Contacts of the strand formed by residues 237 - 241 (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 GLY 237 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A LEU* 3.9 5.4 - - - +
198A ASP 3.1 6.7 + - - -
199A PHE* 3.2 38.4 - - - -
200A THR* 3.3 5.0 + - - -
225A LEU* 4.7 5.4 - - - -
236A LYS* 1.3 77.7 - - - +
238A HIS* 1.3 60.0 + - - +
263A PRO* 4.1 16.8 - - - -
264A ILE* 4.4 2.0 - - - -
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Residues in contact with HIS 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A ILE* 4.4 0.9 - - + -
185A TYR* 4.1 4.9 - + - -
189A VAL* 3.6 29.2 - - + +
200A THR* 2.7 27.6 + - - +
201A KCX 3.5 26.0 - - - -
202A ASP* 2.8 24.1 + - - -
221A CYS* 3.8 14.9 - - + -
225A LEU* 4.2 20.9 - - + +
237A GLY* 1.3 74.5 - - - +
239A TYR* 1.3 63.3 + - - +
240A LEU* 2.9 42.2 + - + +
262A VAL* 5.8 1.8 - - - +
263A PRO* 5.4 0.6 - - - +
264A ILE* 3.2 13.2 - - - +
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Residues in contact with TYR 239 (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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199A PHE* 3.5 44.5 - + + +
200A THR 3.0 7.2 + - - -
201A KCX 3.3 23.3 - - + -
202A ASP* 3.3 23.4 + - - +
238A HIS* 1.3 70.4 - - - +
240A LEU* 1.3 61.4 + - - +
241A ASN 3.5 2.3 + - - -
264A ILE* 3.7 37.0 - - + -
265A VAL* 4.6 0.9 - - - +
266A MET* 3.7 21.3 - - + +
292A HIS* 3.3 35.9 - + + -
325A HIS* 3.6 12.2 + + - -
399A VAL* 3.8 4.3 - - - +
401A GLN* 3.0 33.2 + - - -
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Residues in contact with LEU 240 (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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202A ASP* 3.6 3.8 - - - +
217A ARG* 5.0 0.7 - - - +
218A PHE* 3.7 65.5 - - + +
221A CYS* 4.2 10.1 - - + -
222A ALA 6.1 0.7 - - - +
225A LEU* 6.0 2.2 - - + -
238A HIS* 2.9 36.1 + - + +
239A TYR* 1.3 71.0 - - - +
241A ASN* 1.3 63.7 + - - +
242A ALA* 3.4 1.6 + - - -
257A ALA* 4.4 3.6 - - + -
260A LEU* 4.8 3.1 - - + -
262A VAL* 4.0 32.5 - - + -
264A ILE 3.6 7.5 + - - +
265A VAL* 3.3 11.6 - - + +
266A MET 2.9 18.1 + - - -
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Residues in contact with ASN 241 (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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202A ASP* 2.8 17.7 + - + +
203A ASP 3.4 10.1 + - - -
204A GLU 3.2 25.7 + - - -
206A VAL 3.3 23.6 + - - +
207A ASN* 3.5 7.1 - - - +
217A ARG* 4.0 4.7 + - - +
218A PHE* 3.6 18.4 - - - -
239A TYR 3.5 1.4 + - - -
240A LEU* 1.3 70.0 - - - +
242A ALA* 1.3 59.7 + - - +
243A THR* 2.7 33.0 + - - +
253A ARG* 4.4 7.1 + - - -
266A MET* 3.5 31.0 - - + +
268A ASP* 4.0 2.1 + - - +
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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