Contacts of the helix formed by residues 474 - 482 (chain A) in PDB entry 2W3C
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 LEU 474 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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407A LEU* 4.0 15.0 - - + -
426A CYS* 4.4 5.4 - - - -
429A LEU* 3.6 31.0 - - + -
430A PHE* 3.9 15.5 - - + -
444A LEU* 4.8 4.3 - - + -
458A LEU* 3.8 42.1 + - + +
461A VAL* 3.2 28.3 + - + +
463A LEU* 4.0 18.2 - - + +
472A VAL 3.9 0.4 + - - -
473A SER* 1.3 69.5 - - - +
475A LEU* 1.3 66.6 + - - +
477A GLN* 3.2 2.4 + - - +
478A CYS* 3.0 31.4 + - - -
497A LEU* 6.0 0.4 - - + -
501A TRP* 4.0 8.7 - - + -
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Residues in contact with LEU 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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458A LEU 5.4 0.2 + - - -
459A LEU* 4.3 12.8 - - + +
473A SER* 3.9 7.8 + - - +
474A LEU* 1.3 78.5 - - - +
476A GLN* 1.3 64.8 + - + +
478A CYS* 3.5 4.3 + - - +
479A THR* 3.0 25.8 + - - -
498A LEU* 3.9 17.3 - - + +
501A TRP* 3.5 37.2 - - + -
502A LEU* 3.8 27.1 - - + -
508A ALA 4.3 2.2 - - - +
511A HIS* 3.9 31.0 - - + +
512A PHE* 4.0 23.8 - - + +
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Residues in contact with GLN 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A VAL* 4.0 16.4 - - + -
473A SER* 3.2 20.3 + - - +
475A LEU* 1.3 80.4 - - + +
477A GLN* 1.3 62.5 + - - +
479A THR* 3.3 6.8 + - - +
480A ASN* 2.8 56.6 + - - +
511A HIS 5.2 2.4 - - - +
512A PHE* 5.6 0.9 - - - -
515A ASN* 3.0 37.3 + - - +
517A ALA* 5.2 3.4 - - - +
518A ASN* 3.2 35.2 + - - -
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Residues in contact with GLN 477 (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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430A PHE* 3.4 24.6 - - + -
463A LEU* 3.6 20.0 - - + -
472A VAL* 3.7 18.3 - - + +
473A SER 3.0 18.0 + - - +
474A LEU 3.7 1.8 - - - +
476A GLN* 1.3 78.4 - - - +
478A CYS* 1.3 60.0 + - - +
480A ASN* 3.0 31.2 + - - +
481A ILE* 3.0 40.1 + - - +
484A GLN* 4.7 7.7 - - - +
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Residues in contact with CYS 478 (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* 4.2 19.3 - - - -
430A PHE* 4.5 4.0 - - - -
474A LEU* 3.0 25.8 + - - -
475A LEU 3.6 8.7 - - - +
477A GLN* 1.3 77.2 - - - +
479A THR* 1.3 60.1 + - - +
481A ILE* 3.5 10.3 + - - -
482A LEU* 3.7 7.3 - - - +
494A LEU* 3.5 34.3 - - + +
497A LEU* 4.1 24.2 - - + -
498A LEU* 3.9 20.0 - - + +
501A TRP* 4.7 2.5 - - - -
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Residues in contact with THR 479 (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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475A LEU 3.0 15.0 + - - -
476A GLN* 3.6 12.8 - - - +
477A GLN 3.3 0.2 - - - -
478A CYS* 1.3 75.2 - - - +
480A ASN* 1.3 64.4 + - - +
482A LEU* 3.5 25.1 + - + +
483A SER* 4.1 4.0 + - - -
498A LEU* 3.9 11.1 - - - +
512A PHE* 3.2 37.0 - - + -
518A ASN* 3.4 27.3 + - + +
521A PHE* 4.9 12.6 - - + -
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Residues in contact with ASN 480 (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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472A VAL* 4.1 11.3 - - - +
476A GLN* 2.8 41.2 + - - +
477A GLN* 3.0 35.6 + - - +
479A THR* 1.3 76.8 - - - +
481A ILE* 1.3 63.9 + - - +
482A LEU 3.3 0.5 + - - -
483A SER* 3.3 17.9 + - - -
484A GLN* 3.0 21.0 - - - +
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Residues in contact with ILE 481 (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 5.3 2.5 - - - +
430A PHE* 3.3 37.7 - - + -
477A GLN* 3.0 39.5 + - - +
478A CYS* 3.5 3.1 + - - -
479A THR 3.4 0.6 - - - -
480A ASN* 1.3 75.9 - - - +
482A LEU* 1.3 57.5 + - - +
484A GLN* 3.1 30.4 + - + +
486A SER* 2.6 46.1 + - - +
490A THR* 4.0 7.2 - - - +
491A ARG* 5.7 0.4 - - - -
494A LEU* 3.7 25.1 - - + -
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Residues in contact with LEU 482 (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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478A CYS 3.7 9.4 - - - +
479A THR* 3.5 16.6 - - + +
480A ASN 3.2 0.6 - - - -
481A ILE* 1.3 78.1 - - - +
483A SER* 1.3 57.7 + - - +
484A GLN 3.7 3.3 - - - +
486A SER* 4.4 2.7 - - - -
491A ARG* 3.4 61.3 + - + +
494A LEU* 4.0 13.9 - - + -
495A LEU* 3.8 24.7 - - + -
498A LEU* 3.7 24.0 - - + -
521A PHE* 3.6 34.1 - - + -
522A LEU* 5.2 1.6 - - + -
525A GLN* 4.6 1.2 + - - -
537A VAL* 5.9 0.7 - - + -
541A CYS* 5.5 0.2 - - - -
544A LEU* 5.2 2.2 - - + -
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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