Contacts of the strand formed by residues 321 - 328 (chain A) in PDB entry 2OB1
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 321 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A ARG* 5.9 0.9 - - - -
202A CYS* 5.0 4.0 - - - -
231A TYR* 3.3 31.9 - + + +
232A ASP 3.4 5.4 - - - +
233A PRO* 3.7 33.0 - - + -
243A PHE* 3.9 20.6 - + - -
247A MET* 4.4 9.7 - - - -
285A ASP* 3.1 6.8 - - - +
286A MET* 2.9 44.6 + - + -
317A MET* 3.2 40.2 - - + +
318A GLN* 3.2 16.5 + - - +
320A HIS* 1.3 76.6 - - - +
322A ILE* 1.3 64.0 + - - +
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Residues in contact with ILE 322 (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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230A SER 4.0 2.7 - - - +
231A TYR* 3.3 22.5 - - - -
232A ASP 3.0 17.9 + - - +
234A ILE* 3.7 41.7 - - + -
268A LYS* 3.7 19.5 - - + -
271A TYR* 3.3 43.3 - - + -
283A VAL* 4.2 8.1 - - + -
284A ASN 3.2 10.5 - - - +
285A ASP* 4.1 4.9 - - + +
286A MET* 4.1 4.3 - - - -
321A TYR* 1.3 80.8 - - - +
323A LEU* 1.3 62.0 + - - +
324A MET* 3.9 12.6 - - + +
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Residues in contact with LEU 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLY* 3.4 30.7 - - - +
85A ILE* 3.6 29.4 - - + +
88A ALA* 4.9 2.0 - - + -
229A ILE* 3.7 19.1 - - + -
230A SER 3.3 7.9 - - - +
231A TYR* 4.2 7.9 - - + -
282A ILE* 4.0 0.5 - - - +
283A VAL* 3.4 2.5 - - - -
284A ASN* 2.9 31.5 + - - +
286A MET* 3.9 6.0 - - + -
289A ILE* 3.7 28.9 - - + -
293A GLN* 5.6 3.6 - - - +
322A ILE* 1.3 74.4 - - - +
324A MET* 1.3 59.7 + - - +
325A LYS* 4.1 19.0 + - + +
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Residues in contact with MET 324 (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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228A TRP* 3.5 16.8 - - + +
229A ILE* 3.4 4.2 - - - +
230A SER* 2.8 42.5 + - - +
271A TYR* 3.7 20.4 - - + -
272A ALA* 4.0 21.1 - - + -
275A TRP* 3.4 50.9 - - + +
281A VAL* 4.1 7.4 - - - -
282A ILE 3.4 7.9 - - - +
283A VAL* 4.0 3.8 - - + -
322A ILE* 3.9 3.3 - - + +
323A LEU* 1.3 73.8 - - - +
325A LYS* 1.3 67.4 + - - +
326A ALA* 3.5 21.3 - - + +
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Residues in contact with LYS 325 (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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88A ALA* 3.7 33.8 - - + +
91A GLU* 5.1 11.3 + - - -
227A LEU* 3.9 15.7 - - + -
228A TRP 3.3 4.7 - - - -
229A ILE* 4.7 2.7 - - + -
280A ASN* 3.7 2.1 - - - +
281A VAL* 3.4 1.9 - - - -
282A ILE* 2.7 78.3 + - + +
284A ASN* 5.3 2.8 - - - +
293A GLN* 4.6 14.6 - - - +
323A LEU* 4.6 17.2 - - + +
324A MET* 1.3 78.2 - - - +
326A ALA* 1.3 60.3 + - - +
327A GLN* 4.1 1.5 - - + +
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Residues in contact with ALA 326 (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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220A MET* 4.9 1.1 - - - -
227A LEU* 3.2 2.6 - - - +
228A TRP* 2.6 41.1 + - + +
275A TRP* 3.7 30.5 - - + -
278A ALA* 3.9 11.9 - - + -
280A ASN 3.3 3.6 - - - -
281A VAL* 3.9 3.4 - - + +
324A MET* 3.5 19.0 - - + -
325A LYS* 1.3 74.3 - - - +
327A GLN* 1.3 62.4 + - - +
328A TRP* 3.4 5.5 - - - -
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Residues in contact with GLN 327 (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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92A PHE* 3.9 26.9 - - - +
226A GLY 3.3 8.0 - - - +
227A LEU* 3.3 29.8 - - + +
278A ALA* 3.8 1.9 - - - +
279A PRO* 3.4 7.3 - - - +
280A ASN* 2.7 61.1 + - + +
325A LYS* 5.4 1.5 - - + +
326A ALA* 1.3 73.0 - - - +
328A TRP* 1.3 62.2 + - - +
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Residues in contact with TRP 328 (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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92A PHE* 5.9 0.7 - - - -
196A THR 4.5 2.0 - - - -
198A VAL* 4.5 12.6 - - + -
220A MET* 3.4 56.2 + - + -
223A PHE* 2.8 36.1 + + + -
224A SER 3.3 23.7 - - - +
225A HIS* 2.7 37.2 + - - +
226A GLY* 2.8 46.8 + - - +
227A LEU 3.7 12.3 - - - -
228A TRP* 3.5 19.3 - - + -
278A ALA* 4.6 4.3 - - + -
279A PRO* 3.7 25.5 - - + +
326A ALA 3.4 22.7 - - - -
327A GLN* 1.3 78.5 - - - +
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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