Contacts of the helix formed by residues 228 - 246 (chain B) in PDB entry 2V62
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 SER 228 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B VAL* 3.5 13.0 - - - +
193B TYR* 4.2 3.8 - - - -
199B HIS* 3.7 18.2 - - - -
220B ASP* 4.6 1.1 + - - -
226B ALA 3.4 1.8 + - - -
227B LEU* 1.3 74.8 - - - +
229B ARG* 1.3 65.7 + - - +
230B ARG* 3.3 12.1 + - - +
231B SER* 2.7 23.6 + - - -
232B ASP 3.9 0.3 + - - -
300B TYR* 2.6 51.5 + - - -
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Residues in contact with ARG 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B HIS* 3.5 30.7 + - + +
163B VAL* 3.8 5.8 - - - +
193B TYR* 3.4 38.1 + - + -
194B CYS* 6.2 0.8 - - - -
199B HIS* 4.3 10.9 + - - -
228B SER* 1.3 76.8 + - - +
230B ARG* 1.3 63.4 + - - +
231B SER 3.1 0.9 + - - -
232B ASP 3.1 10.4 + - - -
233B VAL* 3.6 13.0 + - - +
300B TYR 4.8 0.6 + - - -
301B ASP 2.9 27.5 + - - -
302B GLU 3.8 7.2 + - - +
303B LYS* 3.5 37.4 - - - +
304B PRO* 3.7 17.9 - - + -
306B TYR* 3.7 15.7 + - - -
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Residues in contact with ARG 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B TYR* 4.1 9.5 - - - -
220B ASP* 2.9 38.4 + - - +
223B LYS* 4.2 5.3 - - - +
228B SER* 3.8 10.7 + - - +
229B ARG* 1.3 78.9 - - - +
231B SER* 1.3 58.1 + - - +
233B VAL* 3.2 4.5 + - - +
234B GLU* 3.0 35.2 + - - +
295B ALA* 4.7 6.9 - - - +
298B LEU* 2.8 60.8 + - + +
299B ALA* 3.5 10.8 - - - +
300B TYR* 3.3 32.9 + - - +
302B GLU 5.0 2.5 + - - +
304B PRO* 4.8 0.2 - - - +
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Residues in contact with SER 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B VAL* 4.9 0.3 - - - +
218B SER* 3.3 29.3 - - - -
220B ASP* 4.6 10.5 - - - -
227B LEU* 3.7 18.4 - - - +
228B SER 2.7 29.9 + - - -
229B ARG 3.1 0.2 - - - -
230B ARG* 1.3 79.8 - - - +
232B ASP* 1.3 69.9 + - - +
234B GLU* 3.5 6.1 + - - +
235B ILE* 3.0 31.3 + - - +
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Residues in contact with ASP 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B LEU* 3.6 23.0 - - + +
157B ILE* 4.2 0.2 - - - +
158B HIS* 2.9 30.8 + - - +
163B VAL* 3.3 8.8 - - - +
164B HIS* 2.9 23.9 + - - +
165B GLY* 3.0 28.1 + - - -
167B ILE* 3.7 8.1 - - + +
229B ARG 3.1 4.0 + - - +
231B SER* 1.3 85.5 + - - +
233B VAL* 1.3 56.9 + - - +
235B ILE* 3.5 9.0 + - - +
236B LEU* 3.0 29.5 + - - +
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Residues in contact with VAL 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B LEU* 5.1 3.6 - - + -
154B LEU* 4.5 11.9 - - + -
158B HIS* 4.8 2.2 - - + -
229B ARG 3.6 13.9 - - - +
230B ARG* 3.2 8.7 + - - +
232B ASP* 1.3 75.3 - - - +
234B GLU* 1.3 62.7 + - - +
236B LEU* 3.3 5.3 + - - -
237B GLY 3.0 17.8 + - - -
291B PHE* 3.2 33.7 - - + -
295B ALA* 3.7 22.4 - - + -
298B LEU* 4.5 2.9 - - + -
304B PRO* 3.8 27.4 - - + -
306B TYR* 5.3 1.6 - - + -
309B LEU* 3.8 19.5 - - + -
