Contacts of the strand formed by residues 456 - 461 (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 PHE 456 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370B CYS* 3.7 20.9 - - - -
382B TYR* 3.4 4.4 - - - -
383B MET* 2.9 48.1 + - + +
384B GLY 3.0 21.9 + - - +
386B ALA* 4.5 8.1 - - + -
392B VAL* 3.4 43.3 - - + -
393B GLN 4.2 4.7 - - - -
394B ILE* 3.7 37.7 - - + -
410B ILE* 4.7 9.0 - - + -
449B ILE 3.5 2.2 - - - -
450B LYS* 3.8 18.4 - - + -
454B GLY 3.4 15.0 - - - -
455B TYR* 1.3 73.4 - - - +
457B GLN* 1.3 60.4 + - - +
458B PHE 4.1 0.4 - - - -
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Residues in contact with GLN 457 (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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381B GLY* 3.6 22.0 + - - +
382B TYR* 3.6 33.7 + - + -
383B MET* 4.7 2.2 - - - -
448B GLY* 3.3 5.0 - - - -
449B ILE* 2.7 54.0 + - + +
456B PHE* 1.3 73.7 - - - +
458B PHE* 1.3 72.8 + - - +
459B MET* 3.6 13.5 + - - +
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Residues in contact with PHE 458 (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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340B SER* 4.3 17.9 - - - +
361B TYR* 5.0 0.9 - + - -
381B GLY 4.7 3.0 + - - -
383B MET* 3.7 30.7 - - + +
446B ASP* 3.6 35.9 - - + -
447B ARG 3.8 4.7 - - - -
456B PHE 4.1 1.0 - - - -
457B GLN* 1.3 78.3 + - - +
459B MET* 1.3 67.1 + - - +
460B GLY* 3.5 34.3 - - - -
461B ARG* 3.7 6.3 - - + -
467B ASN* 6.2 1.1 - - - -
503B GLU* 5.8 4.5 - - - -
1570B AMP 3.5 39.7 - + + +
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Residues in contact with MET 459 (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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407B GLU* 3.4 25.9 - - - +
447B ARG* 3.0 28.1 + - + +
448B GLY* 3.9 9.6 - - - -
449B ILE* 3.9 29.4 - - + -
457B GLN* 3.6 25.4 - - - +
458B PHE* 1.3 80.9 - - - +
460B GLY* 1.3 60.4 + - - +
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Residues in contact with GLY 460 (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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446B ASP* 3.7 0.9 - - - -
447B ARG* 2.8 33.7 + - - +
458B PHE* 3.5 26.3 - - - -
459B MET* 1.3 78.3 - - - +
461B ARG* 1.3 61.9 + - - -
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Residues in contact with ARG 461 (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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363B GLN* 4.1 2.0 - - - +
444B LEU 3.1 25.9 + - - -
445B GLY* 3.3 16.4 + - - -
446B ASP* 3.0 25.6 + - - -
447B ARG* 4.6 1.9 - - - +
458B PHE* 3.7 7.0 - - + -
460B GLY* 1.3 73.3 - - - -
462B ALA* 1.3 61.6 + - - +
463B ASP* 3.1 42.8 + - - +
465B ILE* 3.2 58.5 - - + +
466B ILE 6.0 0.7 - - - -
467B ASN* 6.1 4.3 - - + -
472B ARG* 5.3 3.6 - - - +
503B GLU* 5.8 1.8 - - - +
564B ARG* 4.9 8.9 + - - +
1570B AMP 3.2 21.9 + - - +
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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