Contacts of the strand formed by residues 488 - 498 (chain B) in PDB entry 2VZE
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 488 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482B LEU* 3.3 38.4 - - + +
483B MET* 3.6 30.9 - - - +
485B HIS 3.1 10.4 + - - +
486B PRO 3.2 2.3 - - - +
487B ALA* 1.3 77.4 - - - +
489B VAL* 1.3 63.4 + - - +
490B GLU 3.8 14.4 - - - +
491B THR* 4.0 10.5 - - - -
509B VAL* 3.7 20.6 - - + -
510B VAL 3.9 3.1 - - - -
527B LEU* 4.1 24.9 - - + -
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Residues in contact with VAL 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B MET* 3.5 17.0 - - - +
486B PRO 4.8 3.4 - - - +
487B ALA 3.8 0.2 + - - -
488B VAL* 1.3 76.3 - - - +
490B GLU* 1.3 70.7 + - + +
510B VAL* 2.9 41.7 + - + +
511B LEU 3.9 4.9 - - - +
512B ALA* 3.8 28.9 - - + -
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Residues in contact with GLU 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B MET* 3.9 5.2 - - - -
488B VAL* 3.5 5.0 - - - +
489B VAL* 1.3 90.5 - - + +
491B THR* 1.3 65.6 + - - +
509B VAL* 3.7 1.4 - - - -
510B VAL* 2.9 46.8 + - + +
550B LEU* 4.3 10.2 + - + +
552B LYS* 2.9 37.9 + - - +
558B ILE* 4.3 15.9 - - + +
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Residues in contact with THR 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B GLU* 3.7 46.0 - - + +
482B LEU* 3.6 24.5 - - + +
483B MET* 3.9 15.1 - - + -
488B VAL* 4.0 10.1 - - - -
490B GLU* 1.3 78.4 - - - +
492B ALA* 1.3 62.7 + - - +
493B VAL* 4.4 0.3 - - - +
507B ALA* 4.2 2.9 - - - +
508B PHE 3.2 13.3 + - - -
509B VAL* 3.9 4.4 - - - +
550B LEU* 3.6 5.5 - - - +
558B ILE* 3.4 20.5 - - - +
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Residues in contact with ALA 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B GLU* 3.5 7.2 - - - +
491B THR* 1.3 76.1 + - - +
493B VAL* 1.3 63.8 + - - +
494B ILE* 4.1 1.6 + - - -
506B LYS 4.1 0.5 - - - +
507B ALA* 3.6 0.2 - - - -
508B PHE* 2.9 39.9 + - - +
550B LEU* 3.8 17.9 - - + +
558B ILE* 3.5 28.9 - - + -
560B ARG* 4.7 6.3 - - + -
563B LEU* 4.0 9.2 - - + -
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Residues in contact with VAL 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B ASP* 5.1 0.9 - - - +
466B ILE* 3.6 13.4 - - + +
475B PRO* 3.4 24.1 - - + +
478B VAL* 3.6 34.1 - - + -
479B GLU* 3.1 26.2 + - + +
482B LEU* 4.1 5.2 - - + -
491B THR* 4.4 0.4 - - - +
492B ALA* 1.3 74.2 - - - +
494B ILE* 1.3 69.8 + - - +
505B VAL* 3.5 24.7 - - + -
506B LYS 3.4 10.5 - - - +
507B ALA* 4.0 16.8 - - + -
560B ARG* 4.0 5.0 - - - +
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Residues in contact with ILE 494 (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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464B ASP 5.5 0.9 - - - -
466B ILE* 3.5 14.9 - - - +
492B ALA 4.8 2.9 - - - +
493B VAL* 1.3 81.8 - - - +
495B SER* 1.3 68.8 + - - +
504B VAL 3.9 0.7 - - - +
506B LYS* 3.1 34.9 + - + +
508B PHE* 3.7 19.5 - - + -
560B ARG* 3.8 36.1 - - + +
563B LEU* 3.3 23.1 - - + +
564B ARG* 3.3 41.5 - - + +
567B GLU* 4.3 4.9 - - + -
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Residues in contact with SER 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465B ILE 5.5 1.1 - - - -
466B ILE* 3.7 14.5 - - - +
494B ILE* 1.3 92.2 - - - +
496B SER* 1.3 63.6 + - - +
503B GLU* 3.4 34.0 - - - -
504B VAL 3.5 6.5 - - - -
564B ARG* 3.6 20.1 - - - +
567B GLU* 4.0 1.4 - - - +
568B TRP* 3.0 24.4 + - - -
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Residues in contact with SER 496 (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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495B SER* 1.3 77.4 - - - +
497B PRO* 1.3 68.7 - - - +
503B GLU* 3.3 4.3 - - - -
504B VAL* 2.7 43.3 + - - +
506B LYS* 3.8 20.9 - - - -
543B LYS* 2.7 33.7 + - - +
567B GLU* 3.6 16.5 - - - +
568B TRP* 3.7 7.0 - - - +
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Residues in contact with PRO 497 (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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496B SER* 1.3 91.2 - - - +
498B ASP* 1.3 60.2 + - - +
499B PRO* 4.3 3.4 - - - +
502B GLY 3.4 8.5 - - - +
543B LYS* 3.0 20.8 + - - +
567B GLU* 3.6 25.8 - - + +
568B TRP* 3.9 35.4 - - + +
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Residues in contact with ASP 498 (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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316B ARG* 4.6 0.7 + - - -
496B SER 3.8 0.6 + - - -
497B PRO* 1.3 72.9 - - - +
499B PRO* 1.3 71.9 - - - +
500B VAL* 2.8 33.4 + - - +
501B ARG* 3.2 14.8 + - - +
502B GLY* 3.0 34.1 + - - +
504B VAL* 3.4 32.1 - - + +
543B LYS* 4.6 10.4 - - - +
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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
------------------------------------------------------------
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