Contacts of the strand formed by residues 543 - 547 (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 GLY 543 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402A TYR* 3.7 8.4 - - - -
403A LEU 3.3 12.6 - - - -
404A ASP* 3.3 9.9 + - - -
405A PHE* 5.2 4.0 - - - -
521A ILE* 6.0 2.7 - - - -
538A TYR* 5.1 0.2 - - - -
539A ALA* 3.8 0.7 - - - -
540A ASP* 2.9 29.8 + - - +
541A THR 3.2 5.3 + - - -
542A ASP* 1.3 79.6 - - - +
544A PHE* 1.3 63.7 + - - -
545A PHE* 4.8 3.6 - - - -
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Residues in contact with PHE 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A VAL 3.8 0.3 - - - +
402A TYR* 3.1 4.2 - - - -
403A LEU* 2.8 67.1 + - + +
405A PHE* 5.4 3.4 - + - -
521A ILE* 5.2 6.7 - - + -
524A THR* 4.1 28.9 - - + -
525A ILE* 4.0 18.2 - - + -
528A ILE* 4.0 35.4 - - + -
536A VAL* 4.0 19.7 - - + -
538A TYR 3.3 12.8 - - - +
539A ALA* 3.7 14.8 - - + -
543A GLY* 1.3 76.5 - - - +
545A PHE* 1.3 67.0 + - - +
546A ALA* 4.3 7.9 - - + -
577A LEU* 4.1 15.5 - - + -
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Residues in contact with PHE 545 (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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400A ILE* 3.7 20.4 - - + -
401A VAL 3.2 4.7 - - - -
402A TYR* 3.5 42.6 - + + -
536A VAL* 3.4 4.2 - - - +
537A LEU* 2.7 30.0 + - + -
538A TYR* 2.9 44.7 + + - +
543A GLY 4.8 1.6 - - - -
544A PHE* 1.3 76.6 - - - +
546A ALA* 1.3 58.4 + - - +
583A TYR* 4.4 10.8 - + - -
588A PHE* 3.6 29.6 - + + -
594A TYR* 3.6 33.2 - + - -
596A VAL* 4.2 15.0 - - + -
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Residues in contact with ALA 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A ILE* 3.4 6.4 - - - +
401A VAL* 2.9 41.8 + - + +
528A ILE* 4.8 0.9 - - + -
534A PHE* 3.8 20.0 - - + -
535A LYS 3.2 14.6 - - - +
536A VAL* 4.0 14.8 - - + -
537A LEU* 4.3 1.8 - - - +
544A PHE* 4.3 11.6 + - + -
545A PHE* 1.3 76.3 - - - +
547A THR* 1.3 61.5 + - - +
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Residues in contact with THR 547 (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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397A TRP* 4.5 13.7 - - + -
398A GLU* 3.1 16.3 + - - +
399A ASN* 2.7 29.1 + - - +
400A ILE* 4.4 2.5 - - - -
534A PHE* 3.4 10.7 - - - -
535A LYS* 2.7 39.5 + - + +
537A LEU* 4.0 22.7 - - + -
546A ALA* 1.3 73.2 - - - +
548A ILE* 1.3 72.2 + - - +
549A PRO* 3.5 13.0 - - + +
556A VAL* 4.2 2.4 - - - +
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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
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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