Contacts of the helix formed by residues 465 - 476 (chain A) in PDB entry 3QRK
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 PRO 465 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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337A ALA* 6.2 4.9 - - + -
341A LEU* 5.5 10.3 - - + -
433A ALA* 6.2 0.2 - - + -
463A GLY 3.5 7.6 - - - +
464A CYS* 1.3 89.7 - - - +
466A GLU* 1.3 56.2 + - - +
467A LYS* 3.2 3.8 - - + +
468A VAL* 2.7 51.3 + - + +
469A TYR* 3.1 10.1 + - - +
496A MET* 5.6 2.9 - - + -
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Residues in contact with GLU 466 (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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460A ARG* 4.8 13.7 - - - +
464A CYS 3.3 4.9 + - - -
465A PRO* 1.3 70.0 - - - +
467A LYS* 1.3 59.2 + - + +
469A TYR* 3.4 8.3 + - - +
470A GLU* 2.9 30.9 + - - +
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Residues in contact with LYS 467 (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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465A PRO* 3.2 3.6 - - + +
466A GLU* 1.3 77.3 - - + +
468A VAL* 1.3 59.4 + - - +
470A GLU* 3.3 27.3 - - - +
471A LEU* 3.2 25.6 + - - +
496A MET* 3.4 53.5 + - + +
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Residues in contact with VAL 468 (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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341A LEU* 4.0 13.9 - - + -
429A LEU* 4.3 18.9 - - + +
433A ALA* 5.5 2.0 - - + -
464A CYS* 3.6 17.9 - - - -
465A PRO* 2.7 39.6 + - + +
467A LYS* 1.3 70.3 - - - +
469A TYR* 1.3 64.6 + - - +
471A LEU* 3.1 10.9 + - - +
472A MET* 3.0 30.2 + - + +
493A PHE* 4.6 5.8 - - + -
496A MET* 3.9 21.3 - - + -
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Residues in contact with TYR 469 (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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458A MET 2.7 25.8 + - - -
459A GLU* 3.5 5.3 - - - -
460A ARG* 3.2 64.0 + - + -
461A PRO* 4.4 0.7 - - + -
464A CYS* 3.8 4.6 - - - -
465A PRO 3.1 6.9 + - - +
466A GLU 3.7 7.6 - - - +
468A VAL* 1.3 75.1 - - - +
470A GLU* 1.3 65.9 + - - +
472A MET* 3.2 25.3 + - - +
473A ARG* 3.0 64.3 + - + +
476A TRP* 4.5 2.9 - + - -
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Residues in contact with GLU 470 (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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466A GLU* 2.9 13.3 + - - +
467A LYS* 3.3 36.7 + - - +
468A VAL 3.2 0.2 - - - -
469A TYR* 1.3 77.9 - - - +
471A LEU* 1.3 62.3 + - + +
473A ARG* 3.5 7.9 + - - +
474A ALA* 3.0 28.6 + - - +
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Residues in contact with LEU 471 (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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429A LEU* 4.0 13.2 - - + -
467A LYS 3.2 15.1 + - - +
468A VAL* 3.1 13.4 + - + +
470A GLU* 1.3 79.8 - - + +
472A MET* 1.3 55.0 + - - +
474A ALA* 3.3 7.1 + - + +
475A CYS* 3.0 36.9 + - - -
484A PRO* 5.0 7.6 - - + -
489A ILE* 4.2 24.0 - - + +
492A ALA* 3.8 26.5 - - + -
493A PHE* 3.5 43.1 - - + -
496A MET* 6.1 1.3 - - + -
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Residues in contact with MET 472 (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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426A GLY* 3.7 16.4 - - - +
429A LEU* 3.8 17.7 - - + +
430A TRP* 3.7 46.9 - - - +
433A ALA* 4.1 3.8 - - + -
461A PRO* 4.4 2.9 - - + -
464A CYS* 3.8 28.7 - - - -
468A VAL* 3.0 20.3 + - + +
469A TYR* 3.3 22.4 - - + +
471A LEU* 1.3 75.4 - - - +
473A ARG* 1.3 57.2 + - - +
475A CYS* 3.0 22.6 + - - +
476A TRP* 3.0 41.8 + - + -
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Residues in contact with ARG 473 (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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455A ASP 5.1 5.1 + - - -
457A ARG* 3.9 27.7 + - - +
458A MET 4.6 0.2 + - - -
469A TYR* 3.0 61.6 + - + +
470A GLU* 3.7 7.0 - - - +
472A MET* 1.3 78.4 - - - +
474A ALA* 1.3 60.9 + - - +
476A TRP* 3.5 27.9 + - - +
477A GLN* 3.6 20.6 + - - +
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Residues in contact with ALA 474 (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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470A GLU 3.0 17.1 + - - +
471A LEU* 3.5 10.3 - - + +
472A MET 3.2 0.2 - - - -
473A ARG* 1.3 72.2 - - - +
475A CYS* 1.3 60.2 + - - +
476A TRP 3.0 6.1 + - - -
477A GLN* 3.2 29.3 + - + +
482A ASP 5.4 1.1 - - - +
483A ARG* 3.7 2.4 - - - -
484A PRO* 3.7 29.3 - - + +
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Residues in contact with CYS 475 (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 VAL* 3.3 42.4 - - - +
423A TRP* 3.3 14.2 - - - -
425A PHE* 4.3 6.3 - - - -
426A GLY* 3.8 21.1 - - - -
429A LEU* 5.0 0.7 - - - -
471A LEU* 3.0 29.1 + - - -
472A MET* 3.0 8.0 + - - +
474A ALA* 1.3 74.3 - - - +
476A TRP* 1.3 59.9 + - + +
477A GLN 3.4 0.4 - - - -
483A ARG* 3.1 20.6 - - - +
484A PRO* 4.7 3.4 - - - -
489A ILE* 4.1 16.6 - - - -
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Residues in contact with TRP 476 (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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423A TRP* 3.2 35.7 - + + -
426A GLY* 3.3 38.6 - - - -
427A VAL* 3.4 12.4 - - + +
430A TRP* 4.2 3.6 - + + -
440A TYR* 5.2 3.6 - - - -
457A ARG* 2.8 57.1 + - + +
458A MET* 3.8 61.0 - - + -
469A TYR* 4.5 1.6 - + - -
472A MET* 3.0 42.1 + - + +
473A ARG* 3.5 19.5 + - - +
474A ALA 3.0 1.2 - - - -
475A CYS* 1.3 86.9 - - + +
477A GLN* 1.3 59.3 + - - +
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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