Contacts of the helix formed by residues 461 - 466 (chain A) in PDB entry 2CQE
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 LYS 461 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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458A PHE* 6.1 1.6 - - + -
459A PRO 3.7 2.9 + - - -
460A CYS* 1.3 72.6 - - - +
462A LEU* 1.3 63.4 + - + +
464A HIS* 2.6 29.8 + - - +
465A THR* 2.7 32.6 + - + +
477A PHE* 5.5 1.8 - - - -
490A LEU* 5.0 6.3 - - + -
493A MET* 3.6 33.7 - - + +
494A LEU* 3.6 33.7 - - + +
497A ASP* 5.1 6.9 - - - +
498A ALA 6.1 0.2 - - - +
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Residues in contact with LEU 462 (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 CYS* 4.1 3.9 - - - -
461A LYS* 1.3 82.8 - - + +
463A TYR* 1.3 56.1 + - - +
464A HIS 2.5 14.7 + - - -
465A THR* 2.7 36.3 + - + +
466A THR* 3.3 6.9 + - + +
467A GLY 3.7 1.6 + - - -
468A ASN 4.2 8.7 - - - +
469A CYS* 4.5 11.9 - - - -
470A ILE* 3.8 30.7 - - + +
471A ASN* 5.9 1.3 - - - +
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Residues in contact with TYR 463 (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 CYS* 3.8 24.8 - - + +
461A LYS 3.3 0.2 - - - -
462A LEU* 1.3 76.8 - - - +
464A HIS* 1.3 79.6 + + - +
467A GLY* 2.7 56.5 - - - +
468A ASN* 4.0 6.1 - - - -
469A CYS* 4.0 14.2 - - + +
478A SER 5.7 0.2 - - - -
479A HIS* 3.7 52.4 + + + +
480A ASP 5.0 1.3 - - - -
481A PRO* 6.4 0.4 - - + -
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Residues in contact with HIS 464 (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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459A PRO* 3.9 9.3 - - + +
460A CYS 2.8 23.8 + - - -
461A LYS* 2.6 10.3 + - - +
462A LEU 2.5 7.5 + - - -
463A TYR* 1.3 97.4 + + - +
465A THR* 1.3 68.6 + - - +
466A THR* 2.6 7.5 + - - -
467A GLY* 3.4 5.4 + - - -
480A ASP 4.6 7.6 + - - -
481A PRO* 5.8 0.4 - - + -
482A LEU* 3.3 49.1 - - + +
490A LEU* 4.0 16.6 - - + -
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Residues in contact with THR 465 (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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461A LYS* 2.7 53.9 + - + +
462A LEU* 2.7 37.7 + - + +
464A HIS* 1.3 71.1 - - - +
466A THR* 1.3 73.9 + - - +
494A LEU* 6.1 3.1 - - + -
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Residues in contact with THR 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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462A LEU* 3.3 0.7 + - - +
464A HIS 2.6 6.7 + - - -
465A THR* 1.3 93.8 + - - +
467A GLY* 1.3 60.3 + - - +
468A ASN* 3.5 26.1 + - - +
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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