Contacts of the helix formed by residues 220 - 228 (chain B) in PDB entry 2WNW
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 TYR 220 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164B ARG* 2.9 32.3 + - - -
167B TYR* 3.7 38.8 - + + -
168B ALA* 3.7 31.4 - - + -
171B ALA* 3.9 16.2 - - + -
215B ALA* 3.7 8.5 - - + -
216B PHE* 3.2 13.4 + + + +
218B VAL 3.5 0.4 - - - -
219B GLN* 1.3 101.9 + - + +
221B LEU* 1.3 67.7 + - - +
222B ARG 3.6 0.7 - - - -
223B PRO* 3.5 4.9 - - - +
224B ARG* 2.9 37.5 + - - +
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Residues in contact with LEU 221 (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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171B ALA* 4.4 9.9 - - + +
174B ILE* 4.1 30.7 - - + -
175B ILE* 5.1 7.2 - - + -
191B LEU* 4.6 17.3 - - + -
192B SER 5.6 0.4 - - - +
193B VAL* 4.5 12.1 - - + -
216B PHE* 2.9 50.1 + - + +
217B ALA* 3.4 18.4 - - - +
220B TYR* 1.3 70.8 - - - +
222B ARG* 1.3 67.8 + - - +
224B ARG* 3.3 4.9 + - - +
225B LEU* 2.9 30.4 + - + +
235B ILE* 4.3 17.9 - - + -
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Residues in contact with ARG 222 (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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217B ALA 3.0 17.9 + - - +
218B VAL* 3.7 17.7 - - + +
221B LEU* 1.3 75.3 - - - +
223B PRO* 1.3 68.5 - - + +
225B LEU* 3.2 8.6 + - - +
226B ALA* 3.0 24.0 + - - +
230B MET 4.7 0.4 + - - -
231B ASP* 3.5 19.5 + - - +
233B MET* 2.9 30.5 + - - +
235B ILE* 3.5 18.9 - - + +
261B GLY* 2.9 33.4 + - - +
263B ASN* 2.8 30.3 + - - +
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Residues in contact with PRO 223 (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 VAL 3.5 12.8 - - - +
219B GLN* 3.7 16.6 - - - +
220B TYR 3.5 14.1 - - - +
222B ARG* 1.3 95.0 - - + +
224B ARG* 1.3 62.6 + - - +
226B ALA* 3.3 8.5 + - + +
227B ARG* 3.1 26.4 + - - +
1449B GOL 3.1 24.5 - - - +
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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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168B ALA* 3.5 34.8 + - - +
171B ALA* 3.7 21.5 - - - -
172B ASP* 2.9 30.1 + - - +
175B ILE* 3.7 20.6 - - + -
219B GLN 4.5 2.2 + - - -
220B TYR* 2.9 42.8 + - - +
221B LEU* 3.3 3.9 + - - +
223B PRO* 1.3 73.3 - - - +
225B LEU* 1.3 65.7 + - - +
227B ARG* 3.4 5.0 + - - +
228B GLN* 3.2 27.9 + - - +
1449B GOL 3.4 48.5 + - - +
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Residues in contact with LEU 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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175B ILE* 3.8 12.3 - - + -
178B LEU* 3.7 30.5 - - + -
191B LEU* 4.4 6.7 - - + -
221B LEU* 2.9 34.0 + - + +
222B ARG* 3.7 11.4 - - - +
224B ARG* 1.3 75.4 - - - +
226B ALA* 1.3 57.4 + - - +
228B GLN* 3.1 7.4 + - - -
230B MET* 2.7 56.9 + - + +
231B ASP* 4.8 1.6 - - - +
233B MET* 4.0 28.5 - - + -
235B ILE* 4.1 18.8 - - + -
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Residues in contact with ALA 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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222B ARG 3.0 12.4 + - - +
223B PRO* 3.5 11.2 - - + +
225B LEU* 1.3 78.6 - - - +
227B ARG* 1.3 58.5 + - + +
228B GLN 3.1 0.2 - - - -
229B GLY* 3.0 18.2 + - - -
231B ASP* 4.3 22.8 - - + +
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Residues in contact with ARG 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 PRO 3.1 12.2 + - - +
224B ARG* 3.9 6.3 - - - +
225B LEU 3.3 0.4 - - - -
226B ALA* 1.3 77.2 - - + +
228B GLN* 1.3 66.6 + - + +
229B GLY 3.4 1.3 - - - -
1449B GOL 3.7 47.1 + - - -
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Residues in contact with GLN 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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175B ILE* 3.9 28.5 - - + +
179B LEU* 3.9 26.5 - - - +
182B ARG* 3.5 21.6 + - - +
224B ARG 3.2 14.1 - - - +
225B LEU 3.1 7.9 + - - +
226B ALA 3.1 0.6 - - - -
227B ARG* 1.3 82.7 + - + +
229B GLY* 1.3 62.4 + - - +
230B MET* 3.2 18.6 + - + -
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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