Contacts of the helix formed by residues 221 - 238 (chain B) in PDB entry 2WP9
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 ASN 221 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145B GLY 4.7 3.4 + - - -
176B LEU* 4.4 4.1 - - - +
213B VAL* 3.5 17.1 - - + +
219B GLY 5.2 1.3 - - - +
220B LEU* 1.3 78.3 - - - +
222B PRO* 1.3 61.7 - - - +
223B THR* 3.1 12.6 + - - -
224B ARG* 2.9 57.7 + - - +
225B ALA* 3.3 11.3 + - - +
101C GLU 3.1 23.4 + - - -
102C THR* 3.8 12.9 - - - +
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Residues in contact with PRO 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B CYS* 4.5 10.5 - - + -
172B PRO* 3.5 40.6 - - + +
173B ALA* 5.5 0.2 - - - -
176B LEU* 4.3 19.1 - - + -
212B CYS* 3.8 24.2 - - + +
213B VAL* 4.4 6.3 - - - +
216B CYS* 5.2 3.6 - - + -
220B LEU* 3.5 11.7 - - + +
221B ASN* 1.3 85.6 - - - +
223B THR* 1.3 60.2 + - - +
225B ALA* 2.9 3.3 + - + +
226B ILE* 2.8 36.9 + - + +
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Residues in contact with THR 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B CYS* 5.5 5.3 - - - -
208B SER* 4.6 16.2 - - - +
210B MET* 4.0 24.9 + - + +
212B CYS* 3.4 14.1 - - - -
213B VAL* 3.3 20.0 - - - +
221B ASN* 3.1 8.9 + - - -
222B PRO* 1.3 77.6 - - - +
224B ARG* 1.3 58.1 + - - +
226B ILE* 3.4 9.9 + - - +
227B GLY* 2.9 26.0 + - - -
94C MET* 6.0 0.2 - - - -
101C GLU* 3.9 28.7 - - + +
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Residues in contact with ARG 224 (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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221B ASN* 2.9 45.0 + - - +
223B THR* 1.3 76.2 - - - +
225B ALA* 1.3 65.8 + - - +
227B GLY* 3.3 1.4 + - - -
228B HIS* 3.1 41.8 + - + +
101C GLU* 3.7 25.8 - - + +
102C THR* 3.5 30.1 - - - +
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Residues in contact with ALA 225 (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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146B LEU* 4.2 3.8 - - + -
175B LEU 4.8 0.2 - - - +
176B LEU* 3.9 34.1 - - + +
179B TYR* 4.0 31.8 - - + -
221B ASN 3.3 4.4 + - - +
222B PRO 2.9 7.7 + - - +
224B ARG* 1.3 77.2 - - - +
226B ILE* 1.3 64.3 + - - +
228B HIS* 2.9 16.5 + - - +
229B ILE* 3.0 18.3 + - - +
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Residues in contact with ILE 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B PHE* 5.0 1.3 - - + -
172B PRO* 4.2 19.7 - - + -
175B LEU* 3.7 33.9 - - + -
203B VAL* 4.0 17.0 - - + -
206B CYS* 3.7 42.4 - - + -
212B CYS* 5.5 2.0 - - - -
222B PRO* 2.8 26.9 + - + +
223B THR* 3.6 6.1 - - - +
225B ALA* 1.3 72.6 - - + +
227B GLY* 1.3 64.4 + - - +
229B ILE* 3.1 9.3 + - - +
230B LYS* 2.9 32.9 + - - +
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Residues in contact with GLY 227 (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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223B THR 2.9 16.6 + - - -
224B ARG 3.3 2.9 + - - -
225B ALA 3.2 0.4 - - - -
226B ILE* 1.3 77.5 - - - +
228B HIS* 1.3 62.8 + - - +
230B LYS* 3.3 13.5 + - - +
231B SER* 3.1 23.1 + - - -
101C GLU* 4.0 16.6 - - - -
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Residues in contact with HIS 228 (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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179B TYR* 3.4 43.8 + + + +
224B ARG* 3.1 44.8 + - + +
225B ALA* 2.9 8.5 + - - +
227B GLY* 1.3 73.3 - - - +
229B ILE* 1.3 66.3 + - - +
231B SER* 3.1 10.3 + - - -
232B MET* 3.0 27.8 + - + +
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Residues in contact with ILE 229 (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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175B LEU* 3.6 47.1 - - + +
178B ALA* 4.4 3.4 - - + -
179B TYR* 4.0 13.4 - - + +
182B LEU* 3.9 26.5 - - + -
194B LEU* 4.7 1.8 - - + -
197B LEU* 4.5 5.4 - - + -
203B VAL* 4.1 14.1 - - + -
225B ALA 3.0 17.2 + - - +
226B ILE* 3.1 9.6 + - - +
