Contacts of the helix formed by residues 225 - 236 (chain B) in PDB entry 4WNP
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 225 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186B MET* 5.7 4.0 - - - +
223B ALA* 3.1 11.3 + - - +
224B SER* 1.3 80.9 - - - +
226B PRO* 1.3 71.3 - - - +
227B GLN* 3.6 7.7 + - - +
228B ASP* 3.0 24.2 + - - +
229B LEU* 3.0 22.9 + - - +
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Residues in contact with PRO 226 (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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185B PRO* 4.0 31.2 - - + -
186B MET* 6.3 1.1 - - - -
193B ILE* 3.8 9.7 - - + +
225B SER* 1.3 87.6 - - - +
227B GLN* 1.3 76.6 + - + +
228B ASP 3.1 1.6 - - - -
229B LEU* 3.0 18.1 + - + +
230B ARG* 3.1 11.1 + - - +
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Residues in contact with GLN 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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225B SER* 4.0 5.5 + - - +
226B PRO* 1.3 83.2 - - + +
228B ASP* 1.3 61.9 + - - +
230B ARG* 3.6 19.6 + - - +
231B LEU* 3.3 31.1 + - + +
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Residues in contact with ASP 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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223B ALA* 4.0 5.2 - - + +
224B SER* 3.2 31.7 + - - +
225B SER* 3.0 31.0 + - - +
227B GLN* 1.3 75.5 - - - +
229B LEU* 1.3 63.6 + - - +
231B LEU* 3.5 9.2 + - - +
232B PHE* 3.0 23.9 + - - +
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Residues in contact with LEU 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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185B PRO* 3.3 28.7 - - + +
186B MET* 4.0 23.1 - - - -
193B ILE* 4.3 4.0 - - + -
221B PHE* 3.6 26.0 - - + +
222B GLN 4.9 0.2 - - - +
223B ALA* 3.7 15.2 - - + +
225B SER 3.0 12.7 + - - +
226B PRO* 3.0 9.6 + - + +
228B ASP* 1.3 75.6 - - - +
230B ARG* 1.3 63.3 + - - +
232B PHE* 3.3 11.2 - - + +
233B TYR* 3.0 60.6 + - + +
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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
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193B ILE* 3.5 44.9 - - + +
194B MET* 4.4 7.1 - - + +
226B PRO 3.1 11.7 + - - +
227B GLN* 3.7 19.2 + - - +
229B LEU* 1.3 76.5 - - - +
231B LEU* 1.3 81.7 + - - +
233B TYR* 3.0 6.3 + - - +
234B GLU* 2.6 74.9 + - - +
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Residues in contact with LEU 231 (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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227B GLN* 3.3 19.3 + - + +
228B ASP* 3.8 9.9 - - - +
230B ARG* 1.3 102.0 - - - +
232B PHE* 1.3 57.6 + - - +
234B GLU* 3.1 18.0 + - + +
235B LYS* 2.9 55.9 + - + +
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Residues in contact with PHE 232 (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 PHE* 4.0 30.3 - + + -
222B GLN 5.5 7.2 - - - -
223B ALA* 5.6 2.2 - - + -
228B ASP* 3.0 17.8 + - - +
229B LEU* 3.3 17.7 - - + +
230B ARG 3.2 0.2 - - - -
231B LEU* 1.3 75.7 - - - +
233B TYR* 1.3 72.4 + + - +
235B LYS* 5.0 0.9 - - - -
236B ASN* 2.6 57.0 + - - +
239B LEU* 3.3 30.3 - - + -
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Residues in contact with TYR 233 (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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186B MET 5.3 3.3 + - - -
188B MET 4.4 6.7 + - - -
190B PRO* 3.8 24.0 - - + -
193B ILE* 3.4 28.5 - - + -
194B MET* 4.2 8.5 - - + -
205B TRP* 3.5 26.0 + + - -
221B PHE* 4.1 9.8 + + - +
229B LEU* 3.0 48.2 + - + +
230B ARG 3.0 7.2 + - - +
232B PHE* 1.3 91.9 - + - +
234B GLU* 1.3 57.6 - - - +
236B ASN 3.3 5.1 - - - +
239B LEU* 3.3 31.9 - - + -
261B ARG* 2.7 37.7 + - - +
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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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194B MET* 3.7 24.3 - - + +
230B ARG* 2.6 56.5 + - - +
231B LEU* 3.1 18.4 + - - +
233B TYR* 1.3 79.1 - - - +
235B LYS* 1.3 60.2 + - + +
236B ASN 3.2 1.0 + - - -
237B LYS* 3.0 26.7 + - - +
261B ARG* 3.9 7.4 + - - +
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Residues in contact with LYS 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 LEU* 2.9 36.4 + - + +
232B PHE* 5.0 0.4 - - - -
234B GLU* 1.3 78.5 - - + +
236B ASN* 1.3 67.1 + - - +
237B LYS* 3.1 19.4 + - - +
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Residues in contact with ASN 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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232B PHE* 2.6 56.0 + - - +
233B TYR 3.3 2.8 - - - +
234B GLU 3.2 1.0 - - - -
235B LYS* 1.3 85.9 - - - +
237B LYS* 1.3 57.6 + - - +
238B THR 3.0 23.7 + - - +
239B LEU* 3.7 10.8 - - + +
261B ARG* 2.8 22.5 + - - -
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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
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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