Contacts of the helix formed by residues 496 - 505 (chain B) in PDB entry 1Z6T
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 MET 496 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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458B LYS* 4.0 35.7 - - + +
461B ILE* 3.8 37.5 - - + -
462B THR* 4.9 4.5 - - - +
465B GLN* 5.4 2.2 - - - +
491B MET* 2.8 15.5 + - - +
494B ALA* 3.6 28.9 - - + +
495B LYS* 1.3 75.2 - - - +
497B HIS* 1.3 57.4 + - - +
498B LYS 3.3 2.9 - - - -
499B GLU* 3.3 45.8 + - + +
500B LEU* 3.0 29.0 + - - +
532B ILE* 4.5 0.7 - - - -
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Residues in contact with HIS 497 (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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495B LYS 3.0 14.8 + - - -
496B MET* 1.3 72.5 - - - +
498B LYS* 1.3 94.3 + - + +
500B LEU* 3.7 2.6 - - - +
501B CYS* 3.0 31.7 + - - -
532B ILE* 3.9 32.4 + - + +
533B LEU* 4.0 16.6 - - + -
534B ASP* 5.8 7.2 - - + -
537B ASP* 4.8 10.5 - - - +
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Residues in contact with LYS 498 (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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496B MET 3.3 0.6 - - - -
497B HIS* 1.3 100.7 - - + +
499B GLU* 1.3 66.7 + - - +
501B CYS* 3.5 5.1 + - - +
502B ALA* 3.0 27.9 + - - +
537B ASP* 5.9 0.9 - - - +
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Residues in contact with GLU 499 (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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461B ILE* 4.8 0.2 - - + -
465B GLN* 3.8 24.6 + - - +
491B MET* 3.7 22.7 - - + +
496B MET* 3.3 47.5 + - + +
498B LYS* 1.3 82.4 - - - +
500B LEU* 1.3 61.1 + - - +
502B ALA* 3.3 7.0 + - - +
503B LEU* 2.9 30.0 + - - +
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Residues in contact with LEU 500 (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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488B ALA* 3.7 33.2 - - + +
491B MET* 3.8 14.5 - - + -
492B ALA* 4.4 2.7 - - + +
496B MET 3.0 17.9 + - - +
497B HIS 3.7 3.8 - - - +
498B LYS 3.3 0.2 - - - -
499B GLU* 1.3 77.4 - - - +
501B CYS* 1.3 57.1 + - - +
503B LEU* 3.3 1.2 + - - +
504B MET* 2.9 61.1 + - + +
529B TYR* 4.1 22.2 - - + +
532B ILE* 3.9 24.9 - - + -
533B LEU* 4.2 16.4 - - + -
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Residues in contact with CYS 501 (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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497B HIS 3.0 25.2 + - - +
498B LYS* 3.7 5.2 - - - +
500B LEU* 1.3 75.5 - - - +
502B ALA* 1.3 59.9 + - - +
505B PHE* 2.9 74.7 + - + +
533B LEU* 3.9 16.2 - - - -
537B ASP* 3.6 24.5 - - - +
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Residues in contact with ALA 502 (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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498B LYS 3.0 17.1 + - - +
499B GLU* 3.3 7.8 + - - +
501B CYS* 1.3 76.0 - - - +
503B LEU* 1.3 63.1 + - - +
505B PHE 4.8 1.7 - - - +
506B SER* 4.0 11.3 - - - -
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Residues in contact with LEU 503 (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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470B PRO* 3.7 32.5 - - + -
487B LEU* 4.1 13.9 - - + -
488B ALA* 4.1 31.0 - - + +
491B MET* 4.0 22.4 - - + -
499B GLU 2.9 17.7 + - - +
500B LEU 3.6 3.4 - - - +
502B ALA* 1.3 77.5 - - - +
504B MET* 1.3 64.8 - - + +
506B SER* 3.4 6.8 - - - -
509B TRP* 3.2 66.5 - - + +
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Residues in contact with MET 504 (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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488B ALA* 4.1 10.3 - - + -
500B LEU* 2.9 43.7 + - + +
503B LEU* 1.3 86.5 - - + +
505B PHE* 1.3 64.6 + - + +
506B SER 2.8 16.7 + - - +
509B TRP* 4.2 11.1 - - - +
510B ILE* 4.5 4.2 - - - +
522B LEU* 3.8 10.8 - - + -
525B GLU* 3.6 29.8 - - + +
526B PHE* 3.5 59.9 - - + +
529B TYR* 4.8 4.5 - - - -
544B PHE* 4.2 2.9 - - - -
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Residues in contact with PHE 505 (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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500B LEU 6.0 0.2 - - - -
501B CYS* 2.9 54.6 + - + +
502B ALA* 4.8 1.6 - - - +
503B LEU 3.6 0.4 - - - -
504B MET* 1.3 79.3 - - + +
506B SER* 1.3 55.9 + - - +
526B PHE* 3.9 16.2 - + - -
533B LEU* 4.4 4.3 - - + -
537B ASP* 3.4 29.4 - - - -
540B VAL* 3.3 26.7 - - + -
541B SER* 3.5 26.9 - - - -
544B PHE* 3.6 21.5 - + + -
575B GLU* 5.1 1.8 - - - +
579B GLN* 2.6 30.3 + - - +
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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