Contacts of the helix formed by residues 496 - 505 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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458A LYS* 3.9 37.7 - - + +
461A ILE* 3.8 37.7 - - + -
462A THR* 4.8 3.6 - - - +
465A GLN* 5.3 2.7 - - - +
491A MET* 2.8 18.7 + - - +
494A ALA* 3.5 30.3 - - + +
495A LYS* 1.3 68.2 - - - +
497A HIS* 1.3 59.4 + - - +
498A LYS 3.3 2.5 - - - -
499A GLU* 3.4 46.7 + - + +
500A LEU* 3.0 28.8 + - - +
532A ILE* 4.5 0.6 - - - +
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Residues in contact with HIS 497 (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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495A LYS* 3.1 28.5 + - + -
496A MET* 1.3 69.9 - - - +
498A LYS* 1.3 68.9 + - + +
500A LEU* 3.8 2.0 - - - +
501A CYS* 3.0 32.7 + - - -
532A ILE* 2.8 37.2 + - + +
533A LEU* 3.8 21.3 - - + -
534A ASP 5.6 2.2 - - - +
537A ASP* 5.4 4.0 - - - +
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Residues in contact with LYS 498 (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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496A MET 3.3 0.4 - - - -
497A HIS* 1.3 86.0 - - + +
499A GLU* 1.3 71.4 + - - +
501A CYS* 3.7 4.9 - - - +
502A ALA* 3.0 28.7 + - + +
537A ASP* 6.0 0.4 - - - -
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Residues in contact with GLU 499 (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 LYS* 5.7 0.5 - - - -
461A ILE* 4.8 0.2 - - + -
465A GLN* 3.7 24.4 + - - +
491A MET* 3.7 21.9 - - + +
496A MET* 3.4 47.8 + - + +
498A LYS* 1.3 89.4 - - + +
500A LEU* 1.3 60.9 + - - +
502A ALA* 3.2 7.0 + - - +
503A LEU* 2.9 31.7 + - - +
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Residues in contact with LEU 500 (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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488A ALA* 3.6 33.4 - - + +
491A MET* 3.7 13.6 - - + -
492A ALA* 4.1 4.0 - - + -
496A MET 3.0 16.9 + - - +
497A HIS 3.8 4.0 - - - +
499A GLU* 1.3 77.6 - - - +
501A CYS* 1.3 56.7 + - - +
503A LEU* 3.4 0.7 + - - +
504A MET* 2.9 62.9 + - + +
529A TYR* 4.0 24.5 - - + +
532A ILE* 3.7 28.5 - - + -
533A LEU* 4.4 10.3 - - + -
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Residues in contact with CYS 501 (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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497A HIS 3.0 25.5 + - - +
498A LYS* 3.7 5.8 - - - +
500A LEU* 1.3 74.5 - - - +
502A ALA* 1.3 60.2 + - - +
505A PHE* 2.8 73.6 + - + +
533A LEU* 3.8 15.5 - - - -
537A ASP* 3.6 28.9 - - - +
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Residues in contact with ALA 502 (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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498A LYS* 3.0 18.2 + - + +
499A GLU* 3.2 8.0 + - - +
501A CYS* 1.3 77.0 - - - +
503A LEU* 1.3 61.9 + - - +
505A PHE 4.8 1.8 - - - +
506A SER* 4.1 10.7 + - - -
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Residues in contact with LEU 503 (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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470A PRO* 3.6 38.1 - - + -
487A LEU* 3.9 24.2 - - + -
488A ALA* 4.2 17.5 - - + +
491A MET* 4.0 20.4 - - + -
499A GLU 2.9 16.2 + - - +
500A LEU* 3.7 3.1 - - + +
502A ALA* 1.3 77.8 - - - +
504A MET* 1.3 71.3 + - + +
506A SER* 3.2 9.9 - - - -
509A TRP* 3.2 53.4 - - + +
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Residues in contact with MET 504 (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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488A ALA* 4.0 7.9 - - + -
500A LEU* 2.9 47.9 + - + +
503A LEU* 1.3 84.3 - - + +
505A PHE* 1.3 62.4 + - + +
506A SER 2.9 15.6 + - - +
509A TRP* 4.2 12.6 - - + +
510A ILE* 4.6 4.3 - - - +
522A LEU* 3.9 19.2 - - + +
525A GLU* 3.5 31.4 - - + +
526A PHE* 3.5 49.1 - - + +
529A TYR* 4.5 7.0 - - - -
544A PHE* 3.9 4.5 - - - -
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Residues in contact with PHE 505 (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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501A CYS* 2.8 59.5 + - + +
502A ALA* 4.8 1.6 - - - +
504A MET* 1.3 76.5 - - + +
506A SER* 1.3 54.3 + - - +
526A PHE* 3.9 15.3 - + - -
533A LEU* 4.3 5.4 - - + -
537A ASP* 3.2 34.5 - - - -
540A VAL* 3.4 22.9 - - + -
541A SER* 3.4 26.0 - - - -
544A PHE* 3.5 25.6 - + + -
575A GLU* 5.4 1.6 - - - +
579A GLN* 2.7 23.4 + - - +
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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