Contacts of the helix formed by residues 438 - 444 (chain B) in PDB entry 2WSC
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 VAL 438 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1807A BCR 4.6 9.9 - - + -
1812A CLA 3.8 35.9 - - + -
434B LEU* 3.1 37.9 + - + +
435B GLY 3.3 1.8 + - - -
437B TYR* 1.3 73.6 - - - +
439B HIS* 1.3 52.2 + - - +
441B ASP* 2.3 32.3 + - - -
442B VAL* 2.5 18.7 + - + -
1763B CLA 2.7 54.1 - - + -
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Residues in contact with HIS 439 (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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435B GLY 2.9 18.0 + - - +
438B VAL* 1.3 76.9 - - - +
440B ASN* 1.3 54.3 + - - +
442B VAL* 3.6 10.5 - - - -
443B MET* 2.9 54.3 + - + +
451B LYS 3.3 10.9 + - - -
452B GLN* 4.7 0.2 - - - -
453B ILE* 3.3 35.9 - - + +
1763B CLA 2.5 85.5 + + + -
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Residues in contact with ASN 440 (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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436B LEU 5.2 0.4 - - - -
437B TYR* 3.7 19.3 - - - +
439B HIS* 1.3 80.7 - - - +
441B ASP* 1.4 56.4 + - - +
443B MET 4.3 0.2 - - - -
444B LEU* 3.0 16.8 + - - +
452B GLN* 2.5 54.8 + - - +
453B ILE* 2.4 36.2 + - - +
518B LEU* 4.9 4.8 - - - +
614B THR* 2.5 42.2 + - - +
615B TYR* 3.4 6.2 - - + +
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Residues in contact with ASP 441 (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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668A TYR* 2.0 48.8 + - - -
677A LEU* 3.0 20.6 - - + +
680A LEU* 4.0 5.5 - - - +
1812A CLA 4.1 10.2 - - + +
437B TYR 3.4 14.1 + - - +
438B VAL 2.3 22.8 + - - +
440B ASN* 1.4 67.9 - - - +
442B VAL* 1.3 57.5 + - - -
443B MET 3.3 1.3 - - - -
444B LEU 2.8 18.3 - - - +
615B TYR* 3.3 20.7 - - + -
616B LEU* 4.5 1.6 - - + -
617B MET* 3.0 24.0 + - - +
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Residues in contact with VAL 442 (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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677A LEU* 3.8 16.7 - - + +
1765A CLA 3.6 31.2 - - + -
1812A CLA 5.2 2.5 - - + -
438B VAL* 2.5 32.8 + - + +
439B HIS* 3.6 6.7 - - - +
441B ASP* 1.3 68.7 - - - +
443B MET* 1.3 61.0 + - + +
444B LEU 2.9 10.4 - - - +
445B ALA* 4.5 0.5 - - - +
446B PHE* 3.0 34.9 + - + +
1763B CLA 3.1 51.4 - - + -
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Residues in contact with MET 443 (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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439B HIS* 2.9 52.0 + - + +
442B VAL* 1.3 74.6 - - + +
444B LEU* 1.3 63.6 + - - +
446B PHE* 3.4 11.5 - - + +
448B THR* 3.1 38.6 + - + +
451B LYS* 3.5 35.7 - - + +
452B GLN* 4.2 12.6 - - - +
1763B CLA 3.3 66.2 - - + +
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Residues in contact with LEU 444 (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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668A TYR* 3.5 17.7 - - + -
440B ASN 3.0 28.0 + - - +
441B ASP 2.8 13.2 - - - +
442B VAL 2.9 4.5 - - - +
443B MET* 1.3 72.4 - - - +
445B ALA* 1.3 70.7 + - - +
446B PHE 2.9 9.3 + - - -
447B GLY 4.6 1.6 - - - +
448B THR 4.8 0.7 - - - +
449B PRO* 3.4 43.3 - - + -
452B GLN* 3.2 24.7 - - - +
611B GLU 5.8 0.7 - - - +
615B TYR* 3.5 26.9 - - + -
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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