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Residues in contact with GLU 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B SER* 3.9 7.1 - - - -
219B LEU* 2.9 36.3 + - - +
220B ASP* 5.0 4.2 + - - +
230B ARG* 3.0 21.8 + - - +
231B SER* 3.5 7.1 - - - +
233B VAL* 1.3 74.9 - - - +
235B ILE* 1.3 64.6 + - - +
237B GLY* 3.0 4.2 + - - -
238B TYR* 2.6 59.0 + - + +
268B LEU* 4.3 16.1 - - + +
292B LEU* 4.0 13.3 - - + +
295B ALA* 4.3 8.2 - - + +
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Residues in contact with ILE 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B GLY* 3.5 39.0 - - - +
166B ASP* 4.0 1.1 - - - +
167B ILE* 3.3 39.0 - - + +
216B PHE* 3.4 31.4 - - + +
217B THR* 4.6 3.1 - - - +
218B SER* 3.9 17.7 - - - +
227B LEU* 6.0 1.6 - - + -
231B SER* 3.0 24.0 + - - +
232B ASP* 3.7 11.9 - - - +
234B GLU* 1.3 75.2 - - - +
236B LEU* 1.3 64.0 + - - +
238B TYR* 3.3 5.0 + - - +
239B CYS* 3.0 20.8 + - - -
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Residues in contact with LEU 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B GLY* 3.5 34.5 - - - +
150B MET* 3.7 32.5 - - + -
151B LEU* 4.0 19.1 - - + +
154B LEU* 4.2 7.2 - - + -
167B ILE* 4.4 16.6 - - + +
232B ASP 3.0 18.1 + - - +
233B VAL* 3.6 5.8 - - - +
235B ILE* 1.3 79.6 - - - +
237B GLY* 1.3 55.6 + - - +
239B CYS* 3.3 5.4 + - - +
240B MET* 2.9 36.8 + - + +
243B TRP* 4.6 9.6 - - + -
291B PHE* 4.1 13.0 - - + -
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Residues in contact with GLY 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B VAL 3.0 10.9 + - - -
234B GLU 3.0 4.8 + - - -
236B LEU* 1.3 73.4 - - - +
238B TYR* 1.3 59.9 + - - +
240B MET* 3.3 6.1 + - - +
241B LEU* 2.9 29.6 + - - +
288B ILE* 3.9 5.1 - - - +
291B PHE* 3.6 22.2 - - - -
292B LEU* 3.9 19.3 - - - -
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Residues in contact with TYR 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B PHE* 3.4 35.0 - - + -
217B THR 3.7 15.0 - - - -
219B LEU* 4.0 0.3 - - - +
234B GLU* 2.6 57.0 + - + +
235B ILE* 3.3 4.7 + - - +
237B GLY* 1.3 77.0 - - - +
239B CYS* 1.3 56.8 + - - +
241B LEU* 3.4 7.5 + - + +
242B ARG* 2.9 29.5 + - - +
248B LEU* 3.7 5.0 - - - +
250B TRP* 3.8 31.9 - + + -
264B LYS* 3.5 29.9 - - + +
267B LEU* 4.1 16.8 - - + -
268B LEU* 3.7 20.3 - - + +
292B LEU* 4.7 4.9 - - + -
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Residues in contact with CYS 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B ILE* 3.3 38.4 - - - -
168B LYS* 3.8 10.5 - - - -
216B PHE* 4.0 21.1 - - - -
235B ILE 3.0 16.5 + - - -
236B LEU* 3.4 10.5 - - - +
237B GLY 3.2 0.2 - - - -
238B TYR* 1.3 73.7 - - - +
240B MET* 1.3 61.7 + - - +
242B ARG* 3.1 1.7 + - - +
243B TRP* 2.8 59.8 + - + -
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Residues in contact with MET 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B VAL* 3.6 35.0 - - + +
144B LEU* 4.7 1.6 - - - -
147B GLY* 3.8 21.5 - - - -
236B LEU* 2.9 28.0 + - + +
237B GLY* 3.3 4.0 + - - +
239B CYS* 1.3 76.5 - - - +
