Contacts of the strand formed by residues 284 - 287 (chain A) in PDB entry 1BWC
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 CYS 284 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A ILE* 3.7 31.6 - - - -
183A LEU* 4.3 8.5 - - + -
187A PRO* 3.5 33.4 - - + -
189A ARG 3.2 3.8 + - - -
190A SER* 3.2 11.1 - - - +
191A VAL 2.8 27.2 + - - +
206A LEU* 5.0 4.3 - - - -
282A VAL* 3.4 4.7 - - - +
283A ASP* 1.3 81.2 - - - +
285A LEU* 1.3 59.3 + - - +
286A LEU* 4.5 13.5 - - - -
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Residues in contact with LEU 285 (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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174A GLY* 3.1 14.5 - - - +
175A ILE* 2.7 34.7 + - - +
191A VAL* 3.4 34.1 - - + +
193A VAL* 4.1 15.3 - - + -
251A VAL* 4.9 4.0 - - + -
254A VAL* 3.6 37.5 - - + -
261A LEU* 4.0 20.1 - - + +
263A VAL* 3.9 13.0 - - + -
282A VAL* 4.1 5.5 - - + +
284A CYS* 1.3 72.7 - - - +
286A LEU* 1.3 53.8 + - - +
287A TRP* 3.9 24.0 - - + -
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Residues in contact with LEU 286 (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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175A ILE* 3.4 31.4 - - + +
176A THR 3.8 15.0 - - - +
177A SER* 4.9 4.0 - - - +
180A PHE* 4.0 23.3 - - + -
191A VAL 2.9 8.7 + - - -
192A ILE* 3.5 45.1 - - + -
193A VAL* 2.8 28.4 + - - +
202A MET* 3.9 21.3 - - + -
206A LEU* 5.4 0.4 - - + -
284A CYS* 4.5 7.2 - - - -
285A LEU* 1.3 74.6 - - - +
287A TRP* 1.3 63.7 + - - +
288A ALA* 3.5 11.9 + - + -
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Residues in contact with TRP 287 (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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160A PRO* 5.3 2.6 - - - +
161A SER 4.5 16.3 - - - +
162A THR* 4.2 12.6 - - + -
163A PRO* 3.9 36.7 - - + +
168A ILE* 4.1 9.4 - - + -
171A ALA* 2.9 40.0 + - + -
174A GLY* 3.7 15.2 - - - -
175A ILE 2.8 19.7 + - - +
176A THR* 3.9 18.9 - - - +
177A SER 4.4 3.3 + - - -
193A VAL* 3.7 36.1 - - + -
251A VAL* 3.9 29.6 - - + -
254A VAL* 4.6 2.9 - - + -
285A LEU* 3.9 19.5 - - + -
286A LEU* 1.3 71.5 - - - +
288A ALA* 1.3 61.1 + - - +
289A ILE* 3.8 10.9 + - + -
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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