Contacts of the helix formed by residues 478 - 482 (chain A) in PDB entry 6WLY
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 THR 478 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440A ASP* 2.7 25.6 + - - -
442A LYS* 2.8 16.0 + - - +
477A GLY* 1.3 73.4 - - - -
479A PRO* 1.3 73.3 - - + +
480A TYR 4.8 0.2 - - - +
481A TRP* 2.8 53.9 + - + +
482A MET* 3.3 9.3 + - - +
505B LYS 4.2 3.8 - - - +
506B ARG 3.6 16.4 - - - +
507B TYR 3.5 17.3 - - - +
508B THR* 3.5 5.2 - - - -
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Residues in contact with PRO 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A GLY 4.0 1.6 - - - +
478A THR* 1.3 89.1 - - + -
480A TYR* 1.3 65.9 + - + +
481A TRP 3.1 1.2 + - - -
482A MET* 3.2 27.7 + - + +
520A PRO* 3.7 35.2 - - + +
523A ALA* 5.6 0.2 - - - -
524A MET* 3.8 27.3 - - + +
527A ILE* 3.5 13.4 - - - +
505B LYS 5.2 3.1 - - - +
507B TYR 4.0 1.6 - - - +
509B VAL* 3.9 27.8 - - + -
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Residues in contact with TYR 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A THR* 3.0 2.4 + - + -
479A PRO* 1.3 75.1 - - + +
481A TRP* 1.3 70.0 + + + +
482A MET 3.5 0.2 - - - -
499A TRP* 5.4 0.2 + - - -
503A ILE* 3.6 18.4 - - - +
513A PRO* 3.7 21.4 - - + +
514A PRO* 3.6 18.5 - - - +
515A TYR 3.2 20.6 - - - -
516A PHE* 3.7 20.0 - + - -
518A GLU 2.7 19.7 + - - -
520A PRO* 3.3 22.7 - - + -
523A ALA* 3.5 24.0 - - + -
527A ILE* 3.8 16.4 - - - +
505B LYS* 3.1 52.8 - - + +
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Residues in contact with TRP 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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440A ASP* 6.0 0.7 - - - +
441A ILE 3.6 25.8 - - - +
442A LYS* 3.4 16.2 - - + +
444A ASP* 4.6 2.2 - - - -
478A THR* 2.8 48.8 + - + +
480A TYR* 1.3 92.1 - + + +
482A MET* 1.3 57.9 + - - -
499A TRP* 3.8 4.3 - - - -
500A SER* 2.7 40.3 + - - +
503A ILE* 3.4 30.0 - - + +
504A MET 4.1 1.5 - - - +
507A GLU* 2.8 39.9 + - - +
513A PRO* 3.7 22.4 - - + -
516A PHE* 4.5 4.5 - + - -
506B ARG* 3.6 33.2 - - + -
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Residues in contact with MET 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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475A LEU* 4.3 9.4 - - + -
476A VAL 4.2 3.4 - - - +
477A GLY* 3.4 36.6 - - - +
478A THR 3.4 15.9 - - - +
479A PRO* 3.2 23.5 + - + +
480A TYR 3.5 0.4 - - - -
481A TRP* 1.3 78.3 - - - +
483A ALA* 1.3 66.2 + - - +
486A LEU* 4.0 19.1 - - + -
487A ILE* 3.6 27.8 - - + +
499A TRP* 3.3 12.9 + - - -
500A SER* 4.6 1.3 - - - -
524A MET* 4.0 13.0 - - - -
527A ILE* 3.5 14.7 - - - +
509B VAL* 3.5 21.5 - - + -
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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