Contacts of the helix formed by residues 235 - 256 (chain A) in PDB entry 5WVD
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 THR 235 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A GLN 4.6 6.7 - - - +
234A ALA* 1.3 76.6 - - - +
236A PHE* 1.3 58.6 + - - +
237A TYR* 3.5 9.7 + - - +
238A ASP* 2.8 35.4 + - - +
239A LYS* 3.0 29.6 + - - +
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Residues in contact with PHE 236 (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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235A THR* 1.3 73.4 - - - +
237A TYR* 1.3 60.1 + - - +
239A LYS* 3.6 15.5 + - + +
240A ARG* 3.1 77.6 + - + +
318A ALA* 4.0 10.1 - - + -
319A LYS* 4.0 35.9 - - + -
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Residues in contact with TYR 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A THR* 3.3 8.6 + - - +
236A PHE* 1.3 80.9 - - + +
238A ASP* 1.3 66.1 + - - +
240A ARG* 3.5 3.2 + - - +
241A CYS* 3.1 52.5 + - - -
316A ARG 5.9 2.2 - - - -
318A ALA* 4.2 20.9 - - + -
321A ARG* 5.7 4.5 - - - -
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Residues in contact with ASP 238 (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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167A ALA* 3.6 25.9 - - + +
169A ARG* 3.1 37.6 + - + +
234A ALA* 4.1 4.6 - - + -
235A THR* 2.8 42.1 + - - +
237A TYR* 1.3 82.0 - - - +
239A LYS* 1.3 62.9 + - - +
241A CYS* 3.6 17.5 + - - +
242A ASP* 3.7 6.4 + - - +
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Residues in contact with LYS 239 (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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162A HIS* 3.2 79.3 + - + +
165A GLY* 4.0 16.4 - - - -
166A ILE 4.6 0.4 - - - +
167A ALA* 4.4 1.6 - - - -
234A ALA* 3.6 30.9 + - + -
235A THR 3.0 18.6 + - - +
236A PHE* 3.7 14.2 - - + +
238A ASP* 1.3 76.6 - - - +
240A ARG* 1.3 63.3 + - + +
242A ASP* 3.4 10.7 + - - +
243A LEU* 3.7 2.8 - - - +
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Residues in contact with ARG 240 (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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236A PHE* 3.1 54.2 + - + +
237A TYR 4.2 1.6 - - - +
238A ASP 3.4 0.2 - - - -
239A LYS* 1.3 76.4 - - + +
241A CYS* 1.3 56.6 + - - +
242A ASP 3.3 0.2 - - - -
243A LEU* 3.3 18.4 + - - +
244A TRP 3.1 16.6 + - - -
318A ALA* 3.0 39.7 + - + +
319A LYS 3.7 8.3 + - - -
321A ARG* 2.8 55.7 + - - +
322A LEU 4.0 6.3 - - - -
323A SER* 3.6 30.0 - - - +
326A GLN* 5.0 2.0 + - - -
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Residues in contact with CYS 241 (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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169A ARG* 6.5 0.4 - - - -
237A TYR* 3.1 53.9 + - - +
238A ASP* 3.6 10.1 - - - +
239A LYS 3.3 0.4 - - - -
240A ARG* 1.3 75.6 - - - +
242A ASP* 1.3 59.2 + - - +
243A LEU 3.3 0.2 - - - -
244A TRP* 3.6 9.6 + - - +
245A SER* 3.0 29.3 + - - -
321A ARG* 4.0 8.3 - - - +
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Residues in contact with ASP 242 (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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158A LEU* 3.7 20.6 - - + +
162A HIS* 3.3 15.7 + - - +
167A ALA* 3.4 3.3 - - - -
168A HIS* 2.8 34.1 + - - +
169A ARG* 3.0 28.1 + - - -
170A ASP 4.6 0.2 + - - -
171A LEU* 3.4 17.2 + - + +
238A ASP 3.7 8.7 + - - +
239A LYS 3.4 9.1 + - - +
240A ARG 3.3 0.4 - - - -
241A CYS* 1.3 76.0 - - - +
243A LEU* 1.3 60.0 + - - +
245A SER* 3.3 5.9 + - - -
246A LEU* 2.9 23.6 + - - +
