Contacts of the strand formed by residues 262 - 267 (chain B) in PDB entry 4AY1
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 262 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B ILE* 4.0 10.3 - - + -
209B LEU* 4.2 29.4 - - + -
249B VAL* 4.6 6.3 - - + +
252B TRP* 4.6 6.3 - - + -
253B ILE* 4.3 13.7 - - + -
257B MET* 3.7 17.9 - - + -
258B PRO 3.7 13.9 - - - +
259B SER* 3.0 15.1 + - - +
261B LYS* 1.3 77.6 - - - +
263B VAL* 1.3 63.7 + - - +
264B MET 4.5 0.4 - - - +
354B LEU* 3.4 28.4 - - + +
355B GLY 2.8 25.0 + - - -
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Residues in contact with VAL 263 (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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28B LYS* 4.2 16.4 - - + +
30B VAL* 3.9 13.7 - - + -
206B PHE* 3.4 35.0 - - + -
207B ILE 3.0 12.4 + - - +
208B ASN* 3.8 5.7 - - - +
209B LEU* 3.0 25.8 + - - +
261B LYS 4.4 0.7 - - - +
262B VAL* 1.3 77.6 - - - +
264B MET* 1.3 58.9 + - - +
265B GLY 3.5 0.3 + - - -
355B GLY* 4.5 8.1 - - - -
356B GLY* 3.7 3.8 - - - -
357B ALA 3.4 35.9 - - - +
358B MET* 3.6 10.9 - - + +
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Residues in contact with MET 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B LEU* 4.4 6.7 - - + -
211B SER* 3.8 10.5 - - - +
245B VAL* 3.4 28.9 - - + -
249B VAL* 4.2 7.6 - - + -
262B VAL* 3.8 2.5 + - + -
263B VAL* 1.3 70.0 - - - +
265B GLY* 1.3 66.4 + - - +
266B ILE* 3.6 18.9 + - + +
345B LYS* 3.5 42.8 - - + +
348B PHE* 3.7 22.0 - - + -
349B LEU* 4.1 15.9 - - + -
354B LEU* 3.9 17.3 - - + -
356B GLY 3.0 12.7 + - - +
357B ALA* 3.3 5.5 - - - +
358B MET 2.8 20.0 + - - +
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Residues in contact with GLY 265 (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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209B LEU 2.9 26.2 + - - -
211B SER* 2.8 26.7 + - - +
212B PHE* 4.0 6.5 - - - -
228B SER* 4.9 0.9 + - - -
245B VAL* 5.2 1.7 - - - +
263B VAL 3.5 1.4 + - - -
264B MET* 1.3 76.5 - - - +
266B ILE* 1.3 64.1 + - - +
267B PRO* 4.5 0.2 - - - +
345B LYS* 5.6 0.9 + - - +
358B MET* 3.3 21.8 - - - -
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Residues in contact with ILE 266 (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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212B PHE* 4.0 4.2 - - - -
264B MET* 3.9 24.5 - - + +
265B GLY* 1.3 80.6 - - - +
267B PRO* 1.3 71.7 - - + +
268B THR 4.0 0.2 + - - -
337B ASP* 4.8 0.4 - - - +
342B MET* 3.5 39.7 - - + +
345B LYS* 4.4 21.8 - - + +
346B VAL* 4.8 5.8 - - + -
357B ALA* 3.9 24.0 - - + -
358B MET 2.6 11.4 + - - +
359B ILE* 3.4 13.3 - - + +
360B TRP 3.1 20.6 + - - -
383B VAL* 4.3 17.5 - - + -
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Residues in contact with PRO 267 (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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212B PHE* 3.9 12.1 - - + -
227B ASN* 3.4 21.5 - - - +
228B SER* 3.7 20.4 - - - +
266B ILE* 1.3 90.8 - - + +
268B THR* 1.3 63.0 + - - +
269B TYR* 3.5 29.3 - - + +
337B ASP* 3.4 25.3 - - - +
342B MET* 3.3 18.3 - - - +
345B LYS* 4.1 1.8 - - - +
360B TRP 3.3 7.0 - - - +
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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