Contacts of the strand formed by residues 293 - 297 (chain C) in PDB entry 3BRW
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 VAL 293 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C LYS 4.9 0.6 + - - -
195C PHE* 3.3 25.9 - - + -
196C GLY 3.3 15.8 + - - -
291C ASP* 4.0 6.3 - - - +
292C ILE* 1.3 84.3 - - + +
294C ALA* 1.3 66.6 + - - +
314C LEU* 5.3 0.2 - - - -
316C ALA* 3.3 25.4 - - + +
317C TYR* 4.8 2.2 - - - +
318C VAL* 5.5 0.9 - - + +
369C LEU* 3.6 28.5 - - + +
372C ALA* 3.8 12.3 - - + -
373C GLU* 3.6 40.3 + - + +
376C CYS* 4.8 0.2 - - - -
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Residues in contact with ALA 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195C PHE* 4.9 0.2 - - - -
196C GLY* 3.4 19.1 - - - +
198C ILE* 5.2 4.9 - - + -
288C ILE* 4.7 7.9 - - + -
291C ASP* 5.4 0.4 - - + +
293C VAL* 1.3 78.3 - - - +
295C VAL* 1.3 66.8 + - - +
314C LEU* 4.4 9.4 - - + -
316C ALA 3.0 7.1 + - - +
317C TYR* 3.5 29.0 - - + -
318C VAL* 3.1 27.9 + - - +
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Residues in contact with VAL 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195C PHE* 4.8 0.9 - - + -
196C GLY 2.6 19.7 + - - +
197C VAL* 4.5 11.4 - - + +
198C ILE* 2.9 31.5 + - - +
223C PHE* 5.0 12.3 - - + -
227C LEU* 5.8 5.4 - - + -
266C PHE* 4.5 17.5 - - + -
294C ALA* 1.3 76.7 - - - +
296C VAL* 1.3 65.9 + - - +
297C PHE* 4.1 1.8 - - + +
318C VAL* 3.7 24.9 - - + +
320C VAL* 4.3 17.9 - - + -
365C LEU* 5.5 7.0 - - + -
369C LEU* 4.1 17.0 - - + -
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Residues in contact with VAL 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198C ILE* 3.8 18.8 - - + +
199C TYR 5.1 1.1 - - - -
200C GLN* 3.9 25.8 - - + +
210C LEU* 5.9 1.1 - - + -
295C VAL* 1.3 78.9 - - - +
297C PHE* 1.3 61.8 + - - +
298C GLN* 3.5 1.4 + - + +
304C PHE* 3.7 43.3 - - + -
317C TYR* 4.2 21.8 - - + -
318C VAL 2.9 14.7 + - - +
319C VAL* 3.4 15.5 - - + +
320C VAL 3.3 19.4 + - - -
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Residues in contact with PHE 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197C VAL* 6.2 0.7 - - + -
198C ILE 3.0 18.5 + - - +
199C TYR* 3.3 15.4 - + - -
200C GLN* 3.0 26.5 + - - -
217C SER* 4.0 2.5 - - - -
219C ALA* 3.3 38.4 - - + -
220C PHE* 3.3 35.9 - + + -
223C PHE* 3.6 37.5 - + + -
295C VAL* 4.1 2.5 - - + +
296C VAL* 1.3 70.0 - - - +
298C GLN* 1.3 74.4 + - - +
299C ASP* 3.7 13.2 - - - -
320C VAL* 3.7 25.1 - - + +
322C ALA* 4.1 5.4 - - + -
332C TYR* 4.2 4.5 - + - -
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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
------------------------------------------------------------
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