Contacts of the strand formed by residues 456 - 462 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454B GLY 3.3 1.1 - - - -
455B GLU* 1.3 82.3 - - - +
457B ALA* 1.3 57.7 + - - +
474B LYS* 3.8 32.3 - - + -
475B ALA 3.4 11.7 - - - +
476B TYR* 4.4 7.2 - - + -
477B PRO* 4.6 0.7 - - - -
506B TRP* 3.4 10.2 - - - -
507B VAL* 2.8 38.3 + - + +
508B SER 4.1 4.9 - - - +
509B ARG* 4.2 4.0 - - - -
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Residues in contact with ALA 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B PHE* 4.8 3.6 - - + -
272B LEU* 4.8 2.0 - - + -
456B ALA* 1.3 71.0 - - - +
458B LEU* 1.3 61.9 + - - +
459B LEU* 3.6 10.9 + - + +
474B LYS* 3.1 8.8 - - - -
475B ALA* 2.8 48.1 + - + +
503B PHE* 3.8 20.9 - - + -
505B SER 3.6 4.3 - - - -
506B TRP* 3.5 23.1 - - + -
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Residues in contact with LEU 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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456B ALA 3.9 2.2 + - - -
457B ALA* 1.3 72.7 - - - +
459B LEU* 1.3 70.1 + - - +
460B HIS* 5.0 5.8 - - + +
472B GLU* 4.3 13.2 - - + +
473B PHE 3.7 3.1 - - - +
474B LYS* 4.6 1.3 - - - -
503B PHE* 4.0 0.7 - - - -
504B VAL* 2.9 47.7 + - + +
505B SER* 2.8 25.1 + - - +
507B VAL* 3.8 17.4 - - + +
511B TYR* 3.9 30.5 - - + +
513B LEU* 3.7 29.6 - - + -
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Residues in contact with LEU 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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231B PHE* 5.5 0.7 - - + -
233B LEU* 3.8 31.6 - - + -
457B ALA* 3.8 24.2 - - + +
458B LEU* 1.3 83.8 - - - +
460B HIS* 1.3 67.6 + - - +
472B GLU* 3.4 5.7 - - - -
473B PHE* 2.8 37.5 + - + +
475B ALA* 4.1 9.4 - - + +
481B LEU* 3.7 35.9 - - + -
501B PHE* 4.0 16.8 - - + -
502B VAL 3.2 6.7 - - - +
503B PHE* 3.8 16.6 - - + -
504B VAL* 4.1 0.7 - - - -
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Residues in contact with HIS 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458B LEU* 5.0 6.6 - - + +
459B LEU* 1.3 82.6 - - - +
461B TYR* 1.3 58.9 + - - +
462B VAL* 3.6 19.0 + - + +
469B ASN* 3.4 37.9 + - + +
471B GLY 3.5 2.7 - - - -
472B GLU* 4.3 19.4 + - + +
500B VAL 3.4 2.6 - - - +
501B PHE* 3.5 4.2 - - - -
502B VAL* 2.8 34.5 + - + +
504B VAL* 3.6 30.5 - - + +
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Residues in contact with TYR 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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238B LEU* 3.6 23.7 - - + +
253B MET* 3.7 13.3 - - + +
460B HIS* 1.3 71.9 - - - +
462B VAL* 1.3 54.4 + - - +
469B ASN 3.7 0.5 - - - -
470B LEU* 2.7 53.3 + - + +
471B GLY 2.9 11.5 + - - +
473B PHE* 3.8 21.3 - + + -
495B LEU* 3.9 20.4 - - + -
496B PRO 2.6 29.5 + - - -
497B ILE* 3.4 11.1 + - - -
499B GLY* 3.0 39.6 + - - -
500B VAL 3.6 7.4 - - - -
501B PHE* 3.7 25.2 - + + -
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Residues in contact with VAL 462 (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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460B HIS* 3.7 27.6 - - + +
461B TYR* 1.3 79.8 - - - +
463B ASP* 1.3 77.6 + - - +
464B PRO* 3.4 5.0 - - + +
467B GLY* 3.6 17.9 - - - +
468B ARG 3.4 11.0 - - - +
469B ASN* 4.6 4.5 - - + -
470B LEU* 4.3 2.0 - - - -
499B GLY* 3.2 6.8 - - - -
500B VAL* 2.8 38.6 + - + +
502B VAL* 3.9 19.5 - - + -
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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