Contacts of the strand formed by residues 321 - 328 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B ARG* 5.7 2.2 - - - -
202B CYS* 5.0 4.7 - - - -
231B TYR* 3.3 33.2 - + + +
232B ASP 3.3 6.5 - - - +
233B PRO* 3.7 32.5 - - + +
243B PHE* 3.9 14.4 - + - -
247B MET* 4.4 9.5 - - - -
285B ASP* 3.2 7.8 - - - +
286B MET* 3.0 43.0 + - + -
317B MET* 3.2 48.9 - - + +
318B GLN* 3.2 14.2 + - - +
319B THR 3.4 0.4 - - - -
320B HIS* 1.3 76.2 - - - +
322B ILE* 1.3 63.4 + - - +
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Residues in contact with ILE 322 (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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230B SER 4.0 6.5 - - - +
231B TYR* 3.3 21.1 - - - -
232B ASP 2.9 21.6 + - - +
234B ILE* 3.7 36.3 - - + -
268B LYS* 3.6 27.6 - - + -
271B TYR* 3.3 44.9 - - + -
283B VAL* 4.2 6.5 - - + -
284B ASN 3.3 8.1 - - - +
285B ASP* 4.2 3.6 - - - -
286B MET* 4.1 4.3 - - - -
321B TYR* 1.3 81.1 - - - +
323B LEU* 1.3 62.3 + - - +
324B MET* 4.1 4.0 - - + +
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Residues in contact with LEU 323 (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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84B GLY* 3.4 35.9 - - - +
85B ILE* 3.8 17.9 - - + -
88B ALA* 5.1 4.7 - - + -
229B ILE* 3.6 30.1 - - + -
230B SER 3.5 7.9 - - - +
231B TYR* 4.4 7.2 - - + -
282B ILE 4.0 0.5 - - - +
283B VAL* 3.5 4.3 - - - -
284B ASN* 2.7 34.3 + - - +
286B MET* 3.8 16.1 - - - -
289B ILE* 4.2 20.9 - - + -
293B GLN* 5.3 2.2 - - - +
322B ILE* 1.3 73.2 - - - +
324B MET* 1.3 58.8 + - - +
325B LYS* 4.1 14.5 + - + +
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Residues in contact with MET 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B TRP* 3.4 15.8 - - + +
229B ILE* 3.3 5.7 - - - +
230B SER* 2.8 43.3 + - - +
271B TYR* 3.7 21.8 - - + -
272B ALA* 4.0 18.8 - - + -
275B TRP* 3.3 59.0 - - + +
281B VAL* 4.0 7.9 - - - -
282B ILE 3.5 7.6 - - - +
283B VAL* 4.0 6.7 - - + -
322B ILE* 4.0 0.8 - - + -
323B LEU* 1.3 71.9 - - - +
325B LYS* 1.3 66.7 + - - +
326B ALA* 3.5 19.1 - - - +
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Residues in contact with LYS 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ALA* 3.8 30.9 - - + +
91B GLU* 5.6 5.1 + - - -
227B LEU* 3.8 15.5 - - + -
228B TRP 3.3 5.8 - - - -
229B ILE* 4.8 3.1 - - + -
280B ASN* 3.7 2.3 + - - +
281B VAL* 3.5 1.7 - - - -
282B ILE* 2.8 77.1 + - + +
284B ASN* 5.0 4.3 - - - +
289B ILE* 6.3 0.7 - - - -
293B GLN* 4.6 15.8 - - - +
323B LEU* 4.8 16.8 - - + +
324B MET* 1.3 78.4 - - - +
326B ALA* 1.3 59.7 + - - +
327B GLN* 4.1 1.3 - - - +
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Residues in contact with ALA 326 (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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220B MET* 4.9 1.6 - - - -
227B LEU* 3.2 3.5 - - - +
228B TRP* 2.7 41.1 + - + +
275B TRP* 3.7 32.1 - - + -
278B ALA* 4.0 7.0 - - + -
280B ASN 3.3 4.0 - - - -
281B VAL* 4.0 8.1 - - + -
324B MET* 3.5 18.1 - - + -
325B LYS* 1.3 73.1 - - - +
327B GLN* 1.3 62.3 + - - +
328B TRP* 3.5 4.7 - - - -
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Residues in contact with GLN 327 (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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92B PHE* 4.0 25.7 - - - +
226B GLY 3.3 9.0 - - - +
227B LEU* 3.6 29.8 - - + +
278B ALA* 3.7 2.1 - - - +
279B PRO* 3.3 19.4 - - - +
280B ASN* 2.7 47.8 + - + +
325B LYS* 4.1 1.6 - - + +
326B ALA* 1.3 71.9 - - - +
328B TRP* 1.3 62.3 + - - +
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Residues in contact with TRP 328 (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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92B PHE* 6.0 0.2 - - - -
196B THR* 4.4 3.1 - - - -
198B VAL* 4.4 13.7 - - + -
219B ILE 4.8 0.7 - - - -
220B MET* 3.4 55.8 + - + -
223B PHE* 2.8 36.5 + + + -
224B SER 3.2 25.6 - - - +
225B HIS* 2.8 33.8 + - - +
226B GLY* 2.9 56.8 + - - +
227B LEU 3.8 3.8 - - - -
228B TRP* 3.6 15.9 - - + -
277B ALA 5.7 0.2 - - - +
278B ALA* 4.6 4.9 - - + -
279B PRO* 3.6 24.5 - - + +
326B ALA 3.5 20.2 - - - -
327B GLN* 1.3 77.3 - - - +
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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