Contacts of the strand formed by residues 515 - 520 (chain B) in PDB entry 2VKX
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 515 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508B VAL* 4.5 9.4 - - + -
509B GLU 3.2 12.3 - - - +
510B PRO* 4.3 3.6 - - + -
511B TYR* 4.7 0.7 - - - -
514B THR* 1.3 78.1 - - - +
516B GLN* 1.3 63.1 + - - +
517B VAL* 3.7 1.5 + - + -
562B THR* 3.4 5.0 - - - -
563B ILE* 3.1 53.5 + - + +
566B LEU* 3.9 5.6 - - + -
593B PHE* 4.0 15.7 - - + -
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Residues in contact with GLN 516 (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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511A TYR* 4.6 1.2 - - - -
514A THR* 3.1 36.1 + - - +
516A GLN* 4.4 8.5 - - - +
562A THR* 3.9 9.5 - - - +
507B GLN* 3.9 1.6 - - - +
508B VAL* 3.3 2.8 - - - -
509B GLU* 2.8 46.8 + - + +
511B TYR* 3.8 30.6 + - + -
515B ALA* 1.3 73.0 - - - +
517B VAL* 1.3 62.4 + - - +
518B GLN* 4.0 0.5 + - - +
560B ILE* 3.8 30.2 - - + +
561B VAL 3.9 3.6 - - - -
562B THR* 4.0 14.0 + - + +
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Residues in contact with VAL 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505B ILE* 3.8 21.3 - - + -
507B GLN 3.4 2.9 - - - +
508B VAL* 4.4 15.9 - - + -
515B ALA 4.6 5.4 - - - +
516B GLN* 1.3 74.8 - - - +
518B GLN* 1.3 72.0 + - - +
519B PHE* 4.1 1.0 - - - -
560B ILE* 3.2 8.3 - - - -
561B VAL* 2.9 46.1 + - + +
563B ILE* 4.6 13.7 - - + -
574B VAL* 4.4 20.2 - - + -
576B LEU* 4.1 25.6 - - + -
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Residues in contact with GLN 518 (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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630A PRO* 3.9 26.5 - - - +
505B ILE* 3.5 5.5 - - - +
506B ASP* 3.0 27.1 + - - +
507B GLN* 2.7 43.8 + - + +
516B GLN 4.0 0.6 + - - +
517B VAL* 1.3 73.4 - - - +
519B PHE* 1.3 65.0 + - - +
559B GLY 3.3 22.4 - - - +
560B ILE* 3.7 11.7 - - + +
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Residues in contact with PHE 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503B PRO* 4.1 8.5 - - + -
504B SER 2.9 23.3 - - - +
505B ILE* 4.0 0.4 - - - -
506B ASP* 3.2 13.2 + - - +
517B VAL* 4.1 8.7 - - + -
518B GLN* 1.3 82.7 - - - +
520B ASP* 1.3 71.4 + - - +
521B GLU* 4.0 22.4 + - + +
533B TYR* 4.0 35.2 - + + -
555B ALA* 4.5 12.8 - - + -
556B SER* 5.9 0.4 - - - -
559B GLY 4.5 6.5 + - - +
560B ILE* 4.7 5.8 - - - -
561B VAL* 3.9 27.8 - - + -
576B LEU* 3.6 24.2 - - + -
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Residues in contact with ASP 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503B PRO* 3.3 6.9 - - - +
504B SER* 2.8 42.3 + - - +
506B ASP* 3.3 25.3 - - - +
519B PHE* 1.3 77.0 - - - +
521B GLU* 1.3 68.1 + - - +
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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