Contacts of the strand formed by residues 262 - 267 (chain B) in PDB entry 1IAS
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 PHE 262 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B MET* 4.0 11.0 - - + +
198B GLN* 3.9 2.5 - - - -
246B ALA* 4.6 6.5 - - + -
249B TYR* 3.4 51.9 - + + -
250B GLN* 3.8 31.6 - - + -
255B ARG* 2.8 28.3 + - - +
260B LEU 3.3 5.4 + - - -
261B GLY* 1.3 71.0 - - - -
263B ILE* 1.3 65.2 + - - +
264B ALA* 3.2 42.0 - - - -
265B ALA* 3.6 11.7 - - + -
278B LEU* 4.0 22.2 - - + -
279B VAL 4.0 5.4 - - - -
280B SER* 4.4 3.8 - - - -
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Residues in contact with ILE 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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177B LEU* 4.1 21.8 - - + -
181B ILE* 4.4 11.4 - - + -
184B MET* 5.3 5.1 - - - +
193B LEU* 3.6 34.4 + - + +
198B GLN* 3.8 6.1 + - - +
201B ILE* 4.2 15.9 - - + -
229B VAL* 3.5 31.2 - - + -
255B ARG* 5.5 1.6 - - - +
261B GLY 3.9 3.4 - - - +
262B PHE* 1.3 85.3 - - - +
264B ALA* 1.3 63.8 + - + +
279B VAL* 2.7 22.1 + - + +
280B SER* 3.6 14.8 - - - -
281B ASP* 3.8 14.6 - - - +
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Residues in contact with ALA 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B GLN* 3.3 42.6 - - + +
201B ILE* 4.9 4.9 - - + -
202B ALA* 5.3 0.4 - - + -
262B PHE* 3.2 13.7 - - - -
263B ILE* 1.3 89.6 - - + +
265B ALA* 1.3 58.6 + - - +
278B LEU* 3.4 3.0 - - - -
279B VAL* 2.6 44.0 + - + +
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Residues in contact with ALA 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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198B GLN* 2.8 24.4 + - - +
199B ARG 4.6 0.7 + - - -
202B ALA* 5.2 0.7 - - - -
242B TRP* 4.6 7.9 - - + -
246B ALA* 4.2 10.8 - - + -
250B GLN* 4.8 6.1 - - - +
262B PHE* 3.7 10.5 - - + -
264B ALA* 1.3 75.0 - - - +
266B ASP* 1.3 66.5 + - - +
277B TRP 3.5 6.7 - - - -
278B LEU* 3.5 20.4 - - + -
279B VAL* 6.3 0.2 - - - -
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Residues in contact with ASP 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ARG* 2.8 44.4 + - - +
202B ALA* 3.6 24.1 - - + +
203B ARG* 2.9 32.6 + - - +
242B TRP* 3.8 8.3 - - - -
265B ALA* 1.3 78.3 - - - +
267B ASN* 1.3 71.1 + - - +
268B LYS* 4.0 6.1 - - - +
275B GLN 3.9 0.4 - - - +
276B LEU* 3.7 1.4 - - - -
277B TRP* 2.9 38.4 + - + +
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Residues in contact with ASN 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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172A SER* 4.7 5.7 - - - -
173A GLU* 3.2 25.5 - - - +
199B ARG* 3.0 20.4 - - - +
203B ARG* 2.7 31.7 + - - -
242B TRP* 4.4 9.8 - - + -
266B ASP* 1.3 77.2 + - - +
268B LYS* 1.3 58.3 + - - +
274B THR* 4.9 0.4 - - + -
275B GLN 3.2 6.3 - - - -
276B LEU* 3.5 23.6 - - + -
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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