Contacts of the strand formed by residues 286 - 290 (chain A) in PDB entry 1ISR
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 286 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A VAL* 5.6 0.2 - - + -
224A TRP* 3.5 45.5 - - + +
226A TYR 4.7 4.1 + - - +
227A VAL* 3.5 26.4 - - + +
228A SER* 3.0 25.1 + - - -
285A ARG* 1.3 80.4 + - + +
287A VAL* 1.3 65.7 + - - +
288A VAL* 4.9 1.8 - - + -
313A SER* 3.5 25.8 - - - +
315A ILE* 3.6 25.4 - - + -
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Residues in contact with VAL 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A SER* 3.8 17.7 - - - +
230A VAL* 4.2 21.3 - - + -
277A LEU* 5.0 12.1 - - + -
284A ALA 5.2 0.2 - - - +
285A ARG 3.4 16.8 - - - +
286A VAL* 1.3 75.2 - - - +
288A VAL* 1.3 72.3 + - - +
289A CYS* 3.8 3.3 + - + +
299A LEU* 5.6 2.2 - - + -
312A PHE* 3.6 27.8 - - + -
313A SER 2.9 9.7 + - - +
314A LEU* 3.3 23.8 - - + +
315A ILE* 2.8 26.2 + - - -
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Residues in contact with VAL 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A MET* 3.6 30.7 - - + -
219A VAL* 4.6 11.9 - - + -
227A VAL* 4.6 13.5 - - + -
228A SER 3.1 15.2 + - - +
229A ALA* 3.6 4.0 - - + -
230A VAL 3.0 26.5 + - - +
241A MET* 3.9 5.6 - - + +
244A PHE* 4.2 39.3 - - + -
286A VAL* 4.9 1.3 - - + -
287A VAL* 1.3 74.5 - - - +
289A CYS* 1.3 63.4 + - - +
290A PHE* 4.0 3.4 - - + +
315A ILE* 3.4 14.4 - - + +
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Residues in contact with CYS 289 (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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215A MET* 4.9 0.2 - - - -
230A VAL* 3.1 17.7 - - + -
287A VAL* 3.8 6.6 + - + +
288A VAL* 1.3 74.7 - - - +
290A PHE* 1.3 52.2 - - - +
291A CYS* 2.0 58.3 + - + +
295A THR* 5.1 3.4 - - - -
296A VAL* 4.5 12.8 - - + -
299A LEU* 5.1 13.7 - - - -
314A LEU* 5.6 5.2 - - + -
315A ILE 2.8 14.4 + - - +
316A GLY* 3.2 6.7 - - - -
317A SER 3.0 21.8 + - - -
320A TRP* 5.6 3.4 - - + -
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Residues in contact with PHE 290 (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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208A ASP* 4.0 24.7 - - + -
211A GLN* 4.1 17.5 - - + -
212A ALA* 4.4 10.8 - - - -
215A MET* 3.5 32.3 - - - -
230A VAL 3.2 6.7 + - - -
231A HIS* 3.4 8.5 - - + +
232A THR* 3.4 16.3 + - - -
236A TYR* 3.9 39.0 - + - -
237A GLY* 3.5 17.8 - - - +
240A GLY* 3.5 38.4 - - - -
241A MET* 4.3 12.1 - - + +
244A PHE* 5.6 4.7 - + + -
288A VAL* 4.0 4.5 - - + +
289A CYS* 1.3 67.3 - - - +
291A CYS* 1.3 58.4 + - - +
317A SER* 3.5 11.0 - - - -
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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