Contacts of the strand formed by residues 460 - 468 (chain B) in PDB entry 3R2W
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 SER 460 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440B ASP* 2.7 32.5 + - - -
458B ASN 3.4 3.8 + - - -
459B VAL* 1.3 74.0 - - - +
461B LEU* 1.3 63.5 + - - +
462B LYS* 4.6 7.6 - - - +
481B ALA 2.8 10.2 + - - +
482B VAL* 3.2 26.5 - - - +
483B LEU* 2.8 28.1 + - - +
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Residues in contact with LEU 461 (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 PHE* 5.9 0.4 - - + -
439B PRO* 4.0 22.2 - - + -
440B ASP* 3.1 15.8 + - - +
441B MET* 3.1 31.0 - - - +
444B LEU* 3.6 14.7 - - + +
447B LEU* 3.8 34.3 - - + -
455B PHE* 4.7 12.3 - - + -
459B VAL* 4.1 16.2 - - + -
460B SER* 1.3 75.8 + - - +
462B LYS* 1.3 64.4 + - - +
465B VAL* 3.9 26.9 - - + -
483B LEU* 3.8 21.5 - - + -
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Residues in contact with LYS 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440B ASP* 5.6 2.0 - - - +
443B GLU* 3.2 56.9 + - + +
444B LEU* 3.8 3.4 - - - +
460B SER* 4.6 9.2 - - - +
461B LEU* 1.3 78.0 - - - +
463B GLY* 1.3 62.4 + - - +
465B VAL* 4.1 2.4 - - - +
482B VAL* 3.8 24.6 - - - +
483B LEU 2.9 24.5 + - - +
484B GLU* 3.2 31.7 - - + +
485B ASN 3.4 1.7 + - - -
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Residues in contact with GLY 463 (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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443B GLU* 2.7 18.6 + - - +
444B LEU* 3.7 3.5 - - - +
445B ASP* 2.8 31.8 + - - -
446B HIS 3.3 6.2 - - - +
462B LYS* 1.3 74.7 - - - +
464B THR* 1.3 59.6 + - - -
485B ASN* 3.8 17.5 - - - -
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Residues in contact with THR 464 (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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445B ASP* 3.8 14.8 - - + +
446B HIS* 3.3 37.2 - - + +
463B GLY* 1.3 74.7 - - - -
465B VAL* 1.3 58.9 + - - +
466B ILE* 4.2 7.2 - - - -
485B ASN* 2.9 49.1 + - - +
486B LYS 3.1 4.8 + - - +
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Residues in contact with VAL 465 (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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444B LEU* 5.0 1.6 - - + -
446B HIS 3.1 7.7 + - - +
447B LEU* 3.4 24.6 - - + +
448B THR* 3.1 23.2 + - - +
461B LEU* 3.9 21.8 - - + -
462B LYS 4.1 4.9 - - - +
464B THR* 1.3 77.8 - - - +
466B ILE* 1.3 62.7 + - - +
467B ILE* 3.9 20.2 - - + -
483B LEU* 3.4 44.9 - - + +
485B ASN 4.7 0.4 - - - +
486B LYS 3.4 7.4 - - - +
488B VAL* 5.7 0.7 - - + -
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Residues in contact with ILE 466 (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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446B HIS* 5.4 4.3 - - + +
448B THR* 3.5 28.0 - - + +
464B THR* 5.4 4.7 - - - -
465B VAL* 1.3 78.7 - - - +
467B ILE* 1.3 58.0 + - - +
468B ILE* 4.1 26.0 - - + -
486B LYS 2.8 13.1 + - - +
487B ILE* 3.3 26.2 - - + -
488B VAL* 2.7 33.3 + - - +
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Residues in contact with ILE 467 (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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447B LEU* 4.9 0.4 - - + -
448B THR 2.8 10.8 + - - +
449B VAL* 3.4 16.6 - - + +
450B SER 3.1 26.2 + - - +
453B VAL* 4.4 9.0 - - + -
455B PHE* 3.5 39.9 - - + -
461B LEU* 5.1 0.2 - - + -
465B VAL* 3.9 22.4 - - + -
466B ILE* 1.3 76.9 - - - +
468B ILE* 1.3 63.1 + - - +
475B ILE* 4.2 13.2 - - + -
477B ILE* 4.0 15.3 - - + -
483B LEU* 4.8 4.3 - - + -
488B VAL* 3.4 31.2 - - + +
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Residues in contact with ILE 468 (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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448B THR 5.3 1.1 - - - +
450B SER* 3.4 22.7 - - - +
466B ILE* 4.1 21.5 - - + -
467B ILE* 1.3 78.8 - - - +
469B ALA* 1.3 64.5 + - - +
470B ASN* 3.9 20.1 + - - +
475B ILE* 3.4 4.8 - - - +
487B ILE* 6.2 2.0 - - + -
488B VAL 2.9 8.9 + - - +
489B SER* 3.3 29.2 - - - -
490B GLY 3.8 1.6 + - - -
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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