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Residues in contact with LEU 243 (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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158A LEU* 4.2 9.0 - - + -
162A HIS* 3.7 17.5 - - + +
239A LYS* 3.7 16.8 - - + +
240A ARG* 3.3 23.6 + - - +
242A ASP* 1.3 75.3 - - - +
244A TRP* 1.3 62.4 + - - +
246A LEU* 3.6 11.1 + - + +
247A GLY 3.3 14.4 + - - -
313A LEU* 3.4 22.4 - - + +
321A ARG* 4.3 4.5 - - - -
322A LEU 3.4 28.3 - - - +
323A SER* 3.9 2.5 - - - -
324A ALA* 3.7 33.7 - - + +
327A VAL* 4.1 13.2 - - + -
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Residues in contact with TRP 244 (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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240A ARG 3.1 5.7 + - - -
241A CYS* 3.7 11.9 - - - +
243A LEU* 1.3 75.3 - - - +
245A SER* 1.3 72.4 + - - +
247A GLY 3.2 2.6 + - - -
248A VAL* 3.0 46.2 + - + +
260A PHE* 3.6 32.8 - + - -
313A LEU 3.5 19.5 - - - -
314A LEU* 3.5 29.5 + - + +
315A VAL 4.3 0.7 - - - -
316A ARG* 6.0 0.8 - - - +
321A ARG* 3.6 34.0 - - - +
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Residues in contact with SER 245 (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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171A LEU* 3.3 32.8 + - - +
241A CYS 3.0 16.9 + - - -
242A ASP* 3.3 6.7 + - - -
244A TRP* 1.3 92.4 - - - +
246A LEU* 1.3 57.9 + - - +
248A VAL* 3.3 8.7 + - - +
249A VAL* 3.0 31.4 + - - +
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Residues in contact with LEU 246 (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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150A VAL* 6.3 0.4 - - + -
151A VAL* 3.9 26.5 - - + +
154A VAL* 3.8 24.9 - - + -
155A ALA* 4.2 26.0 - - + +
158A LEU* 4.3 7.4 - - + -
171A LEU* 3.8 11.4 - - + +
242A ASP 2.9 15.2 + - - +
243A LEU* 3.7 20.9 - - + +
244A TRP 3.3 0.4 - - - -
245A SER* 1.3 74.5 - - - +
247A GLY* 1.3 58.0 + - - +
249A VAL* 3.3 13.1 + - + +
250A LEU* 3.0 27.4 + - - +
313A LEU* 4.1 17.3 - - + -
327A VAL* 4.3 7.9 - - + -
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Residues in contact with GLY 247 (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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243A LEU 3.3 5.5 + - - -
244A TRP 3.2 8.7 + - - -
246A LEU* 1.3 76.0 - - - +
248A VAL* 1.3 60.9 + - - +
250A LEU* 4.1 5.3 - - - +
251A TYR* 3.3 22.2 + - - +
310A ILE* 4.3 7.5 - - - +
313A LEU* 3.8 25.9 - - - +
314A LEU* 3.8 15.3 - - - +
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Residues in contact with VAL 248 (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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173A PRO* 6.1 0.7 - - + -
244A TRP* 3.0 47.8 + - + +
245A SER* 3.5 9.6 - - - +
246A LEU 3.3 0.4 - - - -
247A GLY* 1.3 74.1 - - - +
249A VAL* 1.3 59.9 + - + +
251A TYR* 3.3 4.7 + - - +
252A ILE* 3.0 44.8 + - + +
258A PRO* 5.3 2.7 - - + -
259A PRO* 4.1 22.8 - - + +
260A PHE* 5.1 0.9 - - + -
314A LEU* 3.9 12.1 - - + -
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Residues in contact with VAL 249 (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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132A ILE* 5.1 5.2 - - + -
150A VAL* 5.1 3.1 - - + -
154A VAL* 5.9 0.2 - - + -
171A LEU* 4.7 2.2 - - + -
172A LYS* 4.0 9.0 - - - +
173A PRO* 3.8 27.5 - - + +
176A ILE* 3.8 30.1 - - + -
245A SER 3.0 17.7 + - - +
246A LEU* 3.3 19.7 + - + +
248A VAL* 1.3 76.2 - - + +
250A LEU* 1.3 52.4 + - - +
252A ILE* 3.2 10.8 + - - +
253A MET* 2.8 53.2 + - + +
