Contacts of the strand formed by residues 264 - 268 (chain B) in PDB entry 1IR1
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
----------------------------------------------------------
199B PHE* 4.7 7.4 - - + -
237B GLY* 4.3 8.3 - - - -
238B HIS 3.4 33.7 - - - +
239B TYR* 3.6 40.4 - - + -
240B LEU* 3.6 3.7 + - - +
262B VAL* 3.6 8.9 - - - +
263B PRO* 1.3 82.7 - - + +
265B VAL* 1.3 78.0 + - - +
289B LEU* 4.7 1.6 - - - -
290B LEU* 3.4 33.0 - - + +
291B LEU 4.7 0.7 - - - +
292B HIS* 4.0 10.8 - - + +
325B HIS* 3.9 19.3 - - + +
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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
----------------------------------------------------------
218B PHE* 5.7 1.6 - - + -
239B TYR* 4.6 0.4 - - - -
240B LEU* 3.3 20.6 - - + +
242B ALA* 5.0 6.1 - - + -
254B ALA* 5.0 6.7 - - + -
257B ALA* 3.6 30.7 - - + -
264B ILE* 1.3 85.3 - - - +
266B MET* 1.3 61.9 + - - +
280B LEU* 5.1 8.3 - - + -
284B CYS* 3.9 22.2 - - - -
289B LEU* 4.4 16.4 - - + -
290B LEU 3.1 11.2 + - - +
291B LEU* 3.5 7.2 - - + -
292B HIS 2.9 23.0 + - - -
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Residues in contact with MET 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B KCX 3.9 18.2 - - - +
202B ASP 3.5 25.4 - - - +
204B GLU* 4.1 5.2 - - - -
239B TYR* 3.7 29.8 - - + +
240B LEU 2.9 8.4 + - - +
241B ASN* 3.4 39.9 - - - +
242B ALA* 3.0 29.3 + - - +
265B VAL* 1.3 76.7 - - - +
267B HIS* 1.3 63.9 + - - +
268B ASP* 3.8 15.7 - - - +
280B LEU* 4.7 0.3 - - - +
291B LEU* 4.3 2.9 - - - -
292B HIS* 3.1 18.6 - - + +
294B HIS* 4.0 15.5 - - + -
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Residues in contact with HIS 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B THR* 3.6 32.7 - - - +
244B ALA 5.3 1.0 + - - -
250B MET* 3.8 14.2 - - - -
266B MET* 1.3 76.9 - - - +
268B ASP* 1.3 77.8 + - - +
269B TYR* 3.2 8.5 + - - -
272B GLY* 4.2 12.3 - - - -
273B GLY 4.2 4.3 - - - -
276B ALA* 4.3 4.1 - - + +
277B ASN* 3.0 53.0 + - + +
280B LEU* 3.6 24.6 - - + +
291B LEU* 4.2 5.8 - - + -
292B HIS 2.9 6.5 + - - -
293B ILE* 3.5 7.2 - - + +
294B HIS* 3.0 21.9 + - - -
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Residues in contact with ASP 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B GLU* 2.7 35.7 - - - +
207B ASN* 5.2 0.2 - - - +
241B ASN* 4.0 0.2 + - - -
243B THR* 2.9 30.4 + - + +
266B MET* 3.8 10.6 - - - +
267B HIS* 1.3 75.6 + - - +
269B TYR* 1.3 57.3 + - - +
270B LEU 3.4 2.2 - - - -
271B THR* 3.2 19.5 + - - +
272B GLY* 3.0 26.5 + - - -
294B HIS* 3.5 27.0 - - - +
296B ALA* 4.5 10.2 - - + +
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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
------------------------------------------------------------
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