Contacts of the strand formed by residues 481 - 486 (chain B) in PDB entry 2VRW
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 GLY 481 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412B THR 3.9 0.5 - - - +
413B SER* 3.7 10.7 - - - -
414B VAL* 3.8 11.4 + - - +
472B LEU* 6.2 0.4 - - - -
473B LEU 3.6 7.9 - - - -
474B ILE* 4.0 14.8 - - - -
480B GLN* 1.3 91.2 + - - +
482B TYR* 1.3 64.6 + - - -
483B GLU* 5.9 0.6 - - - +
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Residues in contact with TYR 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B ILE* 4.0 18.4 - - + -
412B THR 3.3 8.1 - - - +
413B SER* 4.1 20.9 - - - -
415B GLU* 4.9 4.9 + - - -
433B ILE* 4.1 16.2 - - + -
445B ALA* 4.3 13.1 - - + +
447B VAL* 3.6 33.5 - - + +
452B PHE* 3.8 23.0 - + - -
472B LEU* 3.3 9.7 - - - +
473B LEU* 2.8 49.5 + - + +
474B ILE* 4.6 0.4 - - - +
480B GLN* 3.6 21.0 + - + +
481B GLY* 1.3 74.8 - - - -
483B GLU* 1.3 63.2 + - - +
484B LEU* 4.1 18.6 - - + -
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Residues in contact with GLU 483 (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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410B LYS 3.7 0.5 - - - +
411B ILE* 3.3 9.5 - - - +
412B THR* 2.7 53.2 + - - +
417B ARG 5.1 0.7 - - - +
470B MET* 3.8 22.4 - - + +
471B PHE 3.8 4.5 - - - -
472B LEU* 3.5 21.7 - - + +
481B GLY 5.9 0.2 - - - +
482B TYR* 1.3 71.7 - - - +
484B LEU* 1.3 62.0 + - - +
485B PHE* 3.6 26.1 + - + -
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Residues in contact with LEU 484 (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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409B LEU* 4.4 7.4 - - + -
410B LYS 3.7 2.2 - - - -
411B ILE* 3.7 29.8 - - + -
431B LEU* 4.1 15.7 - - + -
433B ILE* 5.3 0.4 - - + -
470B MET* 3.1 23.1 - - - -
471B PHE* 3.0 30.8 + - + +
473B LEU* 4.3 13.7 - - + -
482B TYR* 4.1 16.2 - - + -
483B GLU* 1.3 76.4 - - - +
485B PHE* 1.3 63.0 + - - +
486B PHE* 3.8 22.7 - - + -
499B PHE* 3.9 33.7 - - + -
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Residues in contact with PHE 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B LEU* 3.4 8.9 - - - +
410B LYS* 2.7 53.8 + - + +
412B THR* 3.8 13.7 - - + -
419B LYS* 3.6 31.6 - - + -
467B TRP* 3.1 29.0 - - + +
468B SER* 4.2 9.6 - - - -
469B HIS 3.5 1.8 - - - -
470B MET* 3.5 26.9 - - + -
483B GLU* 3.6 43.5 - - + -
484B LEU* 1.3 73.3 - - - +
486B PHE* 1.3 60.9 + - - +
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Residues in contact with PHE 486 (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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408B GLU 4.4 5.4 - - - -
409B LEU* 3.6 33.0 - - + -
467B TRP* 3.2 22.0 + - - -
469B HIS* 2.9 24.3 + - - +
471B PHE* 3.4 27.8 - + - -
484B LEU* 3.8 23.3 - - + -
485B PHE* 1.3 75.7 - - - +
487B LYS* 1.3 65.8 + - - +
488B THR 3.3 4.2 + - - +
491B LEU* 4.2 7.0 - - + -
492B LYS* 3.9 32.8 - - + +
495B TRP* 3.3 54.3 - + + -
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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