Contacts of the strand formed by residues 226 - 232 (chain B) in PDB entry 3WOR
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 ALA 226 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B VAL* 3.5 3.8 - - - +
83B THR* 2.9 33.5 + - + +
84B ASN 4.2 2.0 - - - +
85B HIS* 4.2 8.5 - - - -
88B ALA* 3.9 26.7 - - + -
92B ILE* 4.9 0.4 - - + -
198B LEU* 5.2 0.7 - - + -
200B TYR 3.5 13.0 - - - +
201B ALA* 4.4 10.8 - - + -
202B PRO* 4.5 0.9 - - - -
225B PHE* 1.3 87.0 - - - +
227B PHE* 1.3 65.5 + - - +
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Residues in contact with PHE 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B VAL* 4.3 1.1 - - + -
80B LEU* 3.9 31.6 - - + -
81B VAL 3.2 5.2 - - - +
82B VAL* 3.8 30.1 - - + -
198B LEU* 3.7 7.1 - - - +
199B ALA* 2.8 23.0 + - + -
200B TYR* 2.8 41.3 + + + +
225B PHE* 3.7 16.4 - + - -
226B ALA* 1.3 78.1 - - - +
228B TYR* 1.3 62.7 + - - +
256B PHE* 5.6 1.8 - + - -
701B LEU* 4.5 8.5 - - + -
705B MET* 3.6 38.8 - - + -
714B LEU* 4.5 2.5 - - + -
718B MET* 3.7 29.2 - - + -
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Residues in contact with TYR 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LEU* 4.2 30.1 - - + +
80B LEU* 3.5 7.8 - - - +
81B VAL* 2.8 48.0 + - + +
83B THR* 4.3 11.2 - - + +
87B CYS 3.6 7.4 + - - -
88B ALA* 3.4 38.6 - - + -
91B ALA* 4.0 23.3 + - + +
118B ALA* 4.2 6.2 - - + +
122B ALA* 5.5 4.8 - - + +
123B ARG 5.5 1.3 - - - -
124B VAL* 5.1 2.2 - - + -
196B VAL* 3.7 25.1 - - + -
197B ARG 3.0 15.3 - - - +
198B LEU* 4.2 10.5 - - + -
199B ALA* 4.3 4.7 - - - -
227B PHE* 1.3 81.0 - - - +
229B ARG* 1.3 62.7 + - - +
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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
----------------------------------------------------------
78B ASN* 3.1 29.0 + - - +
79B GLY 3.4 10.5 - - - +
80B LEU* 4.0 10.7 - - + +
112B THR* 3.5 17.8 - - - +
115B GLU* 2.6 46.0 + - - +
124B VAL* 6.3 0.2 - - - -
196B VAL* 3.6 2.2 - - - -
197B ARG 2.6 33.7 + - - -
199B ALA* 4.5 1.9 - - + +
228B TYR* 1.3 78.5 - - - +
230B ALA* 1.3 68.9 + - - +
231B TYR* 3.5 17.5 - - + -
247B PRO* 4.1 13.5 - - - -
714B LEU* 3.7 18.8 - - - +
717B GLU* 2.8 43.6 + - - -
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Residues in contact with ALA 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B PHE* 4.2 12.3 - - + -
79B GLY 3.0 16.4 + - - +
81B VAL* 4.8 5.5 - - + +
124B VAL* 4.8 6.3 - - + -
193B ILE* 3.9 31.0 - - + -
195B ASP 3.9 4.3 - - - -
196B VAL* 4.9 2.7 - - - +
229B ARG* 1.3 76.9 - - - +
231B TYR* 1.3 58.1 + - - +
247B PRO* 3.3 7.1 - - - +
248B TYR* 2.8 33.3 + - + +
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Residues in contact with TYR 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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112B THR* 3.2 26.1 + - - -
115B GLU* 2.5 31.0 + - - -
193B ILE* 3.4 14.7 - - - +
194B LYS 4.8 0.7 + - - -
195B ASP* 3.0 35.9 + - - +
197B ARG* 3.4 42.8 + - + -
229B ARG* 3.5 27.4 - - + -
230B ALA* 1.3 74.4 - - - +
232B VAL* 1.3 69.0 + - - +
238B PRO* 5.2 0.2 - - - +
239B ALA 4.8 2.3 + - - +
245B ASN* 3.5 17.9 - - + -
246B VAL 3.2 22.4 - - - -
247B PRO* 3.4 17.3 - - + -
248B TYR 4.0 0.7 - - - +
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Residues in contact with VAL 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B LEU* 5.7 1.3 - - + -
193B ILE* 4.3 9.6 - - + -
231B TYR* 1.3 80.0 - - - +
233B GLY* 1.3 71.4 + - - +
236B GLY* 3.6 23.6 - - - +
237B LYS 3.4 10.8 - - - +
238B PRO* 4.1 15.7 - - + -
239B ALA* 4.8 2.2 - - - +
245B ASN* 3.2 10.8 - - - +
246B VAL* 2.7 44.4 + - + +
247B PRO 4.6 0.9 - - - +
248B TYR* 4.0 35.6 - - + +
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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
------------------------------------------------------------
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