Contacts of the helix formed by residues 676 - 684 (chain B) in PDB entry 2QY0
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 TYR 676 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526B HIS* 3.5 48.2 - + - -
528B ASP* 5.5 0.4 + - - -
538B GLU* 3.7 4.3 + - - -
539B GLY* 3.5 22.6 + - - -
541B ILE* 3.8 26.9 - - + -
619B ASN* 3.3 34.0 + - + +
671B THR* 3.4 30.0 - - + +
672B LYS 3.5 16.4 - - - -
673B VAL 2.9 8.2 + - - +
675B ASN* 1.3 81.4 - - - +
677B VAL* 1.3 60.0 + - - +
678B ASP* 3.3 2.9 - - - -
679B TRP* 3.1 11.9 + - + +
680B ILE* 2.8 29.3 + - + +
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Residues in contact with VAL 677 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561B LEU* 4.2 16.4 - - + -
562B PRO* 3.5 39.7 - - + +
673B VAL* 3.6 18.6 - - + +
674B LEU* 3.4 14.5 + - + +
675B ASN 3.6 0.8 - - - -
676B TYR* 1.3 76.8 - - - +
678B ASP* 1.3 68.6 + - - +
680B ILE* 3.2 6.3 + - - +
681B LYS* 3.0 49.9 + - + +
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Residues in contact with ASP 678 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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675B ASN 5.4 1.5 + - - +
676B TYR 3.3 0.4 - - - -
677B VAL* 1.3 84.0 - - - +
679B TRP* 1.3 61.5 + - - +
681B LYS* 3.4 9.3 + - - +
682B LYS* 3.1 23.2 + - - +
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Residues in contact with TRP 679 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524B SER* 3.5 29.2 - - - -
525B VAL 3.7 8.3 - - - -
526B HIS* 3.5 51.1 - + + +
527B PRO* 3.7 17.0 - - + +
541B ILE* 4.3 20.2 - - + -
542B ALA* 4.4 3.4 - - - -
543B LEU* 4.5 13.0 - - + -
676B TYR* 3.1 19.4 + - + +
678B ASP* 1.3 76.5 - - - +
680B ILE* 1.3 81.9 + - + +
682B LYS* 3.4 10.2 + - + +
683B GLU* 3.1 49.7 + - + +
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Residues in contact with ILE 680 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475B LEU* 3.9 22.4 - - + -
481B LEU* 4.1 23.3 - - + -
541B ILE* 4.3 4.9 - - + -
543B LEU* 4.3 9.6 - - + -
561B LEU* 3.9 34.3 - - + -
673B VAL* 4.1 12.1 - - + -
676B TYR 2.8 25.0 + - - +
677B VAL* 3.2 8.3 + - - +
679B TRP* 1.3 93.5 - - + +
681B LYS* 1.3 58.3 + - - +
683B GLU* 3.2 2.4 + - - +
684B MET* 2.9 43.5 + - + +
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Residues in contact with LYS 681 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561B LEU* 4.7 12.7 - - + +
677B VAL* 3.0 42.1 + - + +
678B ASP* 4.0 9.2 - - - +
680B ILE* 1.3 77.9 - - - +
682B LYS* 1.3 59.7 + - - +
684B MET* 3.3 23.6 + - + +
685B GLU* 3.5 16.8 + - - +
801B GOL 5.4 2.0 - - - +
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Residues in contact with LYS 682 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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678B ASP 3.1 16.8 + - - +
679B TRP* 3.9 11.4 - - + +
681B LYS* 1.3 75.5 - - - +
683B GLU* 1.3 70.8 + - + +
685B GLU* 3.3 17.6 + - + +
686B GLU* 4.1 4.3 + - - -
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Residues in contact with GLU 683 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479B TRP* 3.2 20.6 - - + -
522B ARG* 3.5 22.3 + - - +
524B SER* 2.5 29.9 + - - +
543B LEU* 3.8 16.2 - - + -
679B TRP* 3.1 53.1 + - + +
680B ILE 3.7 3.1 - - - +
682B LYS* 1.3 83.6 - - + +
684B MET* 1.3 56.4 + - - +
685B GLU 3.2 4.0 + - - -
686B GLU 4.1 1.2 + - - -
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Residues in contact with MET 684 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475B LEU* 4.3 11.0 - - + +
476B GLY* 5.5 2.2 - - - +
479B TRP* 3.6 57.2 + - + +
543B LEU* 4.0 10.1 - - + -
680B ILE* 2.9 43.6 + - + +
681B LYS* 3.6 16.6 - - + +
682B LYS 3.2 1.0 - - - -
683B GLU* 1.3 75.1 - - - +
685B GLU* 1.3 57.3 + - - +
686B GLU 3.8 0.9 - - - -
801B GOL 3.7 29.2 - - - +
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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