Contacts of the strand formed by residues 228 - 234 (chain A) in PDB entry 6WNX
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205A HIS* 4.6 5.4 + - - -
206A HIS* 3.3 18.7 + - - -
223A CYS* 3.4 4.3 - - - +
224A SER 3.1 25.8 + - - +
226A ASP* 2.9 22.3 + - - -
227A ARG* 1.3 80.1 - - - +
229A ILE* 1.3 63.6 + - - +
245A VAL* 4.2 19.7 - - - -
246A LEU 3.8 5.8 - - - -
247A VAL* 5.0 6.5 - - - +
253A VAL* 4.0 0.7 - - - +
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Residues in contact with ILE 229 (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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221A VAL* 3.3 30.3 - - + -
222A THR 3.3 6.5 - - - +
223A CYS* 4.1 3.1 - - + -
228A SER* 1.3 78.7 - - - +
230A ALA* 1.3 65.1 + - - +
231A VAL* 4.6 0.7 - - + -
245A VAL* 3.4 7.4 - - - +
246A LEU* 2.9 55.4 + - + +
249A HIS* 4.4 5.6 - - + -
253A VAL* 4.0 17.3 - - + -
256A VAL* 4.2 4.0 - - + -
263A ILE* 5.0 1.3 - - + -
265A SER* 3.3 35.0 - - - +
275A TRP* 3.9 23.8 - - + +
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Residues in contact with ALA 230 (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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205A HIS* 3.9 18.8 - - + +
206A HIS* 3.7 9.4 - - - +
221A VAL* 3.1 7.6 - - - +
222A THR* 2.8 51.6 + - - +
229A ILE* 1.3 73.5 - - - +
231A VAL* 1.3 61.9 - - - +
232A TRP* 3.4 17.6 + - + +
242A LEU* 4.2 5.2 - - + -
244A ARG 3.8 4.0 - - - -
245A VAL* 4.7 0.9 - - - +
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Residues in contact with VAL 231 (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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219A LEU* 4.0 25.8 - - + -
220A MET 3.5 6.1 - - - +
221A VAL* 4.2 11.4 - - + -
229A ILE* 4.6 2.0 - - + -
230A ALA* 1.3 76.3 - - - +
232A TRP* 1.3 57.5 + - - +
242A LEU* 3.5 4.0 - - - +
243A ARG* 2.8 36.5 + - + +
244A ARG 3.0 20.1 + - - +
246A LEU* 4.2 17.5 - - + -
263A ILE* 4.1 17.0 - - + -
277A THR 5.6 0.4 - - - +
280A CYS* 4.1 29.8 - - - -
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Residues in contact with TRP 232 (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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189A VAL* 6.1 0.7 - - + -
203A LEU* 4.1 34.5 - - + -
204A ILE 5.0 1.8 - - - -
205A HIS* 3.8 31.4 - + + -
206A HIS* 5.0 2.0 - + - -
219A LEU* 3.4 11.1 - - - +
220A MET* 2.7 59.5 + - + +
222A THR* 3.2 31.8 + - + +
230A ALA* 3.4 24.8 - - + +
231A VAL* 1.3 75.4 - - - +
233A ASP* 1.3 62.1 + - - +
240A ILE* 3.9 26.9 - - + -
241A THR 3.2 9.0 - - - +
242A LEU* 3.5 39.7 - - + -
243A ARG* 4.7 0.9 - - - -
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Residues in contact with ASP 233 (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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218A GLY 3.6 6.0 - - - +
219A LEU* 4.4 2.6 - - - +
232A TRP* 1.3 71.6 - - - +
234A MET* 1.3 58.4 + - - +
235A ALA* 3.8 3.1 - - + +
239A ASP 3.9 1.2 - - - +
240A ILE* 3.3 6.2 - - - +
241A THR* 2.9 46.9 + - - +
243A ARG* 3.4 45.0 + - - +
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Residues in contact with MET 234 (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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179A VAL* 5.0 7.6 - - + -
181A VAL* 4.1 18.6 - - + -
191A VAL* 5.1 3.8 - - + -
215A PHE* 3.8 43.5 - - + -
218A GLY* 2.6 39.0 + - - +
219A LEU 4.1 3.6 - - - +
220A MET* 4.1 20.6 - - + +
232A TRP 3.7 0.2 + - - -
233A ASP* 1.3 70.0 - - - +
235A ALA* 1.3 64.7 + - - +
236A SER* 3.3 7.0 - - - +
237A ALA* 5.6 2.0 - - - -
239A ASP 3.9 2.9 - - - -
240A ILE* 3.6 33.2 - - + -
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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