Contacts of the helix formed by residues 291 - 295 (chain A) in PDB entry 1R6W
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 THR 291 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A LEU* 4.5 4.9 - - + -
263A SER* 2.7 37.1 + - - +
265A ILE* 3.5 32.4 - - + +
266A GLU 4.9 0.2 + - - -
271A LEU* 3.8 11.5 - - - +
289A LEU 2.9 4.2 + - - -
290A ASP* 1.3 77.3 - - - +
292A LEU* 1.3 67.3 + - - +
293A ASP 3.2 3.1 - - - +
294A LEU* 3.2 32.7 + - + +
295A MET* 3.8 8.4 - - - +
735A 164 4.2 15.5 - - + -
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Residues in contact with LEU 292 (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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268A SER* 4.1 24.9 - - - +
271A LEU* 3.7 18.1 - - + +
289A LEU 4.2 1.5 + - - +
290A ASP* 3.8 1.2 + - - -
291A THR* 1.3 79.0 + - - +
293A ASP* 1.3 62.5 - - - +
294A LEU 3.1 0.2 - - - -
295A MET* 3.0 45.5 + - - +
297A ALA 4.6 4.9 - - - +
298A GLN* 4.2 8.5 - - + +
303A TRP* 3.6 38.1 - - + -
306A SER* 3.7 21.3 - - - +
308A LEU* 3.6 15.6 - - + +
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Residues in contact with ASP 293 (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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14A ASP* 2.8 24.1 - - - +
290A ASP* 4.3 14.6 + - - +
291A THR* 3.2 1.4 - - - +
292A LEU* 1.3 82.5 - - - +
294A LEU* 1.3 54.0 + - - +
295A MET 3.3 6.1 - - - +
306A SER* 4.9 3.8 + - - -
308A LEU* 4.3 15.7 - - - +
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Residues in contact with LEU 294 (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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13A MET* 3.5 21.2 - - + +
14A ASP* 2.8 30.4 + - + +
17A VAL* 3.8 29.7 - - + +
109A LEU* 5.2 8.7 - - + -
265A ILE* 4.6 9.9 - - + -
290A ASP 5.0 3.4 - - - +
291A THR* 3.4 39.0 - - + +
292A LEU 3.1 0.8 - - - -
293A ASP* 1.3 80.3 - - - +
295A MET* 1.3 57.7 + - - +
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Residues in contact with MET 295 (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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11A ILE* 4.2 15.0 - - + -
12A PRO 3.9 4.5 - - - -
13A MET* 3.9 12.6 - - + -
14A ASP* 3.7 8.7 - - - +
27A ARG* 3.9 25.4 - - + -
265A ILE* 3.7 16.8 - - + +
266A GLU 3.5 29.6 - - - +
267A SER* 4.0 11.2 - - - -
291A THR 3.8 13.7 - - - +
292A LEU* 3.0 24.3 + - + +
293A ASP 4.4 1.9 - - - +
294A LEU* 1.3 82.3 - - - +
296A GLN* 1.3 63.3 + - - +
297A ALA 3.4 13.5 - - - +
308A LEU* 3.4 21.0 - - - +
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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