Contacts of the helix formed by residues 185 - 207 (chain A) in PDB entry 1WBP
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 PRO 185 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A GLY 4.4 1.6 - - - +
184A LEU* 1.3 88.3 - - + +
186A LEU* 1.3 60.1 + - - +
187A PRO* 3.9 3.6 - - + -
188A CYS* 2.8 26.8 + - - +
189A VAL* 3.0 9.9 + - - +
482A PRO 3.5 15.5 - - - +
483A LEU* 3.6 31.0 - - + +
485A PRO* 3.8 32.3 - - + -
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Residues in contact with LEU 186 (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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184A LEU 3.4 3.0 + - - +
185A PRO* 1.3 71.6 - - - +
187A PRO* 1.3 69.0 - - + +
188A CYS 3.1 0.9 + - - -
189A VAL* 3.2 4.9 + - + +
190A LYS* 3.1 35.7 + - - +
545A ALA* 4.0 17.0 - - + +
618A TRP* 3.5 40.6 - - + -
622A GLU* 3.9 33.9 - - + +
652A TRP* 4.5 26.0 - - + +
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Residues in contact with PRO 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A PRO* 3.2 5.2 - - + -
186A LEU* 1.3 94.7 - - + +
188A CYS* 1.3 58.4 + - - +
190A LYS* 4.0 14.3 - - + +
191A LYS* 3.7 17.2 + - - +
485A PRO* 3.6 35.0 - - + +
488A ALA* 3.6 18.9 - - + +
655A SER* 5.8 4.0 - - - +
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Residues in contact with CYS 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A LEU* 4.7 6.5 - - + -
185A PRO* 2.8 15.1 + - + +
187A PRO* 1.3 76.2 - - - +
189A VAL* 1.3 65.5 + - - +
190A LYS 3.1 1.8 - - - -
191A LYS* 3.1 5.5 + - - +
192A ILE* 3.0 27.3 + - - +
482A PRO 3.3 26.9 - - - +
484A GLU 3.6 18.6 - - - -
485A PRO* 3.9 9.4 - - - -
488A ALA* 3.9 23.1 - - - +
491A LEU* 3.9 14.5 - - + +
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Residues in contact with VAL 189 (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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184A LEU* 3.6 22.9 - - + +
185A PRO 3.0 14.5 + - - +
186A LEU* 3.2 10.7 + - + +
188A CYS* 1.3 77.3 - - - +
190A LYS* 1.3 62.1 + - - +
192A ILE* 3.3 8.5 + - - -
193A ILE* 2.9 44.7 + - + +
541A ALA 4.0 19.1 - - - +
544A LEU* 4.0 25.4 - - + +
545A ALA* 4.0 10.3 - - + +
652A TRP* 4.3 13.5 - - + -
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Residues in contact with LYS 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A LEU* 3.2 27.4 - - - +
187A PRO* 4.0 11.7 - - + +
188A CYS 3.1 0.4 - - - -
189A VAL* 1.3 78.4 - - - +
191A LYS* 1.3 61.6 + - - +
194A GLN* 2.9 29.6 + - - +
622A GLU* 5.9 1.3 + - - -
652A TRP* 3.0 69.8 + - + +
653A LEU* 3.7 21.5 - - - +
655A SER* 3.3 33.9 + - - +
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Residues in contact with LYS 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A PRO 3.7 13.7 - - - +
188A CYS 3.1 8.8 + - - +
190A LYS* 1.3 82.0 - - - +
192A ILE* 1.3 65.8 - - + +
194A GLN* 2.9 28.3 + - - +
195A GLN* 3.0 41.6 + - - +
488A ALA* 3.6 24.9 - - + +
489A GLU* 3.3 30.1 - - - +
491A LEU* 5.4 2.5 - - + -
653A LEU 2.9 28.1 + - - -
654A ASN* 4.9 1.8 - - - +
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Residues in contact with ILE 192 (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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172A LEU* 3.6 36.6 - - + -
184A LEU* 3.4 32.8 - - + -
188A CYS 3.0 19.7 + - - +
189A VAL* 3.7 4.3 - - - +
191A LYS* 1.3 75.0 - - - +
193A ILE* 1.3 64.6 + - - +
195A GLN* 3.0 8.4 + - - +
196A VAL* 2.9 34.9 + - + +
221A LEU* 5.5 0.4 - - + -
482A PRO* 5.4 0.9 - - + -
491A LEU* 4.3 22.2 - - + -
493A VAL* 4.1 25.4 - - + +
544A LEU* 3.8 13.7 - - + -
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Residues in contact with ILE 193 (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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189A VAL* 2.9 30.3 + - + +
