77.3 - - - +
152P MET* 1.3 57.9 + - - +
154P GLY* 2.9 20.1 + - - -
155P ASP 4.7 1.3 - - - +
159P MET* 3.7 30.2 - - + +
222P GLN* 4.0 25.8 - - - +
227P PHE* 4.1 11.2 - - + -
228P THR 4.6 2.5 - - - +
229P SER* 3.7 8.8 - - - -
232P HIS* 3.5 44.6 - - + +
235P PHE* 4.2 13.9 - - + -
6S VAL* 3.9 14.8 - - + +
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Residues in contact with MET 152 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148P HIS* 3.0 51.7 + - + +
149P HIS* 3.3 17.5 + - + +
151P LEU* 1.3 75.2 - - - +
153P GLU* 1.3 61.9 + - + +
154P GLY 3.2 1.2 + - - -
229P SER* 3.7 23.7 - - - +
230P ASN* 5.4 1.7 + - - -
232P HIS* 4.3 15.9 - - + +
236P GLU* 6.2 1.1 - - - -
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Residues in contact with GLU 153 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149P HIS* 3.0 24.2 + - + +
150P SER* 3.7 4.0 - - - +
152P MET* 1.3 81.1 - - + +
154P GLY* 1.3 62.0 + - - +
155P ASP* 3.4 5.9 + - + +
229P SER* 5.1 0.7 - - - -
4S GLY* 5.4 1.4 - - - -
12T GLY* 4.1 5.7 - - - -
13T ALA* 3.2 35.1 + - - +
14T ARG 5.2 0.5 + - - -
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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