Contacts of the strand formed by residues 535 - 540 (chain A) in PDB entry 2VWK
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 LYS 535 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393A GLU* 3.3 27.6 - - + +
397A TRP* 4.0 30.5 - - + -
529A GLU* 3.8 5.4 - - - +
534A PHE* 1.3 73.6 - - - +
536A VAL* 1.3 69.5 + - - +
537A LEU* 3.4 11.0 + - + +
546A ALA* 3.2 3.8 - - - -
547A THR* 2.7 38.9 + - + +
549A PRO* 4.3 19.7 - - + +
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Residues in contact with VAL 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A LYS* 3.7 37.3 + - + +
393A GLU* 3.9 11.4 - - - +
525A ILE* 3.8 20.2 - - + -
528A ILE* 3.6 31.2 - - + -
529A GLU* 3.1 16.9 + - + +
535A LYS* 1.3 71.4 - - - +
537A LEU* 1.3 63.5 + - - +
538A TYR 3.9 14.4 - - - +
544A PHE* 4.0 22.7 - - + -
545A PHE 3.4 11.7 - - - +
546A ALA* 4.0 2.2 - - + -
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Residues in contact with LEU 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A LYS* 5.9 0.9 - - - -
391A GLU 5.5 0.7 - - - -
392A PRO* 3.2 5.4 - - - +
393A GLU* 3.0 35.4 + - + +
397A TRP* 3.5 52.3 - - + +
400A ILE* 3.6 37.2 - - + -
535A LYS* 3.8 18.8 - - + +
536A VAL* 1.3 75.6 - - - +
538A TYR* 1.3 62.5 + - - +
545A PHE 2.7 10.2 + - - +
546A ALA 4.5 2.2 - - - -
547A THR* 4.0 11.4 - - + -
588A PHE* 3.7 27.3 - - + -
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Residues in contact with TYR 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389A VAL* 4.3 4.0 - - + -
390A LYS* 4.0 13.0 - - - -
392A PRO* 4.2 15.0 - - + -
536A VAL* 3.5 4.1 - - - +
537A LEU* 1.3 82.9 - - - +
539A ALA* 1.3 70.2 + - - +
540A ASP* 2.5 44.1 + - - -
544A PHE* 3.3 4.0 - - - +
545A PHE* 2.9 51.3 + + + +
588A PHE* 3.6 30.5 - + + -
590A THR 3.9 10.8 - - - -
591A LYS* 4.1 6.1 - - - -
592A LYS* 2.6 33.7 + - - -
594A TYR* 3.9 18.8 - + - -
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Residues in contact with ALA 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388A TYR* 3.6 8.1 - - + +
389A VAL* 3.4 8.7 - - - +
390A LYS* 3.2 47.4 + - + +
521A ILE* 4.9 0.2 - - + -
525A ILE* 3.6 26.0 - - + -
536A VAL* 4.4 0.2 - - + -
538A TYR* 1.3 81.5 - - - +
540A ASP* 1.3 68.4 + - - +
543A GLY 3.8 4.5 - - - -
544A PHE* 3.7 7.2 - - + -
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Residues in contact with ASP 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388A TYR* 3.8 16.5 - - - -
389A VAL* 4.1 7.1 - - - +
521A ILE* 3.7 15.8 - - - +
538A TYR* 2.5 40.6 + - + -
539A ALA* 1.3 72.2 - - - +
541A THR* 1.3 62.7 + - - +
542A ASP* 3.1 21.0 - - + +
543A GLY* 2.9 20.9 + - - +
591A LYS* 4.9 3.0 - - - +
592A LYS* 3.5 28.8 + - - +
594A TYR* 5.0 2.4 - - - -
606A ARG* 4.1 6.6 + - - -
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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