Contacts of the strand formed by residues 479 - 483 (chain D) in PDB entry 2W3S
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 479 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215B HIS* 3.1 9.5 + - - -
471D VAL* 3.8 22.2 - - + -
472D GLN 3.1 8.5 - - - +
473D ILE* 3.8 22.0 - - + -
477D GLY 4.0 8.3 - - - +
478D SER* 1.3 81.3 - - - +
480D ALA* 1.3 60.9 + - - +
481D LEU* 4.4 0.9 - - + +
500D ALA* 5.6 2.0 - - + -
504D LEU* 4.1 18.2 - - + -
506D ILE* 4.1 11.2 - - + -
510D GLN 2.9 11.1 + - - +
511D VAL* 4.2 21.1 - - + -
512D ARG 2.8 31.4 + - - -
582D PHE* 4.8 1.8 - - + -
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Residues in contact with ALA 480 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B HIS* 4.2 8.8 - - + +
519B SER* 5.8 3.4 - - - -
470D LEU 4.2 0.2 - - - +
471D VAL* 3.5 6.6 - - - +
472D GLN* 2.9 45.0 + - + +
474D TYR* 3.9 24.6 - - + +
478D SER 4.4 0.2 + - - -
479D VAL* 1.3 73.0 - - - +
481D LEU* 1.3 59.7 + - - +
512D ARG* 3.5 6.7 - - + +
514D THR* 4.4 15.9 - - + -
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Residues in contact with LEU 481 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470D LEU 4.2 0.7 - - - -
471D VAL* 3.8 20.0 - - + -
479D VAL* 3.9 2.6 - - + -
480D ALA* 1.3 73.5 - - - +
482D ASN* 1.3 72.1 + - - +
483D HIS* 4.5 0.4 - - + -
496D MET* 3.4 46.2 - - + +
497D VAL* 3.8 11.0 - - + +
500D ALA* 4.4 4.3 - - + -
511D VAL* 3.7 17.5 - - + -
512D ARG 2.7 12.9 + - - +
513D ILE* 3.5 15.0 - - + +
514D THR* 2.8 32.2 + - - -
540D VAL* 3.7 29.8 - - + -
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Residues in contact with ASN 482 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469D ALA* 3.3 6.8 - - - +
470D LEU* 2.9 43.6 + - + +
481D LEU* 1.3 75.6 - - - +
483D HIS* 1.3 69.0 + - - +
514D THR* 2.5 29.7 + - - +
515D ALA 3.0 24.4 + - - -
516D THR* 4.6 0.2 - - - +
517D ASP 4.6 4.3 + - - +
520D LYS* 3.6 30.9 - - - +
521D VAL* 3.4 20.6 + - - +
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Residues in contact with HIS 483 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468D GLY 3.5 11.7 - - - +
469D ALA* 4.1 0.9 - - - +
481D LEU* 4.5 3.8 - - + -
482D ASN* 1.3 86.9 - - - +
484D GLY* 1.3 62.5 + - - +
485D GLY* 3.0 47.2 + - - +
492D LEU* 3.9 8.5 - - + -
493D HIS* 2.8 31.8 + + - -
496D MET* 3.5 28.7 - - + +
513D ILE* 3.5 17.7 - - + +
514D THR 5.4 1.5 + - - +
516D THR* 3.7 16.5 + - - +
521D VAL* 4.3 2.4 - - - +
536D ASN* 3.6 16.4 + - + +
540D VAL* 4.1 14.4 - - + -
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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