Contacts of the helix formed by residues 446 - 451 (chain A) in PDB entry 2WSK
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 446 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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440A THR* 4.0 0.9 - - - -
444A GLY 3.9 0.2 + - - -
445A PHE* 1.3 79.1 - - - +
447A LEU* 1.3 68.7 + - - +
449A ASP* 3.3 24.3 + - - +
450A CYS* 3.3 15.2 + - - -
513A LEU* 4.4 14.8 - - + -
516A ASP* 3.7 9.0 - - - +
520A HIS* 2.9 41.9 + - + +
522A GLN* 3.6 35.6 + - + +
525A ASN 5.6 0.2 + - - -
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Residues in contact with LEU 447 (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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439A VAL* 3.6 30.5 - - + -
440A THR* 3.7 6.3 - - + +
446A THR* 1.3 71.1 - - - +
448A ARG* 1.3 64.2 + - - +
450A CYS* 3.1 22.8 + - - +
451A VAL* 3.8 6.1 + - - +
496A ILE* 3.8 33.4 - - + +
499A LEU* 3.9 22.7 - - + -
500A LEU* 3.5 36.1 - - + +
516A ASP* 3.0 39.1 + - + +
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Residues in contact with ARG 448 (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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446A THR* 3.3 1.0 + - - -
447A LEU* 1.3 79.7 - - - +
449A ASP* 1.3 60.9 + - - +
451A VAL* 3.0 27.7 + - - +
452A CYS* 3.3 18.8 + - - -
482A LEU* 4.0 30.3 - - - +
483A GLY 4.8 5.3 - - - +
496A ILE* 4.3 21.8 - - + -
516A ASP* 4.6 1.0 + - - +
519A GLY* 2.9 39.7 + - - +
520A HIS 3.7 12.8 + - - +
521A SER* 4.1 13.8 - - - -
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Residues in contact with ASP 449 (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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445A PHE* 3.8 21.1 - - + -
446A THR* 3.3 18.1 + - - +
448A ARG* 1.3 76.6 - - - +
450A CYS* 1.3 57.4 + - - +
451A VAL 3.1 0.2 - - - -
452A CYS* 3.6 0.9 - - - -
453A PHE* 2.9 50.2 + - + +
482A LEU* 3.8 2.9 - - - +
521A SER* 2.7 25.1 + - - -
522A GLN* 2.9 26.3 + - - +
524A GLY* 3.1 20.5 + - - -
525A ASN 4.6 1.7 - - - +
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Residues in contact with CYS 450 (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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401A ARG* 3.6 40.6 - - - -
405A LEU* 4.1 16.8 - - + +
440A THR* 4.2 7.2 - - - -
445A PHE* 3.7 11.4 - - - -
446A THR 3.3 19.2 + - - -
447A LEU* 3.1 18.1 + - + +
448A ARG 3.1 0.8 - - - -
449A ASP* 1.3 77.3 - - - +
451A VAL* 1.3 61.3 + - + +
452A CYS 3.5 0.2 - - - -
472A ASN 5.3 0.7 - - - -
474A SER* 3.2 13.1 - - - -
475A ASN 2.9 27.5 + - - -
499A LEU* 5.3 0.4 - - + -
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Residues in contact with VAL 451 (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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405A LEU* 4.3 9.4 - - + -
447A LEU 4.1 7.6 - - - +
448A ARG* 3.0 18.8 + - + +
450A CYS* 1.3 81.8 - - - +
452A CYS* 1.3 57.7 + - - +
475A ASN 3.1 19.3 - - - +
476A ASN 3.4 0.9 - - - -
477A HIS* 3.2 23.5 - - - +
492A ARG* 3.1 43.6 + - + -
495A SER* 4.2 16.2 - - - -
496A ILE* 3.9 25.1 - - + -
499A LEU* 4.4 9.2 - - + -
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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