Contacts of the helix formed by residues 570 - 576 (chain A) in PDB entry 4ZTZ
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 PRO 570 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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471A CYS* 3.7 20.6 - - - -
474A LEU* 4.4 12.6 - - + -
490A TRP* 3.6 36.6 - - + -
491A ASP 3.5 13.2 - - - +
568A GLY 4.2 2.0 - - - +
569A HIS* 1.3 93.0 - - + +
571A GLY* 1.3 60.7 + - - +
572A TRP* 3.3 24.2 - - + +
573A TYR* 3.0 5.9 + - + +
574A ARG* 2.9 22.9 + - - +
462B MET* 4.2 7.6 - - + -
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Residues in contact with GLY 571 (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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489A GLU* 3.7 20.6 - - - +
491A ASP* 3.9 8.6 - - - +
570A PRO* 1.3 72.6 - - - +
572A TRP* 1.3 57.1 + - - +
574A ARG* 3.0 28.9 + - - +
575A LYS* 2.9 31.9 + - - +
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Residues in contact with TRP 572 (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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467A ALA* 3.3 33.4 - - + -
470A ALA* 4.5 8.1 - - + -
471A CYS* 4.2 19.5 - - + -
485A LEU* 5.7 4.0 - - + -
488A LEU* 3.3 45.8 - - + -
489A GLU* 3.7 8.0 - - - +
490A TRP* 3.5 24.0 - + - -
570A PRO* 3.4 26.2 - - + +
571A GLY* 1.3 76.0 - - - +
573A TYR* 1.3 66.3 + + + +
575A LYS* 3.9 6.7 + - - +
576A LEU* 3.3 42.1 + - + +
598A VAL* 4.2 22.9 - - + +
602A LEU* 3.5 26.9 - - + -
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Residues in contact with TYR 573 (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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467A ALA* 3.5 22.4 - - + -
468A ASN* 2.4 31.0 + - - -
471A CYS* 4.1 13.5 - - + -
566A LEU* 4.9 2.2 - - + -
569A HIS* 3.7 34.1 - + + -
570A PRO* 3.0 17.1 + - + +
572A TRP* 1.3 101.1 - + - +
574A ARG* 1.3 63.5 + - - +
576A LEU* 3.3 9.4 + - + -
577A CYS* 3.2 40.8 + - - -
588A GLY* 4.6 2.1 - - - -
589A PRO* 3.1 29.2 - - + +
460B THR* 3.2 15.9 - - + +
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Residues in contact with ARG 574 (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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491A ASP* 3.5 28.7 + - - +
493A GLN* 3.3 25.6 - - - +
565A HIS* 3.0 45.7 + - + +
566A LEU* 3.0 35.9 + - + +
567A PRO* 2.7 29.2 + - - +
569A HIS 2.9 15.8 + - - +
570A PRO 2.9 16.3 + - - +
571A GLY* 3.0 29.1 + - - +
573A TYR* 1.3 77.8 - - - +
575A LYS* 1.3 61.8 + - - +
577A CYS 3.1 5.0 + - - +
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Residues in contact with LYS 575 (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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489A GLU* 5.2 10.1 + - - -
571A GLY 2.9 15.0 + - - +
572A TRP* 4.2 6.5 - - - +
574A ARG* 1.3 76.8 - - - +
576A LEU* 1.3 57.7 + - + +
577A CYS 3.1 8.5 + - - +
591A LEU* 4.3 9.9 - - - +
596A MET* 5.2 17.5 - - + +
598A VAL* 6.2 4.3 - - + -
13T C 5.6 2.9 - - - +
14T T 5.0 9.5 + - - -
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Residues in contact with LEU 576 (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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467A ALA* 3.9 28.3 - - + -
572A TRP* 3.3 31.5 + - + +
573A TYR* 3.3 9.6 + - + +
574A ARG 3.1 1.4 - - - -
575A LYS* 1.3 78.1 - - + +
577A CYS* 1.3 57.1 + - - +
589A PRO* 3.2 19.1 - - + +
590A SER 2.8 20.7 - - - +
591A LEU* 4.1 10.8 - - + +
592A LEU* 3.8 26.0 - - + -
596A MET* 3.8 34.8 - - + -
598A VAL* 5.3 7.6 - - + -
599A THR* 4.7 7.6 - - + -
602A LEU* 5.3 0.4 - - + -
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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