Contacts of the strand formed by residues 281 - 285 (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 LYS 281 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194B SER* 5.1 6.9 + - - -
195B LEU 5.3 0.6 + - - -
196B SER* 2.8 39.0 + - - +
277B LYS* 3.5 5.9 - - - +
278B LEU 3.1 33.3 + - - +
279B GLY 3.3 5.3 - - - +
280B GLY* 1.4 78.8 - - - +
282B GLY* 1.3 59.8 + - - +
283B TYR* 4.1 13.7 - - + +
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Residues in contact with GLY 282 (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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275B THR* 3.8 14.8 - - - -
276B LEU 3.8 3.4 - - - -
277B LYS* 3.9 15.3 - - - +
281B LYS* 1.3 76.0 - - - +
283B TYR* 1.3 65.2 + - - -
284B LYS* 3.7 22.2 + - - +
329B TYR* 4.7 0.5 + - - -
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Residues in contact with TYR 283 (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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196B SER* 3.5 30.6 + - - -
198B LEU* 4.4 2.6 - - - +
274B ILE 3.7 1.9 - - - +
275B THR* 3.6 3.9 - - - +
276B LEU* 2.8 45.0 + - - +
278B LEU* 3.3 43.5 + - + -
281B LYS* 4.0 15.9 - - + +
282B GLY* 1.3 72.6 - - - -
284B LYS* 1.3 64.3 - - - +
285B LEU* 3.9 1.6 + - - +
325B PHE* 3.7 24.2 - + + -
329B TYR* 3.6 34.5 - + + -
342B PHE* 3.7 33.2 - + + +
343B ALA* 5.9 0.4 - - - -
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Residues in contact with LYS 284 (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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273B ALA* 5.1 8.5 - - + -
274B ILE 3.7 5.8 - - - -
275B THR* 3.8 17.2 - - + +
282B GLY 3.7 19.2 + - - +
283B TYR* 1.3 73.3 - - - +
285B LEU* 1.3 61.1 - - - +
286B SER 4.2 0.7 - - - -
328B ARG* 3.7 21.9 + - - +
329B TYR* 2.7 37.2 + - - +
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Residues in contact with LEU 285 (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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237B MET* 3.8 17.9 - - + -
273B ALA* 3.5 5.0 - - - -
274B ILE* 2.9 32.9 + - + +
276B LEU* 3.6 27.8 - - + -
283B TYR 4.4 1.3 - - - +
284B LYS* 1.3 80.5 - - - +
286B SER* 1.3 63.9 + - - +
289B ASP* 4.0 19.7 - - + -
290B TYR* 3.5 21.3 - - + -
306B PHE* 4.5 11.0 - - + -
324B VAL* 4.3 15.9 - - + +
325B PHE* 4.5 7.2 - - + -
328B ARG* 4.2 18.6 - - + -
329B TYR* 4.3 7.2 - - + -
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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