Contacts of the strand formed by residues 264 - 269 (chain B) in PDB entry 4R95
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 ILE 264 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B VAL* 5.0 1.3 - - + -
263B ILE* 1.4 71.7 - - - +
265B VAL* 1.3 61.5 + - - +
266B ARG 3.7 16.8 - - - +
267B VAL* 3.8 17.9 - - + -
278B CYS 4.0 4.9 - - - +
281B TYR* 4.0 13.2 - - + +
282B ASN* 2.8 33.1 + - - +
286B SER* 3.8 14.4 - - - +
297B LEU* 6.1 0.7 - - + -
346B LEU* 4.5 21.5 - - + -
347B TYR 3.3 15.0 - - - +
348B LEU* 3.7 18.8 - - + -
392B THR* 3.7 31.2 - - + +
394B MET* 4.7 5.4 - - - -
443B CYS* 3.8 4.9 - - - +
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Residues in contact with VAL 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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263B ILE* 4.0 9.2 - - + -
264B ILE* 1.3 76.6 - - - +
266B ARG* 1.3 64.1 + - + +
278B CYS* 3.6 17.8 - - - +
281B TYR* 4.4 1.6 - - - -
347B TYR* 2.9 28.1 + - + +
348B LEU 4.4 0.2 - - - -
349B MET* 3.9 17.0 - - + +
356B SER* 3.8 14.6 - - - +
437B THR* 3.8 28.6 - - + +
440B MET* 3.7 31.2 - - + -
443B CYS* 4.0 12.9 - - - -
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Residues in contact with ARG 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B ILE* 3.7 2.6 - - - +
265B VAL* 1.3 82.9 - - + +
267B VAL* 1.3 73.6 + - - +
268B GLU* 2.8 34.9 + - - +
271B GLY 4.2 5.7 + - - -
273B ASP* 3.3 47.5 + - - +
281B TYR* 4.0 7.2 - - - -
347B TYR* 2.9 58.7 + - + -
437B THR* 5.9 2.2 - - + -
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Residues in contact with VAL 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B ILE* 3.8 19.3 - - + -
266B ARG* 1.3 80.9 - - - +
268B GLU* 1.4 72.7 + - - +
269B ILE* 4.5 9.2 - - + -
273B ASP* 3.6 7.5 + - - +
274B LEU* 2.9 44.1 + - + +
281B TYR* 3.8 35.1 + - + +
297B LEU* 6.4 1.6 - - + -
301B VAL* 5.4 3.8 - - + -
305B ALA* 6.0 0.7 - - + -
344B ILE* 4.7 2.9 - - + -
345B SER 3.4 7.6 - - - +
346B LEU* 3.8 19.1 - - + -
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Residues in contact with GLU 268 (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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266B ARG* 2.8 41.0 + - - +
267B VAL* 1.4 75.3 - - - +
269B ILE* 1.4 66.3 + - - +
270B ASN 4.0 0.4 - - - -
271B GLY* 3.4 31.3 + - - +
272B GLN 3.2 8.7 - - - +
273B ASP* 4.2 0.7 - - - -
343B VAL 4.0 0.2 - - - +
344B ILE* 3.4 5.4 - - - +
345B SER* 2.9 46.8 + - - +
347B TYR* 2.6 34.3 + - + -
358B ARG* 4.4 6.5 + - - -
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Residues in contact with ILE 269 (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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267B VAL* 4.5 8.1 - - + -
268B GLU* 1.4 77.8 - - - +
270B ASN* 1.4 68.5 + - - +
272B GLN* 2.9 25.9 + - - +
274B LEU* 3.9 13.5 - - + -
305B ALA* 4.6 10.8 - - + -
308B SER* 3.2 39.4 + - - +
309B ILE* 4.1 18.6 - - + -
312B ALA* 4.8 2.2 - - + -
342B PRO* 3.5 31.9 - - + -
343B VAL 3.5 2.2 - - - +
344B ILE* 3.8 26.5 - - + -
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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
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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