Contacts of the strand formed by residues 329 - 334 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282D GLY 5.1 0.6 + - - -
283D TYR* 4.0 31.9 - + + -
284D LYS* 2.7 37.9 + - - +
285D LEU* 4.4 2.5 - - + -
325D PHE* 2.8 46.0 + + + +
326D ILE* 3.1 11.8 + - - +
328D ARG* 1.4 111.1 + - + +
330D TYR* 1.4 54.5 + - - +
331D THR* 2.7 27.5 + - - -
342D PHE* 4.0 10.8 - - + -
343D ALA 3.3 14.1 - - - +
344D GLU* 3.7 30.7 + - + -
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Residues in contact with TYR 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D SER* 3.0 34.9 + - - -
167D PHE 3.4 16.2 - - - -
168D TYR* 3.6 31.2 - + + +
180D GLU* 5.3 0.6 + - - -
182D MET* 4.4 2.6 - - - +
186D THR* 4.4 1.6 - - - -
187D ASP* 2.8 31.9 + - - +
190D TYR* 3.9 24.9 - + + +
191D TYR* 3.6 44.9 - + + -
195D LEU* 4.5 3.4 - - + +
326D ILE 3.8 2.8 + - - -
329D TYR* 1.4 66.8 - - - +
331D THR* 1.3 57.9 + - - +
332D VAL* 3.9 15.5 - - + -
341D GLY 3.6 0.9 - - - +
342D PHE* 3.4 5.5 - - - -
343D ALA* 2.8 30.6 + - + +
345D ALA* 3.9 9.1 - - - +
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Residues in contact with THR 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D PHE 4.2 0.2 - - - +
166D SER* 3.2 4.2 - - - -
167D PHE* 2.8 38.4 + - - -
230D VAL* 3.7 15.9 - - + -
326D ILE* 3.3 24.2 - - - +
329D TYR 2.7 21.2 + - - -
330D TYR* 1.3 72.3 - - - +
332D VAL* 1.3 64.2 + - - +
333D PHE* 3.6 32.9 - - + -
340D VAL* 3.8 9.2 - - + -
341D GLY 3.5 2.0 - - - +
342D PHE* 3.7 18.1 - - + -
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Residues in contact with VAL 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D ILE* 3.8 24.2 - - + -
165D PHE 4.3 0.7 - - - +
166D SER* 3.3 22.7 - - - +
186D THR* 3.7 15.0 - - + -
195D LEU* 3.7 28.7 - - + -
197D TYR* 4.7 13.7 - - + +
330D TYR* 3.9 8.3 - - + -
331D THR* 1.3 75.2 - - - +
333D PHE* 1.3 68.6 + - - +
334D ASP* 3.9 2.5 - - + +
340D VAL* 3.2 11.8 - - - +
341D GLY* 2.7 40.3 + - - +
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Residues in contact with PHE 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C THR* 3.8 15.0 - - + -
164D ILE* 3.2 6.6 - - - -
165D PHE* 2.8 74.6 + + + +
167D PHE* 3.5 24.9 - + - -
206D TRP* 3.5 52.3 - + + -
230D VAL* 3.8 22.7 - - + -
232D THR* 4.3 6.1 - - + -
331D THR* 3.6 29.8 - - + -
332D VAL* 1.3 76.3 - - - +
334D ASP* 1.4 58.1 + - - +
335D ARG 3.8 0.7 + - - -
339D ARG 4.1 2.2 - - - -
340D VAL* 4.4 3.4 - - + -
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Residues in contact with ASP 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D ILE* 3.5 24.3 - - + +
197D TYR* 5.0 5.1 - - + -
206D TRP* 3.5 7.9 - - - -
332D VAL* 3.9 3.8 - - + +
333D PHE* 1.4 69.2 - - - +
335D ARG* 1.3 57.5 + - - +
336D ASP* 2.9 11.4 + - - +
337D ASN* 2.9 36.8 + - - +
338D ASN* 3.2 17.3 + - - -
339D ARG* 2.8 68.6 + - + +
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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