Contacts of the strand formed by residues 285 - 291 (chain B) in PDB entry 2B9B
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 GLN 285 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B VAL* 4.5 19.6 - - + +
36B ARG 3.6 11.9 - - - +
37B GLN* 5.5 4.5 - - + -
38B LEU 5.2 0.2 - - - +
283B ALA 4.3 6.2 + - - +
284B THR* 1.3 79.8 - - - +
286B ILE* 1.3 64.6 + - - +
287B ILE* 3.9 15.7 + - + +
309B VAL 3.9 0.3 - - - +
310B MET* 3.5 2.1 - - - -
311B VAL* 2.8 41.7 + - + +
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Residues in contact with ILE 286 (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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34B ASN 3.5 3.3 - - - +
36B ARG* 2.8 42.7 + - - +
38B LEU* 3.5 30.7 - - + -
285B GLN* 1.3 75.3 - - - +
287B ILE* 1.3 61.3 + - - +
288B ASP* 4.2 3.2 + - - +
308B ARG* 3.6 35.4 - - + +
309B VAL 3.4 7.6 - - - +
310B MET* 4.5 8.7 - - + -
319B TYR* 3.3 37.5 - - + -
331B VAL* 3.7 26.9 - - + -
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Residues in contact with ILE 287 (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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21B ASP* 5.5 9.4 - - + +
32B PRO* 4.1 15.7 - - + -
34B ASN 3.2 9.2 - - - +
35B VAL* 4.2 20.6 - - + -
285B GLN* 4.6 17.9 - - - +
286B ILE* 1.3 79.1 - - - +
288B ASP* 1.3 74.5 + - - +
289B LEU* 3.9 16.2 + - + +
308B ARG* 3.3 3.1 - - - +
309B VAL* 2.9 48.1 + - + +
311B VAL* 4.5 18.4 - - + -
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Residues in contact with ASP 288 (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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32B PRO* 3.5 5.9 - - - +
33B THR* 2.9 44.0 + - - +
34B ASN* 2.9 22.7 + - - +
36B ARG* 2.9 29.9 + - - -
286B ILE* 4.4 1.0 - - - +
287B ILE* 1.3 73.0 - - - +
289B LEU* 1.3 60.8 + - - +
307B THR* 3.3 10.5 - - + +
308B ARG* 2.8 42.7 + - - +
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Residues in contact with LEU 289 (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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25B LEU* 5.2 5.4 - - + -
30B VAL* 4.3 20.2 - - + -
31B ILE 4.0 9.2 - - - +
32B PRO* 4.2 8.7 - - + -
33B THR* 5.2 0.4 - - - -
287B ILE* 4.1 19.7 - - + +
288B ASP* 1.3 80.3 - - - +
290B ALA* 1.3 61.1 + - - +
291B THR* 5.3 3.1 - - + +
305B LEU* 4.7 5.6 - - + -
306B PRO 3.6 22.7 - - - +
307B THR* 2.6 33.4 + - - +
309B VAL* 4.0 18.8 - - + -
349B LEU* 3.7 29.8 - - + -
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Residues in contact with ALA 290 (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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30B VAL* 3.2 3.5 - - - +
31B ILE* 2.7 39.4 + - + +
33B THR* 3.4 27.1 - - + -
288B ASP 4.1 0.4 + - - -
289B LEU* 1.3 73.9 - - - +
291B THR* 1.3 65.4 + - - +
370B VAL* 5.8 3.8 - - + -
117C THR* 5.9 6.3 - - + -
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Residues in contact with THR 291 (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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29B GLY 3.1 5.6 - - - -
30B VAL* 3.5 25.6 - - + -
289B LEU* 5.3 3.6 - - + +
290B ALA* 1.3 83.6 - - - +
292B ILE* 1.3 66.0 + - - +
302B MET* 3.3 41.6 - - - +
303B ALA* 3.9 20.5 + - + +
305B LEU* 5.2 8.3 - - + +
367B THR* 4.5 5.9 - - - +
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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