Contacts of the helix formed by residues 485 - 496 (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 SER 485 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355A GLU* 3.5 20.9 - - - -
419A LYS* 4.1 11.7 - - - +
422A VAL* 4.8 0.7 - - - -
483A ARG 3.9 0.8 + - - -
484A PRO* 1.3 77.5 - - - +
486A PHE* 1.3 60.1 + - - +
487A ALA* 3.7 5.1 + - - +
488A GLU* 3.0 37.3 + - - +
489A ILE* 3.0 27.0 + - - +
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Residues in contact with PHE 486 (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 SER* 4.4 5.8 - - - +
351A MET* 3.2 48.9 - - + +
352A GLU* 3.7 22.1 - - - +
355A GLU* 2.9 12.4 + - + +
364A LEU* 4.6 0.2 - - + -
418A ILE* 3.8 15.9 - - + -
421A ASP* 3.5 42.6 - - + -
422A VAL* 3.5 20.2 - - + +
425A PHE* 3.5 30.1 - + + -
485A SER* 1.3 69.5 - - - +
487A ALA* 1.3 61.5 + - - +
489A ILE* 3.5 19.8 - - + +
490A HIS* 2.8 30.8 + - - +
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Residues in contact with ALA 487 (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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352A GLU* 3.5 28.3 - - + +
355A GLU* 2.9 17.5 + - - +
485A SER* 3.3 6.0 - - - +
486A PHE* 1.3 75.2 - - - +
488A GLU* 1.3 63.7 + - + +
490A HIS* 3.4 3.1 + - - +
491A GLN* 3.0 25.5 + - - +
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Residues in contact with GLU 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A ARG 4.8 0.3 - - - +
484A PRO* 3.3 16.7 - - + +
485A SER* 3.0 40.0 + - - +
487A ALA* 1.3 75.6 - - + +
489A ILE* 1.3 59.1 + - - +
491A GLN* 3.2 8.6 + - + +
492A ALA* 3.0 26.9 + - - +
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Residues in contact with ILE 489 (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 SER* 3.8 7.9 - - - -
422A VAL* 3.9 25.4 - - + -
425A PHE* 3.7 25.8 - - + -
471A LEU* 4.2 13.2 - - + -
475A CYS* 4.1 12.8 - - - -
484A PRO* 3.9 15.5 - - + -
485A SER 3.0 20.5 + - - +
486A PHE* 3.1 31.6 + - + +
488A GLU* 1.3 71.8 - - - +
490A HIS* 1.3 67.8 + - - +
492A ALA* 3.2 10.2 + - - +
493A PHE* 3.1 33.2 + - + -
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Residues in contact with HIS 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A THR* 3.9 22.4 - - + +
348A SER* 3.1 26.2 + - - +
349A SER* 3.5 28.1 - - - -
352A GLU* 3.3 27.4 - - + +
486A PHE 2.8 14.0 + - - +
487A ALA 3.7 3.4 - - - +
489A ILE* 1.3 77.5 - - - +
491A GLN* 1.3 61.8 + - - +
493A PHE* 3.1 13.3 + - - +
494A GLU* 2.9 44.9 + - + +
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Residues in contact with GLN 491 (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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352A GLU* 5.9 0.8 + - - -
487A ALA 3.0 14.9 + - - +
488A GLU* 3.2 13.4 + - + +
490A HIS* 1.3 75.4 - - - +
492A ALA* 1.3 62.1 + - - +
494A GLU* 3.0 38.4 + - - +
495A THR* 3.0 36.8 + - - +
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Residues in contact with ALA 492 (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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471A LEU* 3.8 26.5 - - + -
488A GLU 3.0 13.3 + - - +
489A ILE 3.2 9.6 + - - +
491A GLN* 1.3 75.7 - - - +
493A PHE* 1.3 62.4 + - - +
495A THR* 3.8 8.5 - - - +
496A MET* 3.1 29.8 + - - +
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Residues in contact with PHE 493 (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* 3.5 29.4 - - + -
344A ALA* 3.9 25.4 - - + -
345A THR* 3.6 32.8 - - + +
348A SER* 3.5 22.7 - - - -
425A PHE* 4.1 4.3 - + - -
429A LEU* 4.0 9.9 - - + -
468A VAL* 4.6 6.1 - - + -
471A LEU* 3.5 30.3 - - + -
489A ILE* 3.1 33.0 + - + -
490A HIS 3.1 9.1 + - - +
492A ALA* 1.3 76.2 - - - +
494A GLU* 1.3 61.2 + - - +
496A MET* 3.1 30.6 - - + +
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Residues in contact with GLU 494 (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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345A THR* 6.5 0.4 - - + -
490A HIS* 2.9 44.2 + - + +
491A GLN* 3.0 45.2 + - - +
493A PHE* 1.3 75.7 - - - +
495A THR* 1.3 60.6 + - - +
496A MET 3.5 0.2 - - - -
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Residues in contact with THR 495 (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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491A GLN* 3.0 27.2 + - - +
492A ALA* 4.1 9.0 - - - +
494A GLU* 1.3 80.1 - - - +
496A MET* 1.3 63.8 + - - +
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Residues in contact with MET 496 (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* 3.8 43.7 - - + -
465A PRO* 5.6 2.9 - - + -
467A LYS* 3.4 54.2 + - + +
468A VAL* 3.9 18.8 - - + +
471A LEU* 6.1 1.6 - - + -
492A ALA 3.1 12.9 + - - +
493A PHE* 3.1 32.1 - - + +
494A GLU 3.5 1.2 - - - -
495A THR* 1.3 84.7 - - - +
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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