Contacts of the helix formed by residues 496 - 505 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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458D LYS* 3.9 37.7 - - + +
461D ILE* 3.8 38.4 - - + -
462D THR* 5.0 3.1 - - - +
465D GLN* 5.2 2.9 - - - +
491D MET* 2.8 19.2 + - - +
494D ALA* 3.6 29.4 - - + +
495D LYS* 1.3 68.0 - - - +
497D HIS* 1.3 58.5 + - - +
498D LYS 3.3 3.1 - - - -
499D GLU* 3.3 47.5 + - + +
500D LEU* 2.9 28.6 + - - +
532D ILE* 4.5 0.6 - - - +
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Residues in contact with HIS 497 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495D LYS* 3.1 14.2 + - - +
496D MET* 1.3 71.6 - - - +
498D LYS* 1.3 88.4 + - + +
500D LEU* 3.9 2.2 - - - +
501D CYS* 3.0 32.2 + - - -
532D ILE* 4.0 28.3 + - + +
533D LEU* 3.8 21.1 - - + -
534D ASP* 5.4 10.3 + - + -
537D ASP* 4.8 10.8 - - - -
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Residues in contact with LYS 498 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496D MET 3.3 0.2 - - - -
497D HIS* 1.3 98.1 - - + +
499D GLU* 1.3 68.4 + - - +
501D CYS* 3.7 5.1 - - - +
502D ALA* 3.0 28.8 + - - +
537D ASP* 6.1 0.2 - - - -
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Residues in contact with GLU 499 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458D LYS* 5.5 1.2 - - - -
465D GLN* 3.8 22.9 - - - +
491D MET* 3.5 21.7 - - + +
496D MET* 3.3 49.0 + - + +
498D LYS* 1.3 87.5 - - - +
500D LEU* 1.3 57.1 + - - +
502D ALA* 3.3 6.7 + - - +
503D LEU* 2.9 28.6 + - - +
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Residues in contact with LEU 500 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488D ALA* 3.5 45.5 - - + +
491D MET* 3.7 15.4 - - + -
492D ALA* 4.2 2.0 - - + +
496D MET 2.9 16.1 + - - +
497D HIS* 3.9 5.8 - - - +
498D LYS 3.3 0.2 - - - -
499D GLU* 1.3 73.9 - - - +
501D CYS* 1.3 60.5 + - - +
503D LEU* 3.4 0.7 + - - +
504D MET* 2.9 45.8 + - + +
529D TYR* 3.9 28.9 - - + +
532D ILE* 3.9 23.1 - - + -
533D LEU* 4.6 11.0 - - + -
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Residues in contact with CYS 501 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497D HIS 3.0 25.1 + - - +
498D LYS* 3.7 5.4 - - - +
499D GLU 3.3 0.2 - - - -
500D LEU* 1.3 77.7 - - - +
502D ALA* 1.3 57.1 + - - +
505D PHE* 2.8 73.4 + - + +
533D LEU* 3.5 24.7 - - - -
537D ASP* 3.6 19.5 - - - +
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Residues in contact with ALA 502 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498D LYS 3.0 17.1 + - - +
499D GLU* 3.3 7.8 + - - +
501D CYS* 1.3 77.2 - - - +
503D LEU* 1.3 61.6 + - - +
505D PHE 4.9 1.7 - - - +
506D SER* 4.1 11.1 + - - -
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Residues in contact with LEU 503 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470D PRO* 3.6 39.0 - - + -
487D LEU* 3.8 28.3 - - + -
488D ALA* 4.2 17.7 - - + +
491D MET* 3.9 22.9 - - + -
499D GLU 2.9 16.4 + - - +
500D LEU 3.7 2.7 - - - +
502D ALA* 1.3 77.8 - - - +
504D MET* 1.3 63.4 + - + +
506D SER* 3.3 10.0 - - - -
509D TRP* 3.2 52.0 - - + +
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Residues in contact with MET 504 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488D ALA* 4.0 9.0 - - + -
500D LEU* 2.9 44.1 + - + +
503D LEU* 1.3 87.0 - - + +
505D PHE* 1.3 63.3 + - + +
506D SER 2.9 15.9 + - - +
509D TRP* 4.1 12.2 - - - +
510D ILE* 4.5 4.3 - - - +
522D LEU* 3.9 11.0 - - + -
525D GLU* 3.6 30.7 - - + +
526D PHE* 3.5 58.3 - - + +
529D TYR* 4.5 4.7 - - - -
544D PHE* 3.9 4.5 - - - -
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Residues in contact with PHE 505 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501D CYS* 2.8 56.1 + - + +
502D ALA* 4.9 1.6 - - - +
504D MET* 1.3 81.9 - - + +
506D SER* 1.3 53.9 + - - +
526D PHE* 3.8 15.5 - + - -
533D LEU* 4.2 4.9 - - + -
537D ASP* 3.3 34.1 - - - -
540D VAL* 3.3 25.6 - - + -
541D SER* 3.4 27.4 - - - -
544D PHE* 3.4 21.1 - + + -
575D GLU* 5.0 2.0 - - - +
579D GLN* 2.6 25.2 + - - +
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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