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Residues in contact with LEU 250 (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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147A ALA* 4.3 0.7 - - + -
151A VAL* 3.8 23.3 - - + -
246A LEU 3.0 16.2 + - - +
247A GLY* 4.1 4.7 - - - +
248A VAL 3.4 0.2 - - - -
249A VAL* 1.3 72.2 - - - +
251A TYR* 1.3 58.9 + - - +
253A MET* 4.0 15.3 - - + -
254A LEU* 3.1 40.3 + - + +
306A ALA* 4.9 1.3 - - - +
309A LEU* 3.8 31.6 - - + -
310A ILE* 3.8 26.7 - - + +
313A LEU* 5.1 6.1 - - + -
332A TRP* 3.7 30.1 - - + -
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Residues in contact with TYR 251 (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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247A GLY 3.3 14.7 + - - +
248A VAL 3.3 9.2 + - - +
250A LEU* 1.3 75.3 - - - +
252A ILE* 1.3 56.1 + - - +
254A LEU 3.7 0.2 + - - -
255A SER* 2.5 35.7 + - - -
257A TYR* 3.4 36.4 - + - -
259A PRO* 3.6 41.6 + - + +
292A TYR* 4.4 4.7 - + - -
293A GLU 2.4 31.9 + - - -
294A PHE* 3.6 17.3 - + - -
295A PRO* 3.4 17.0 - - - +
299A TRP* 3.6 23.8 + + - -
310A ILE* 3.9 19.9 - - + +
314A LEU* 4.4 1.1 - - + -
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Residues in contact with ILE 252 (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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136A ILE* 3.5 37.0 - - + +
173A PRO* 4.1 30.5 - - + -
248A VAL* 3.0 36.6 + - + +
249A VAL* 3.5 7.4 - - - +
251A TYR* 1.3 74.3 - - - +
253A MET* 1.3 59.5 + - - +
256A GLY* 2.8 32.2 + - - +
257A TYR 3.6 16.8 - - - +
258A PRO* 3.8 21.8 - - + -
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Residues in contact with MET 253 (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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132A ILE* 4.8 9.9 - - + -
136A ILE* 4.1 7.6 - - + -
141A HIS* 3.7 2.6 - - - -
142A PHE* 3.0 65.6 + - + +
147A ALA* 3.5 36.1 - - + +
150A VAL* 3.8 33.0 - - + -
151A VAL* 3.9 16.2 - - + -
249A VAL* 2.8 23.9 + - + +
250A LEU* 3.6 13.2 - - + +
251A TYR 3.3 0.2 - - - -
252A ILE* 1.3 77.1 - - - +
254A LEU* 1.3 60.1 + - - +
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Residues in contact with LEU 254 (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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141A HIS* 3.7 15.9 + - - +
142A PHE 4.5 7.1 - - - +
143A ASN 4.4 2.5 - - - +
144A GLU* 4.0 28.0 - - + +
147A ALA* 3.9 22.4 - - + -
250A LEU* 3.1 36.9 + - + +
253A MET* 1.3 75.9 - - - +
255A SER* 1.3 57.8 + - - +
298A ASP* 4.4 5.8 - - - +
299A TRP* 3.8 31.0 - - + -
302A ILE* 4.1 29.6 - - + +
306A ALA* 4.1 11.4 - - + -
310A ILE* 4.0 8.3 - - + -
332A TRP* 4.6 2.0 - - + -
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Residues in contact with SER 255 (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 LYS* 4.7 1.2 - - - +
141A HIS* 4.2 13.8 - - - +
251A TYR* 2.5 28.9 + - - -
253A MET 3.4 0.2 - - - -
254A LEU* 1.3 79.0 - - - +
256A GLY* 1.3 59.9 + - - +
257A TYR* 3.1 36.6 + - - -
298A ASP* 4.1 16.4 - - - +
299A TRP* 3.6 27.8 - - - -
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Residues in contact with GLY 256 (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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136A ILE* 4.8 11.4 - - - +
140A LYS* 3.4 28.6 + - - +
252A ILE* 2.8 24.9 + - - +
255A SER* 1.3 73.4 + - - +
257A TYR* 1.3 60.7 + - - +
258A PRO* 4.8 0.9 - - - +
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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
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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