Contacts of the strand formed by residues 456 - 461 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A CYS* 3.6 21.5 - - - -
382A TYR* 3.3 4.8 - - - -
383A MET* 2.8 53.8 + - + +
384A GLY 2.9 20.2 + - - +
385A THR* 4.5 0.2 - - - -
386A ALA* 4.3 8.7 - - + -
392A VAL* 3.3 44.2 - - + -
393A GLN* 4.1 7.0 - - - -
394A ILE* 3.6 38.1 - - + -
410A ILE* 4.7 7.9 - - + -
449A ILE 3.4 4.9 - - - +
450A LYS* 4.0 15.5 - - + -
454A GLY 3.5 18.4 - - - -
455A TYR* 1.3 72.8 - - - +
457A GLN* 1.3 60.0 + - - +
458A PHE 4.1 0.2 - - - -
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Residues in contact with GLN 457 (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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381A GLY* 3.8 20.6 + - - +
382A TYR* 3.7 38.4 + - + -
383A MET* 4.6 1.8 - - - -
448A GLY* 3.2 5.0 - - - -
449A ILE* 2.8 52.6 + - + +
455A TYR 3.9 0.6 + - - -
456A PHE* 1.3 74.1 - - - +
458A PHE* 1.3 72.1 + - - +
459A MET* 3.4 19.8 + - - +
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Residues in contact with PHE 458 (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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340A SER* 4.1 20.4 + - - +
359A GLU* 6.0 0.4 - - - +
361A TYR* 4.8 6.1 - + - -
381A GLY 4.5 3.8 + - - -
383A MET* 4.0 23.1 - - + +
446A ASP* 3.6 36.1 - - + -
447A ARG 4.0 8.1 - - - -
456A PHE 4.1 2.4 + - - -
457A GLN* 1.3 75.3 - - - +
459A MET* 1.3 66.4 + - - +
460A GLY* 3.4 33.4 - - - -
461A ARG* 3.7 6.1 - - + -
467A ASN* 6.1 0.7 - - - -
503A GLU* 5.7 4.9 - - - -
1570A AMP 3.6 37.5 - + + +
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Residues in contact with MET 459 (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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407A GLU* 3.9 31.5 - - - +
447A ARG* 3.0 22.3 + - + +
448A GLY* 4.0 3.6 - - - -
449A ILE* 3.9 35.7 - - + -
457A GLN* 3.4 30.0 + - - +
458A PHE* 1.3 78.5 - - - +
460A GLY* 1.3 60.9 + - - +
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Residues in contact with GLY 460 (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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446A ASP* 3.7 1.0 - - - -
447A ARG* 2.8 29.7 + - - +
458A PHE* 3.4 29.4 - - - -
459A MET* 1.3 78.0 - - - +
461A ARG* 1.3 63.2 + - - -
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Residues in contact with ARG 461 (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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363A GLN* 4.1 1.6 - - - +
444A LEU 2.8 28.1 + - - -
445A GLY* 3.4 14.4 + - - -
446A ASP* 3.0 28.2 + - - +
447A ARG* 4.7 1.9 - - - +
458A PHE* 3.7 6.7 - - + -
460A GLY* 1.3 71.7 - - - -
462A ALA* 1.3 61.9 + - - +
463A ASP* 2.9 51.7 + - - +
465A ILE* 3.1 51.5 - - + +
466A ILE 6.0 0.9 - - - -
467A ASN* 6.0 4.3 - - + +
472A ARG* 5.1 5.2 - - - +
503A GLU* 6.0 0.9 - - - +
564A ARG* 4.6 11.9 + - - +
1570A AMP 3.3 20.3 + - - +
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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