Contacts of the strand formed by residues 264 - 268 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A PHE* 4.6 8.1 - - + -
237A GLY* 4.4 8.3 - - - -
238A HIS 3.2 33.6 + - - +
239A TYR* 3.7 40.8 - - + -
240A LEU* 3.6 4.6 + - - +
262A VAL* 3.7 7.3 + - - +
263A PRO* 1.3 83.2 - - + +
265A VAL* 1.3 78.4 + - - +
289A LEU* 4.8 0.9 - - - -
290A LEU* 3.3 33.2 - - + +
291A LEU 4.7 0.2 - - - +
292A HIS* 4.0 10.5 - - + +
325A HIS* 3.8 20.4 - - + +
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Residues in contact with VAL 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A PHE* 5.7 0.9 - - + -
239A TYR* 4.6 0.9 - - - -
240A LEU* 3.3 19.3 - - + +
242A ALA* 5.0 6.3 - - + -
253A ARG 5.7 0.2 - - - +
254A ALA* 5.1 6.3 - - + -
257A ALA* 3.6 31.4 - - + -
264A ILE* 1.3 83.8 - - - +
266A MET* 1.3 63.2 + - - +
280A LEU* 5.1 8.1 - - + -
284A CYS* 3.9 23.1 - - - -
289A LEU* 4.4 15.7 - - + -
290A LEU 3.0 12.8 + - - +
291A LEU* 3.5 7.5 - - + -
292A HIS 2.9 22.0 + - - -
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Residues in contact with MET 266 (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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201A KCX 3.8 19.1 - - - +
202A ASP 3.4 24.2 - - - +
204A GLU* 4.1 4.9 - - - -
239A TYR* 3.7 28.7 - - + +
240A LEU 2.9 8.3 + - - +
241A ASN* 3.5 41.5 - - - +
242A ALA* 3.0 29.3 + - - +
265A VAL* 1.3 74.6 - - - +
267A HIS* 1.3 63.9 + - - +
268A ASP* 3.7 15.9 - - - +
280A LEU* 4.6 0.5 - - - +
291A LEU* 4.2 2.7 - - - -
292A HIS* 3.1 19.3 - - + +
294A HIS* 4.0 14.6 - - + -
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Residues in contact with HIS 267 (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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241A ASN* 4.2 0.2 - - - -
243A THR* 3.5 32.9 - - - +
244A ALA 5.3 0.8 + - - -
250A MET* 3.9 15.0 - - - -
266A MET* 1.3 77.5 - - - +
268A ASP* 1.3 77.1 + - - +
269A TYR* 3.3 7.8 + - - -
272A GLY* 4.1 13.1 - - - -
273A GLY 4.2 3.8 - - - -
276A ALA* 4.3 4.6 - - + +
277A ASN* 2.9 48.7 + - + -
280A LEU* 3.6 25.1 - - + +
291A LEU* 4.1 7.2 - - + -
292A HIS 3.0 6.1 + - - -
293A ILE* 3.5 9.6 - - + +
294A HIS 3.0 21.7 + - - -
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Residues in contact with ASP 268 (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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204A GLU* 2.8 32.4 - - - +
207A ASN* 4.6 0.2 + - - -
243A THR* 2.9 27.6 + - + +
266A MET* 3.7 12.6 - - - +
267A HIS* 1.3 74.5 + - - +
269A TYR* 1.3 57.9 + - - +
270A LEU 3.3 2.6 + - - +
271A THR* 3.2 19.9 + - - +
272A GLY* 2.9 26.7 + - - -
294A HIS* 3.4 28.9 - - - +
296A ALA* 4.5 9.4 - - + +
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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