Contacts of the strand formed by residues 434 - 441 (chain A) in PDB entry 2QR8
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 SER 434 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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430A VAL 4.1 1.0 - - - -
431A GLY* 3.3 24.4 + - - +
432A SER 4.0 0.2 - - - -
433A TYR* 1.3 80.3 - - - +
435A VAL* 1.3 65.9 + - - +
451A LYS* 3.7 23.0 - - - +
452A ILE 3.3 13.0 - - - -
453A ILE* 3.9 19.3 - - - -
454A ASP 4.9 0.4 - - - +
458A ARG* 5.7 2.0 - - - -
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Residues in contact with VAL 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A ASP* 4.0 21.1 - - - +
429A GLY 3.8 9.2 - - - +
430A VAL* 4.0 24.2 - - + +
431A GLY 4.9 2.9 - - - +
434A SER* 1.3 81.3 - - - +
436A CYS* 1.3 61.3 + - - +
437A LYS* 4.0 18.2 - - + -
450A VAL 3.7 0.9 - - - +
451A LYS* 3.5 2.0 - - - -
452A ILE* 2.7 48.2 + - + +
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Residues in contact with CYS 436 (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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427A ASP* 3.5 5.2 - - - +
428A ILE* 2.7 54.8 + - + -
429A GLY* 2.7 24.7 + - - +
435A VAL* 1.3 72.5 - - - +
437A LYS* 1.3 58.6 + - - +
449A ALA* 4.2 10.5 - - - -
450A VAL 3.3 15.9 - - - -
451A LYS* 4.2 12.1 - - + +
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Residues in contact with LYS 437 (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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424A VAL* 3.5 26.9 - - + +
425A LYS 4.3 3.1 + - - +
426A GLU 3.3 10.5 - - - +
427A ASP* 3.4 27.9 + - - +
428A ILE* 3.8 7.1 - - - +
435A VAL* 4.0 15.9 - - + -
436A CYS* 1.3 76.4 - - - +
438A ARG* 1.3 65.6 + - - +
449A ALA* 3.4 3.6 - - - -
450A VAL* 2.7 41.8 + - + +
452A ILE* 4.1 22.0 - - + +
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Residues in contact with ARG 438 (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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424A VAL* 3.9 0.5 - - - -
425A LYS* 2.9 53.1 + - + +
426A GLU* 2.9 48.8 + - - +
428A ILE* 3.8 13.0 - - + +
437A LYS* 1.3 77.8 - - - +
439A CYS* 1.3 66.4 + - - +
440A ILE* 4.2 17.2 - - - +
447A GLU* 3.7 30.1 + - + +
448A PHE 3.5 11.9 - - - +
495A LEU* 3.8 27.4 - - + -
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Residues in contact with CYS 439 (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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418A PHE* 4.2 17.0 - - + -
422A TYR* 3.8 24.0 - - + -
423A GLU 3.2 15.3 - - - +
424A VAL* 4.4 1.8 - - - -
425A LYS* 4.3 1.6 - - - +
438A ARG* 1.3 78.6 - - - +
440A ILE* 1.3 65.5 + - - +
447A GLU* 3.5 4.5 - - - -
448A PHE* 2.9 50.4 + - - +
449A ALA 4.2 0.9 - - - -
450A VAL* 4.1 24.7 - - + -
492A VAL* 4.4 2.7 - - - -
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Residues in contact with ILE 440 (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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422A TYR* 3.2 7.3 - - - -
423A GLU* 2.9 45.0 + - + +
425A LYS* 3.3 31.2 - - - +
438A ARG* 4.2 18.6 - - - +
439A CYS* 1.3 78.8 - - - +
441A HIS* 1.3 75.5 + - - +
442A LYS* 3.1 4.0 + - - +
445A ASN* 4.0 27.8 - - - +
446A MET 3.5 5.4 - - - +
447A GLU* 4.9 6.5 - - + -
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Residues in contact with HIS 441 (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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421A GLY* 3.5 19.2 + - - -
422A TYR* 3.7 31.6 + + + -
440A ILE* 1.3 69.9 - - - +
442A LYS* 1.3 58.9 + - - +
443A ALA* 3.5 23.5 - - + +
444A THR* 2.7 35.4 + - + +
445A ASN* 2.8 32.6 + - - -
446A MET 2.8 16.8 + - - +
448A PHE* 3.8 17.5 - + + -
481A ASP* 5.6 1.0 + - - -
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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