Contacts of the strand formed by residues 456 - 462 (chain A) in PDB entry 2ZL6
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 456 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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454A GLY 3.4 0.6 - - - -
455A GLU* 1.3 79.9 - - - +
457A ALA* 1.3 60.5 + - - +
474A LYS* 3.8 32.3 - - + -
475A ALA 3.4 11.0 - - - +
476A TYR* 4.5 7.6 - - + -
477A PRO* 4.6 1.3 - - - -
506A TRP* 3.4 10.5 - - - -
507A VAL* 2.9 37.3 + - + +
508A SER 4.1 4.7 - - - +
509A ARG* 4.4 3.8 - - - -
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Residues in contact with ALA 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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231A PHE* 4.7 3.6 - - + -
272A LEU* 4.7 2.5 - - + -
456A ALA* 1.3 70.3 - - - +
458A LEU* 1.3 63.0 + - - +
459A LEU* 3.5 11.3 + - + +
474A LYS* 3.2 6.2 - - - -
475A ALA* 2.8 47.6 + - + +
503A PHE* 3.7 20.9 - - + -
505A SER 3.7 4.5 - - - -
506A TRP* 3.6 22.8 - - + -
507A VAL* 4.6 0.9 - - - -
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Residues in contact with LEU 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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456A ALA 3.8 2.2 + - - -
457A ALA* 1.3 72.4 - - - +
459A LEU* 1.3 68.2 + - - +
460A HIS* 4.9 6.1 - - + +
472A GLU* 4.2 13.9 - - + +
473A PHE 3.7 11.0 - - - +
474A LYS* 4.7 1.3 - - + -
503A PHE* 4.0 0.5 - - - -
504A VAL* 2.8 48.1 + - + +
505A SER* 2.8 32.0 + - - +
507A VAL* 3.8 18.2 - - + +
511A TYR* 3.9 30.7 - - + +
513A LEU* 3.7 22.2 - - + -
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Residues in contact with LEU 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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231A PHE* 5.4 0.4 - - + -
233A LEU* 3.7 31.2 - - + -
457A ALA* 3.8 24.5 - - + +
458A LEU* 1.3 83.5 - - - +
460A HIS* 1.3 73.3 + - - +
472A GLU* 3.4 1.9 - - - -
473A PHE* 2.8 36.6 + - + +
475A ALA* 3.9 15.7 - - + +
481A LEU* 3.8 27.4 - - + -
501A PHE* 4.1 15.3 - - + -
502A VAL 3.3 7.2 - - - +
503A PHE* 3.7 20.2 - - + -
504A VAL* 4.1 0.7 - - - +
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Residues in contact with HIS 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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458A LEU* 4.9 6.3 - - + +
459A LEU* 1.3 84.0 - - - +
461A TYR* 1.3 59.4 + - - +
462A VAL* 3.7 18.2 + - + +
469A ASN* 3.5 39.6 + - + +
471A GLY 3.4 2.5 - - - -
472A GLU* 4.2 17.9 + - + +
500A VAL 3.5 2.4 - - - +
501A PHE* 3.5 4.8 - - - -
502A VAL* 2.9 34.8 + - + +
504A VAL* 3.6 28.9 - - + +
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Residues in contact with TYR 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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238A LEU* 3.4 22.9 - - + +
253A MET* 3.6 12.5 - - + +
460A HIS* 1.3 70.8 - - - +
462A VAL* 1.3 55.9 + - - +
469A ASN* 3.7 0.7 - - - +
470A LEU* 2.7 53.3 + - + +
471A GLY 2.9 10.7 + - - +
473A PHE* 3.8 12.8 - + + -
495A LEU* 4.1 20.0 - - + -
496A PRO 2.6 29.7 + - - -
497A ILE* 3.4 10.4 + - - -
499A GLY* 3.0 39.6 + - - -
500A VAL 3.6 8.1 - - - -
501A PHE* 3.7 31.8 - + + -
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Residues in contact with VAL 462 (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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460A HIS* 3.8 27.8 - - + +
461A TYR* 1.3 79.1 - - - +
463A ASP* 1.3 78.6 + - - +
464A PRO* 3.4 5.9 - - + +
467A GLY* 3.7 23.1 - - - +
468A ARG 3.3 4.7 - - - +
469A ASN* 4.7 3.8 - - + -
470A LEU* 4.5 1.6 - - - -
499A GLY* 3.2 6.7 - - - -
500A VAL* 2.8 37.2 + - + +
502A VAL* 3.8 20.2 - - + -
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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