Contacts of the strand formed by residues 492 - 497 (chain D) in PDB entry 2VGB
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 ALA 492 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D ALA* 5.3 6.1 - - + +
469D ALA 3.3 12.6 + - - +
470D ALA* 3.0 13.3 - - + +
471D ILE 2.7 30.8 + - - +
490D ARG 3.4 3.6 + - - +
491D ALA* 1.3 72.7 - - - +
493D VAL* 1.3 57.5 + - - +
494D ILE* 3.5 5.9 + - + -
511D GLY* 4.1 2.2 - - - -
513D PHE* 3.3 31.6 - - + -
545D PHE* 5.6 7.6 - - + -
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Residues in contact with VAL 493 (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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471D ILE* 3.2 12.1 - - + -
473D VAL* 3.7 26.7 - - + -
481D ALA* 4.2 7.6 - - + +
484D LEU* 4.0 17.3 - - + -
485D SER* 4.6 6.3 - - - +
489D PRO* 3.9 28.0 - - + -
491D ALA 4.4 1.3 - - - +
492D ALA* 1.3 70.5 - - - +
494D ILE* 1.3 58.9 + - - +
495D ALA 3.5 0.9 + - - -
511D GLY* 3.0 21.1 + - - +
512D VAL* 3.3 20.4 - - + -
513D PHE* 2.8 27.4 + - - -
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Residues in contact with ILE 494 (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 ALA* 3.8 25.6 - - + -
471D ILE 2.8 11.4 + - - +
472D ILE* 3.3 16.0 - - + +
473D VAL* 2.9 26.4 + - - +
492D ALA* 4.3 5.4 - - + +
493D VAL* 1.3 70.9 - - - +
495D ALA* 1.3 58.6 + - - +
496D VAL* 3.8 3.2 + - + +
513D PHE* 3.5 9.9 - - + +
515D LEU* 3.6 33.7 - - + -
536D GLY* 4.5 13.0 - - - +
540D GLY* 4.4 9.4 - - - -
545D PHE* 3.7 31.6 - - + -
546D LEU* 4.0 12.8 - - + -
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Residues in contact with ALA 495 (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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473D VAL* 3.4 8.1 - - + +
475D THR* 3.8 22.2 - - + -
481D ALA* 3.9 9.4 - - + -
493D VAL 3.5 1.2 + - - -
494D ILE* 1.3 71.4 - - - +
496D VAL* 1.3 57.9 + - - +
497D THR* 3.9 2.8 + - + +
506D VAL* 4.8 4.0 - - + -
512D VAL* 3.8 24.2 - - + -
513D PHE 2.9 10.0 + - - +
514D PRO* 3.4 5.0 - - + +
515D LEU* 2.7 33.8 + - - +
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Residues in contact with VAL 496 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472D ILE* 4.5 7.6 - - + -
473D VAL 2.9 10.5 + - - +
474D LEU* 3.5 12.2 - - + +
475D THR* 3.0 24.5 + - - +
494D ILE* 4.4 8.7 - - + +
495D ALA* 1.3 73.4 - - - +
497D THR* 1.3 63.8 + - - +
515D LEU* 3.6 11.7 - - + +
517D TYR* 4.1 18.6 - - + -
532D ARG* 3.9 36.8 + - + +
535D PHE* 4.1 8.5 - - + -
536D GLY* 4.0 26.9 - - - +
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Residues in contact with THR 497 (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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475D THR* 2.5 33.9 + - + -
476D THR* 3.9 10.9 + - - -
495D ALA* 4.9 3.8 - - + +
496D VAL* 1.3 74.7 - - - +
498D ARG* 1.3 60.9 + - - +
499D SER* 3.5 28.0 + - - +
502D ALA* 4.4 3.4 - - - +
503D ALA* 3.7 26.9 - - + +
514D PRO* 5.6 0.4 - - + -
515D LEU 3.2 9.3 + - - +
516D LEU* 3.3 2.6 - - - +
517D TYR* 2.9 27.3 + - - -
532D ARG* 6.1 3.6 - - - +
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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