190A LYS* 3.9 3.4 - - - +
192A ILE* 1.3 75.0 - - + +
194A GLN* 1.3 64.8 + - - +
196A VAL* 3.2 4.1 + - - -
197A LEU* 2.9 41.8 + - + +
537A THR* 4.4 5.8 - - + +
540A MET* 4.0 17.9 - - + -
541A ALA* 3.6 32.1 - - + -
544A LEU* 3.9 15.9 - - + -
629A PHE* 4.1 26.2 - - + -
633A MET* 5.7 0.4 - - + -
652A TRP* 4.9 3.6 - - + -
653A LEU* 4.5 4.0 - - + -
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Residues in contact with GLN 194 (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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190A LYS 2.9 18.7 + - - +
191A LYS* 2.9 40.8 + - - +
192A ILE 3.2 0.2 - - - -
193A ILE* 1.3 77.5 - - - +
195A GLN* 1.3 64.0 + - + +
198A GLN* 3.1 42.5 + - - +
648A LEU* 3.3 20.3 - - + +
653A LEU* 3.8 28.8 - - + +
654A ASN* 5.6 1.0 - - - +
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Residues in contact with GLN 195 (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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143A MET* 3.2 28.9 - - + +
191A LYS* 3.0 31.2 + - - +
192A ILE* 3.0 8.5 + - - +
194A GLN* 1.3 76.5 - - + +
196A VAL* 1.3 58.3 + - - +
197A LEU 3.1 1.6 - - - -
198A GLN* 2.8 38.2 + - - +
199A GLY 3.0 9.5 + - - -
491A LEU* 3.3 22.0 + - - +
492A LYS* 3.3 8.6 - - - +
493A VAL* 2.9 44.6 + - + +
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Residues in contact with VAL 196 (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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192A ILE* 2.9 32.8 + - + +
193A ILE* 3.2 7.8 + - - +
195A GLN* 1.3 75.0 - - - +
197A LEU* 1.3 59.8 + - + +
199A GLY 3.3 0.9 + - - -
200A LEU* 3.0 42.7 + - + +
214A ILE* 4.3 7.2 - - + -
219A ILE* 4.1 30.3 - - + -
493A VAL* 4.6 3.5 - - + +
495A ILE* 3.6 16.1 - - + +
537A THR* 4.3 4.0 - - + +
540A MET* 3.9 27.6 - - + -
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Residues in contact with LEU 197 (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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193A ILE* 2.9 28.6 + - + +
194A GLN 3.7 4.9 - - - +
196A VAL* 1.3 75.1 - - - +
198A GLN* 1.3 60.6 + - - +
200A LEU* 3.7 10.3 - - + -
201A ASP* 2.9 28.6 + - - +
534A ILE* 5.3 2.7 - - + -
537A THR* 3.3 34.5 - - + -
629A PHE* 4.4 13.9 - - + -
633A MET* 5.2 2.7 - - + -
644A ALA* 3.8 13.9 - - - +
647A CYS* 3.1 43.7 - - + +
648A LEU* 3.7 15.9 - - + +
653A LEU* 4.6 2.2 - - + -
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Residues in contact with GLN 198 (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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139A PRO* 5.2 3.8 + - - +
140A ASN* 3.1 46.7 + - - +
143A MET* 3.5 21.3 - - + +
194A GLN* 3.1 35.4 + - - +
195A GLN* 2.8 28.6 + - - +
197A LEU* 1.3 76.5 - - - +
199A GLY* 1.3 62.8 + - - +
201A ASP* 3.5 0.9 + - - +
202A TYR 3.1 9.5 + - - -
648A LEU* 4.0 18.2 - - + -
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Residues in contact with GLY 199 (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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140A ASN 4.2 2.0 - - - -
143A MET* 3.4 20.8 - - - +
144A VAL* 4.1 8.0 - - - +
195A GLN 3.0 9.5 + - - -
196A VAL 3.3 3.3 + - - -
198A GLN* 1.3 77.5 - - - +
200A LEU* 1.3 58.1 + - - +
202A TYR* 3.2 4.2 + - - +
203A LEU* 2.8 31.5 + - - +
495A ILE* 3.9 14.8 - - - -
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Residues in contact with LEU 200 (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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196A VAL* 3.0 29.5 + - + +
197A LEU* 3.9 10.8 - - + +
199A GLY* 1.3 72.3 - - - +
201A ASP* 1.3 58.6 + - - +
203A LEU* 4.3 9.9 - - + +
204A HIS* 2.7 60.3 + - + +
214A ILE* 3.6 25.6 - - + -
495A ILE* 3.8 9.8 - - + +