241B LEU* 1.3 62.6 + - - +
243B TRP* 3.4 13.2 + - + -
244B LEU* 3.1 26.0 + - - +
288B ILE* 3.7 17.9 - - + +
291B PHE* 3.8 41.7 - - + -
313B LEU* 3.8 22.4 - - + -
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Residues in contact with LEU 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B GLY 2.9 17.2 + - - +
238B TYR* 3.6 6.3 - - - +
240B MET* 1.3 77.7 - - - +
242B ARG* 1.3 56.8 + - - +
245B CYS* 2.9 47.9 + - - +
247B LYS 4.8 0.2 - - - -
248B LEU* 3.8 20.4 - - + -
249B PRO* 4.8 2.0 - - + -
250B TRP* 5.1 0.4 - - + -
267B LEU* 4.3 20.4 - - + -
275B VAL* 3.8 36.3 - - + +
278B TRP* 4.0 16.6 - - + -
285B CYS* 3.8 26.9 - - - -
288B ILE* 4.1 10.2 - - + +
292B LEU* 5.0 3.1 - - + -
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Residues in contact with ARG 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B ASN* 2.9 32.3 + - - +
136B GLY* 3.5 14.5 + - - -
215B GLU* 3.1 23.5 + - - -
216B PHE* 3.7 26.6 - - + -
238B TYR 2.9 17.7 + - - +
239B CYS 3.1 4.7 + - - +
241B LEU* 1.3 78.9 - - - +
243B TRP* 1.3 64.5 + - + +
246B GLY* 2.9 39.2 + - - -
247B LYS* 3.7 23.5 - - - +
248B LEU* 3.9 8.9 - - + +
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Residues in contact with TRP 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B LEU* 6.1 0.2 - - + -
136B GLY 3.9 16.8 - - - -
137B THR* 3.1 10.0 - - - -
138B PHE* 2.9 46.3 + + + +
143B VAL* 3.7 20.4 - - + -
146B LEU* 4.0 32.3 - - + -
150B MET* 5.3 0.2 - - + -
167B ILE* 4.8 0.7 - - + -
168B LYS 4.2 2.9 - - - -
169B ALA* 3.9 35.9 - - + +
172B LEU* 4.0 23.1 - - + -
216B PHE* 5.4 3.6 - - - -
236B LEU* 4.6 12.6 - - + -
239B CYS* 2.8 50.5 + - + +
240B MET* 3.9 21.3 - - + +
242B ARG* 1.3 85.7 - - + +
244B LEU* 1.3 58.2 + - - +
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Residues in contact with LEU 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B THR* 4.2 6.6 - - - +
138B PHE 4.1 6.5 - - - +
140B LYS* 3.4 46.9 - - + +
143B VAL* 4.2 7.6 - - + -
144B LEU* 6.2 0.4 - - + -
240B MET 3.1 16.5 + - - +
241B LEU 4.0 2.2 - - - +
243B TRP* 1.3 78.6 - - - +
245B CYS* 1.3 65.4 + - - +
280B PRO* 4.4 3.3 - - - +
283B SER* 3.6 33.7 + - - +
284B SER 3.4 26.2 - - - +
285B CYS* 3.8 13.9 - - - -
288B ILE* 3.9 13.7 - - + -
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Residues in contact with CYS 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B THR* 4.2 1.8 - - - -
241B LEU* 2.9 29.9 + - - +
244B LEU* 1.3 81.6 - - - +
246B GLY* 1.3 57.3 + - - +
247B LYS* 3.3 5.0 + - - +
278B TRP* 3.7 36.8 - - + +
279B ALA* 3.7 24.9 - - - -
280B PRO* 3.9 11.2 - - + -
285B CYS* 3.8 9.6 - - - -
1331B EDO 3.2 26.5 + - - -
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Residues in contact with GLY 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B ASN* 3.6 19.3 - - - +
137B THR* 3.3 25.5 - - - +
242B ARG* 2.9 31.8 + - - -
245B CYS* 1.3 75.7 - - - +
247B LYS* 1.3 64.8 + - - +
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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