Contacts of the strand formed by residues 369 - 374 (chain A) in PDB entry 2Q8J
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 VAL 369 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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345A VAL* 3.2 15.9 - - + +
347A TRP* 4.3 9.0 - - + -
358A CYS* 4.9 3.8 - - - -
361A TRP* 4.0 52.5 - - + -
362A SER* 3.0 30.4 + - - +
365A SER* 3.5 9.5 + - - +
367A GLN* 3.1 2.6 - - - -
368A ASN* 1.3 85.2 - - - +
370A THR* 1.3 72.4 + - - +
610A VAL* 4.2 8.3 - - + -
611A LEU* 5.5 1.1 - - + -
614A GLN* 4.2 17.7 - - + -
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Residues in contact with THR 370 (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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344A ARG* 3.3 41.1 + - - +
345A VAL 3.1 7.8 + - - -
346A VAL* 3.4 17.6 - - + -
347A TRP* 2.7 30.0 + - - +
362A SER* 4.2 4.7 + - - -
367A GLN* 4.2 17.8 + - - +
369A VAL* 1.3 74.1 + - - +
371A CYS* 1.3 72.8 + - - +
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Residues in contact with CYS 371 (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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346A VAL* 4.5 2.3 - - - +
347A TRP 3.6 2.9 - - - -
355A GLN* 5.0 11.9 - - + +
358A CYS* 2.1 65.3 - - + -
359A GLN* 3.7 7.2 - - + +
362A SER* 4.1 10.3 - - - -
369A VAL* 5.2 0.2 - - - -
370A THR* 1.3 87.7 - - - +
372A ALA* 1.3 64.5 + - - +
373A THR* 5.3 0.2 - - - -
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Residues in contact with ALA 372 (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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346A VAL* 4.4 6.5 - - + -
347A TRP 2.8 14.2 + - - +
348A CYS* 4.3 2.7 - - - -
349A ALA* 2.7 32.8 + - - +
371A CYS* 1.3 75.3 - - - +
373A THR* 1.3 61.3 + - - +
383A LEU* 3.9 21.5 - - + -
388A GLU* 4.5 4.9 - - + +
389A ALA* 4.2 13.9 - - + -
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Residues in contact with THR 373 (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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348A CYS* 5.1 0.2 - - - -
349A ALA 3.2 15.7 - - - +
351A GLY* 3.7 28.5 - - - +
352A PRO* 4.7 0.7 - - + -
355A GLN* 3.0 44.6 + - + +
371A CYS 5.3 0.3 - - - -
372A ALA* 1.3 77.1 + - - +
374A ALA* 1.3 64.2 + - - +
383A LEU* 4.1 9.4 - - - +
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Residues in contact with ALA 374 (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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348A CYS* 4.6 1.1 - - - -
349A ALA 3.1 4.4 + - - -
350A VAL* 3.5 4.2 - - - -
351A GLY* 2.8 24.4 + - - -
373A THR* 1.3 76.1 - - - +
375A SER* 1.3 63.1 + - - +
376A THR 3.4 9.2 + - - +
379A ASP* 3.5 29.6 - - + +
380A CYS* 3.8 18.1 - - - +
383A LEU* 4.6 4.5 - - + -
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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