Contacts of the helix formed by residues 500 - 509 (chain D) in PDB entry 1ZQ1
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 SER 500 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470D TYR* 3.5 36.3 - - - -
472D LEU* 4.0 10.8 - - - -
489D PHE* 3.5 19.9 - - - -
498D LYS 2.4 8.2 + - - -
499D PRO* 1.3 78.6 - - - +
501D LEU* 1.3 57.9 + - - +
502D ALA 3.3 0.7 - - - -
503D ALA 3.9 1.1 - - - -
504D SER* 2.5 43.9 + - - -
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Residues in contact with LEU 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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472D LEU* 5.1 6.0 - - + +
476D LEU* 5.3 5.4 - - + -
499D PRO* 4.6 3.8 - - + +
500D SER* 1.3 78.2 - - - +
502D ALA* 1.3 57.5 + - - +
504D SER* 4.3 5.2 - - - -
505D ILE* 2.7 40.8 + - + +
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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 30.5 - - + -
499D PRO* 4.1 7.3 - - + +
500D SER 4.1 0.6 - - - +
501D LEU* 1.3 79.2 - - - +
503D ALA* 1.3 53.4 + - - +
505D ILE* 4.1 1.1 - - - +
506D LEU* 2.6 44.7 + - + +
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Residues in contact with ALA 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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489D PHE* 3.6 27.8 - - + +
492D LEU* 4.3 17.9 - - + -
493D VAL 5.1 1.1 - - - +
498D LYS* 3.0 22.2 + - + +
500D SER 3.5 0.6 + - - -
502D ALA* 1.3 76.5 - - - +
504D SER* 1.3 68.4 + - - +
506D LEU* 2.8 20.9 + - - +
507D VAL* 2.8 21.0 + - + +
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Residues in contact with SER 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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472D LEU* 3.4 26.2 - - - -
476D LEU* 3.8 20.6 - - - -
480D LEU* 4.3 12.6 - - - -
489D PHE* 3.8 9.0 - - - -
500D SER 2.5 24.7 + - - -
501D LEU* 4.3 0.9 - - - -
503D ALA* 1.3 71.9 - - - +
505D ILE* 1.3 63.2 + - - +
508D VAL* 3.0 30.4 + - - +
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Residues in contact with ILE 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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476D LEU* 4.1 9.2 - - + +
501D LEU* 2.7 29.5 + - + +
502D ALA* 4.1 1.6 - - - +
504D SER* 1.3 72.7 - - - +
506D LEU* 1.3 66.0 + - + +
509D VAL* 2.9 39.1 + - + +
510D LEU* 2.9 2.2 + - - -
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Residues in contact with LEU 506 (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* 5.2 3.8 - - + -
502D ALA* 2.6 36.3 + - + +
503D ALA* 2.8 13.3 + - - +
505D ILE* 1.3 70.6 - - + +
507D VAL* 1.3 64.6 + - + +
510D LEU* 2.7 46.3 + - + +
511D LYS 3.0 3.2 + - - -
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Residues in contact with VAL 507 (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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480D LEU* 4.0 11.7 - - + -
485D ARG* 3.7 29.2 - - + -
488D LEU* 5.2 13.9 - - + -
489D PHE* 5.4 5.4 - - - +
492D LEU* 6.2 2.0 - - + -
503D ALA* 2.8 24.9 + - + +
504D SER 4.1 1.1 - - - +
506D LEU* 1.3 79.3 - - + +
508D VAL* 1.3 66.8 + - - +
509D VAL 3.1 0.3 + - - -
511D LYS* 3.1 26.1 - - + +
512D GLY 4.2 0.2 + - - -
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Residues in contact with VAL 508 (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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476D LEU* 4.2 23.3 - - + +
479D THR* 3.5 34.1 - - + +
480D LEU* 4.7 8.5 - - + -
504D SER 3.0 15.4 + - - +
507D VAL* 1.3 79.7 - - - +
509D VAL* 1.3 60.6 + - - +
512D GLY* 4.8 5.5 + - - -
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Residues in contact with VAL 509 (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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476D LEU* 3.8 25.8 - - + -
505D ILE* 2.9 25.9 + - + +
508D VAL* 1.3 79.9 - - - +
510D LEU* 1.3 69.4 + - - +
511D LYS 3.4 0.7 - - - -
512D GLY* 3.1 17.2 + - - -
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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