Contacts of the strand formed by residues 329 - 334 (chain B) in PDB entry 4OBZ
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 329 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283B TYR* 3.6 38.6 - + + -
284B LYS* 2.7 47.2 + - - +
285B LEU* 4.3 2.9 - - + -
325B PHE* 2.9 44.6 + + + +
326B ILE* 3.0 16.1 + - - +
328B ARG* 1.4 106.0 + - + +
330B TYR* 1.4 55.4 + - - +
331B THR* 2.8 26.5 + - - -
342B PHE* 4.3 8.5 - - + -
343B ALA 3.1 21.8 - - - +
344B GLU* 4.0 12.8 - - + -
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Residues in contact with TYR 330 (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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166B SER* 3.0 36.8 - - - -
167B PHE 3.4 13.9 - - - -
168B TYR* 3.5 32.5 - + + +
180B GLU* 4.9 1.7 + - - -
182B MET* 4.4 2.3 - - - +
186B THR* 4.5 0.4 - - - -
187B ASP* 2.9 34.1 + - - +
190B TYR* 3.8 26.5 - + + +
191B TYR* 3.6 43.5 - + + -
195B LEU* 4.5 2.4 - - + +
326B ILE 3.9 2.4 + - - -
329B TYR* 1.4 66.3 - - - +
331B THR* 1.3 59.0 + - - +
332B VAL* 4.2 13.0 + - + -
341B GLY 3.7 0.7 - - - +
342B PHE* 3.3 5.9 - - - -
343B ALA* 2.9 30.0 + - + +
345B ALA* 4.0 9.7 - - - +
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Residues in contact with THR 331 (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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165B PHE 4.2 0.5 - - - +
166B SER* 3.4 3.8 + - - -
167B PHE* 2.9 34.2 + - - +
230B VAL* 3.7 4.3 - - + -
326B ILE* 3.4 23.6 - - - +
329B TYR 2.8 15.6 + - - -
330B TYR* 1.3 72.8 - - - +
332B VAL* 1.3 65.0 + - - +
333B PHE* 3.7 27.3 - - + -
340B VAL* 3.6 27.6 - - + -
341B GLY 3.4 2.0 - - - +
342B PHE* 3.6 18.9 - - + -
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Residues in contact with VAL 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B ILE* 3.8 30.1 - - + -
165B PHE 3.8 3.6 - - - +
166B SER* 3.5 17.0 - - - +
186B THR* 3.7 13.2 - - + -
195B LEU* 3.7 29.8 - - + -
197B TYR* 4.6 13.9 - - + +
330B TYR* 4.2 6.1 - - + -
331B THR* 1.3 75.3 - - - +
333B PHE* 1.3 68.4 + - - +
334B ASP* 3.9 2.6 + - + +
340B VAL* 3.2 11.4 - - - +
341B GLY* 2.7 39.1 + - - +
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Residues in contact with PHE 333 (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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34A THR* 4.0 14.6 - - + -
164B ILE* 3.2 6.1 - - - -
165B PHE* 2.8 75.0 + + + +
167B PHE* 3.5 24.9 - + - -
206B TRP* 3.4 52.3 - + + -
230B VAL* 3.7 22.9 - - + -
232B THR* 4.3 6.1 - - + -
331B THR* 3.7 29.8 - - + -
332B VAL* 1.3 75.8 - - - +
334B ASP* 1.4 58.9 + - - +
335B ARG 3.8 0.9 + - - -
339B ARG 4.1 2.2 - - - -
340B VAL* 4.4 4.7 - - + -
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Residues in contact with ASP 334 (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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164B ILE* 3.5 23.3 - - + +
197B TYR* 5.0 5.6 - - + -
206B TRP* 3.5 7.2 - - - -
332B VAL* 3.9 2.3 - - + -
333B PHE* 1.4 69.4 - - - +
335B ARG* 1.3 59.8 + - - +
336B ASP* 3.0 10.6 + - - +
337B ASN* 2.8 37.7 + - - -
338B ASN* 3.2 17.5 + - - -
339B ARG* 2.8 68.9 + - + +
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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