533A ASP* 4.0 13.2 - - + +
534A ILE* 4.6 8.7 - - + -
537A THR* 3.2 29.4 - - - +
644A ALA* 4.1 9.6 - - + -
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Residues in contact with ASP 201 (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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138A ASP* 5.4 0.3 - - - +
140A ASN* 3.9 15.1 + - - +
197A LEU 2.9 19.3 + - - +
198A GLN* 3.7 5.4 - - - +
200A LEU* 1.3 75.3 - - - +
202A TYR* 1.3 55.8 + - - +
204A HIS* 4.4 2.4 - - - +
205A THR* 2.7 53.6 + - - +
644A ALA* 3.7 8.9 - - + +
645A ALA* 3.0 38.3 + - - +
648A LEU* 4.2 10.1 - - + +
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Residues in contact with TYR 202 (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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131A VAL* 2.8 32.7 + - + -
134A SER* 3.4 6.3 + - - -
135A ASP* 3.3 37.4 + - + -
138A ASP* 3.1 30.7 - - + -
140A ASN* 3.5 21.5 - - + +
141A ARG* 3.6 28.9 - - + -
144A VAL* 4.6 5.4 - - + -
198A GLN 3.1 4.3 + - - +
199A GLY 3.2 7.6 + - - +
201A ASP* 1.3 79.5 + - - +
203A LEU* 1.3 71.2 + - + +
206A LYS* 3.1 36.9 + - + +
207A CYS* 3.3 26.8 + - - -
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Residues in contact with LEU 203 (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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131A VAL* 3.9 28.3 - - + -
144A VAL* 4.0 20.0 - - + -
199A GLY 2.8 24.2 + - - +
200A LEU* 3.8 20.9 - - + +
202A TYR* 1.3 75.0 - - + +
204A HIS* 1.3 58.3 + - - +
207A CYS* 2.9 14.2 + - - +
208A ARG 2.8 31.0 + - - -
209A ILE* 3.8 30.3 - - + +
211A HIS* 4.5 21.3 - - + +
495A ILE* 4.6 10.3 - - + -
498A LEU* 4.8 6.5 - - + -
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Residues in contact with HIS 204 (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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200A LEU* 2.7 37.3 + - + +
201A ASP* 3.8 4.3 - - - +
203A LEU* 1.3 76.0 - - + +
205A THR* 1.3 61.4 + - - +
208A ARG* 3.3 31.0 + - - -
209A ILE 3.5 15.0 + - - +
211A HIS 5.1 0.2 - - - -
530A THR* 3.0 48.3 + - + +
533A ASP* 2.7 37.8 + - + +
534A ILE* 4.4 7.6 - - + +
643A THR* 6.2 0.2 - - - -
644A ALA* 4.4 18.2 - - + -
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Residues in contact with THR 205 (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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201A ASP* 2.7 36.6 + - - +
202A TYR* 5.0 0.2 - - - -
203A LEU 3.1 0.4 + - - -
204A HIS* 1.3 77.0 - - - +
206A LYS* 1.3 91.7 + - + +
207A CYS 3.4 0.7 + - - -
208A ARG* 3.6 15.2 - - - +
645A ALA* 5.8 0.2 - - - +
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Residues in contact with LYS 206 (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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134A SER* 3.1 22.1 + - - +
135A ASP* 3.3 31.4 + - + +
138A ASP* 3.2 38.9 + - - +
202A TYR* 3.1 31.3 + - + +
205A THR* 1.3 95.3 - - + +
207A CYS* 1.3 59.5 + - - +
208A ARG* 5.1 1.6 - - - +
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Residues in contact with CYS 207 (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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130A SER* 4.2 1.0 + - - -
131A VAL* 3.8 14.8 - - - -
134A SER* 3.4 24.0 - - - +
202A TYR* 3.3 39.7 + - - -
203A LEU* 2.9 14.8 + - - +
206A LYS* 1.3 76.4 - - - +
208A ARG* 1.3 74.0 + - - +
209A ILE* 3.2 28.9 - - + +
503A TRP* 3.9 10.9 - - - -
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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
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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) + - + + + + + -
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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