Contacts of the strand formed by residues 289 - 294 (chain R) in PDB entry 6QX2
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 289 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277R ILE* 4.5 4.7 - - + -
281R VAL* 3.8 45.8 - - + +
286R ILE* 4.1 18.0 + - + -
287R ASP 3.8 0.6 - - - -
288R GLY* 1.3 76.8 - - - +
290R THR* 1.3 59.2 + - - +
291R ASP 3.5 26.0 - - - +
292R LEU* 5.0 5.2 - - + -
306R ILE* 3.6 26.7 - - + -
307R ASP 3.5 3.4 - - - +
308R VAL* 5.4 0.7 - - + -
317R ILE* 3.8 27.1 - - + -
321R LEU* 4.2 17.7 - - + -
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Residues in contact with THR 290 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252R ARG* 4.0 11.3 + - - +
289R ILE* 1.3 73.5 - - - +
291R ASP* 1.3 64.0 + - - +
307R ASP* 2.9 26.4 + - - +
309R ARG* 3.3 50.7 - - + +
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Residues in contact with ASP 291 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289R ILE* 3.5 14.5 - - - +
290R THR* 1.3 81.8 + - - +
292R LEU* 1.3 75.1 + - - +
293R ARG* 2.7 36.5 + - - +
305R VAL 4.6 0.4 - - - -
306R ILE* 3.5 1.7 - - - -
307R ASP* 3.0 39.0 + - + +
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Residues in contact with LEU 292 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274R ILE* 3.5 38.8 - - + +
277R ILE* 3.7 18.2 - - + -
278R ALA* 3.6 28.5 - - + +
281R VAL* 6.0 1.1 - - + -
289R ILE* 5.0 5.2 - - + -
291R ASP* 1.3 84.8 + - - +
293R ARG* 1.3 63.1 + - - +
304R VAL* 4.3 14.4 - - + -
305R VAL 3.4 5.8 - - - +
306R ILE* 3.7 28.7 - - + -
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Residues in contact with ARG 293 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252R ARG* 6.0 1.4 - - - +
274R ILE* 5.6 1.1 - - - -
291R ASP* 2.7 40.9 + - - +
292R LEU* 1.3 76.6 - - - +
294R ASP* 1.3 58.3 + - - +
295R GLU* 2.8 40.7 + - + +
304R VAL* 3.6 6.2 - - - +
305R VAL* 2.8 59.5 + - + +
307R ASP* 3.0 25.9 + - - -
422U SER* 5.0 16.2 - - - +
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Residues in contact with ASP 294 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114R ASP* 4.1 10.9 - - - +
270R LYS* 3.9 12.1 - - - +
274R ILE* 3.6 31.8 - - + +
293R ARG* 1.3 71.1 - - - +
295R GLU* 1.3 58.5 + - - +
296R THR* 2.5 37.2 + - - +
303R ARG 3.6 4.0 - - - +
304R VAL* 3.9 6.4 - - - +
449U SER* 4.2 10.6 + - - -
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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