228B HIS* 1.3 76.1 - - - +
230B LYS* 1.3 58.4 + - - +
232B MET* 3.0 10.7 + - - +
233B LEU* 2.8 46.9 + - + +
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Residues in contact with LYS 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B VAL* 4.2 11.9 - - + -
204B PHE* 3.7 38.1 - - + -
206B CYS* 2.7 32.9 + - - -
207B THR* 4.8 2.2 - - - +
208B SER* 4.9 6.7 + - - -
226B ILE* 2.9 35.5 + - + +
227B GLY* 3.4 11.4 - - - +
229B ILE* 1.3 76.7 - - - +
231B SER* 1.3 62.3 + - - +
233B LEU* 3.2 9.3 + - - +
234B LEU* 3.0 29.6 + - + +
91C HIS* 5.5 2.6 - - - -
95C ASP* 4.9 8.6 + - - +
16D PHE* 4.2 21.9 - - + -
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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
----------------------------------------------------------
227B GLY 3.1 13.7 + - - -
228B HIS* 3.1 13.0 + - - -
230B LYS* 1.3 74.2 - - - +
232B MET* 1.3 54.1 + - - +
234B LEU* 3.1 11.9 + - - +
235B GLN* 2.8 36.5 + - - +
95C ASP 5.3 5.2 + - - -
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Residues in contact with MET 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B TYR* 4.1 24.7 - - + -
182B LEU* 4.2 23.8 - - - +
183B ILE* 4.9 7.0 - - + -
190B THR* 3.7 29.6 - - + -
194B LEU* 3.9 21.5 - - + +
228B HIS* 3.0 13.7 + - + +
229B ILE* 3.0 7.0 + - - +
231B SER* 1.3 75.2 - - - +
233B LEU* 1.3 63.8 + - - +
235B GLN* 3.2 7.6 + - - +
236B ARG* 3.1 25.3 + - - +
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Residues in contact with LEU 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B LEU* 3.5 40.8 - - + +
197B LEU* 3.5 22.7 - - + +
198B SER* 3.7 14.6 - - - +
203B VAL* 4.0 9.4 - - + -
204B PHE* 3.8 22.2 - - + -
229B ILE* 2.8 40.4 + - + +
230B LYS* 3.5 7.0 - - - +
232B MET* 1.3 72.8 - - - +
234B LEU* 1.3 56.1 + - - +
236B ARG* 3.5 1.5 + - - -
237B ASN* 2.9 37.4 + - - +
13D VAL* 4.1 12.5 - - + +
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Residues in contact with LEU 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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204B PHE* 5.4 2.2 - - + -
230B LYS* 3.0 22.9 + - + +
231B SER* 3.6 9.0 - - - +
233B LEU* 1.3 71.3 - - + +
235B GLN* 1.3 68.9 + - - +
236B ARG 3.0 2.7 + - - -
238B ALA* 3.1 31.8 + - + +
95C ASP 6.1 1.6 - - - +
96C PHE* 6.1 4.3 - - + -
13D VAL* 3.6 23.3 - - + -
16D PHE* 4.0 30.5 - - + -
17D ILE* 3.8 26.0 - - + -
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Residues in contact with GLN 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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231B SER 2.8 20.0 + - - +
232B MET* 3.2 7.8 + - - +
234B LEU* 1.3 73.7 - - - +
236B ARG* 1.3 58.6 + - - +
238B ALA 4.8 4.2 - - - +
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Residues in contact with ARG 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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191B ASP* 3.3 45.4 + - - +
194B LEU* 4.1 21.3 - - + -
195B ASP* 2.7 41.0 + - - -
232B MET 3.1 15.7 + - - +
233B LEU* 4.0 2.9 - - - +
234B LEU 3.0 0.6 - - - -
235B GLN* 1.3 80.3 - - + +
237B ASN* 1.3 73.3 + - - +
238B ALA 3.7 0.7 - - - -
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Residues in contact with ASN 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B LEU 4.7 1.2 + - - -
195B ASP* 4.4 7.2 + - - +
198B SER* 2.9 32.1 + - - -
233B LEU* 2.9 25.2 + - - +
234B LEU 3.9 0.2 - - - -
236B ARG* 1.3 96.2 + - - +
238B ALA* 1.3 59.9 + - - +
11D ASN* 5.5 8.9 + - - +
13D VAL* 4.1 21.7 - - + +
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Residues in contact with ALA 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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234B LEU* 3.1 29.5 + - + +
235B GLN 4.8 4.0 - - - +
236B ARG 3.7 1.7 - - - -
237B ASN* 1.3 79.5 - - - +
13D VAL* 4.3 1.6 - - + -
17D ILE* 3.5 32.1 - - + -
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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