Contacts of the helix formed by residues 364 - 369 (chain C) in PDB entry 6ZGI
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 ASP 364 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335C LEU* 3.7 17.6 - - + +
338C PHE* 3.5 7.6 - - - -
362C VAL* 3.2 12.1 + - + -
363C ALA* 1.3 71.7 - - - +
365C TYR* 1.3 62.2 + - - +
366C SER* 3.0 24.0 + - - -
367C VAL* 3.5 26.1 - - - +
527C PRO* 4.0 26.5 - - + +
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Residues in contact with TYR 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415B THR* 3.2 27.0 + - + -
420B ASP* 5.2 0.5 + - - -
338C PHE* 3.8 23.6 - - + -
363C ALA* 3.4 11.0 + - + -
364C ASP* 1.3 71.0 + - - +
366C SER* 1.3 59.5 + - - +
367C VAL* 3.0 6.1 - - - -
368C LEU* 2.9 34.4 + - + +
369C TYR* 3.7 29.6 + + - -
377C PHE* 6.4 0.9 - + - -
384C PRO 4.1 11.3 + - - -
387C LEU* 4.3 26.1 - - + +
388C ASN* 3.4 30.2 + - - -
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Residues in contact with SER 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B TYR* 4.6 8.1 - - - -
364C ASP* 3.0 19.6 + - - -
365C TYR* 1.3 79.5 - - - +
367C VAL* 1.3 62.3 + - - +
368C LEU 3.1 0.9 - - - -
369C TYR* 3.2 49.3 + - - +
370C ASN* 4.6 2.1 - - - +
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Residues in contact with VAL 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C LEU* 4.3 22.2 - - + -
338C PHE* 3.9 28.3 - - + -
364C ASP* 3.5 29.6 - - - +
365C TYR 3.0 1.7 - - - +
366C SER* 1.3 79.5 + - - +
368C LEU* 1.3 60.4 + - + +
369C TYR 3.3 0.4 - - - -
370C ASN* 3.0 18.6 - - - +
371C SER* 4.4 4.9 + - - -
1312C NAG 5.5 0.7 - - - +
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Residues in contact with LEU 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338C PHE* 4.0 45.8 - - + +
342C PHE* 4.3 28.5 - - + -
365C TYR* 2.9 22.7 + - + +
367C VAL* 1.3 79.1 - - + +
369C TYR* 1.3 64.9 + - + +
370C ASN 3.4 0.9 - - - -
371C SER* 4.1 6.7 - - - +
372C ALA* 3.2 38.7 + - + +
374C PHE* 4.2 23.0 - - + -
1312C NAG 6.0 1.1 - - - +
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Residues in contact with TYR 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B GLY* 3.6 11.6 - - - -
417B LYS* 3.8 52.3 - - + -
420B ASP* 3.1 21.2 + - - -
421B TYR* 4.0 27.4 - + - -
455B LEU* 4.1 16.4 - - + -
365C TYR* 3.7 27.7 - + - -
366C SER* 3.2 41.4 + - - +
367C VAL 3.3 0.4 - - - -
368C LEU* 1.3 80.8 - - + +
370C ASN* 1.3 61.0 + - + +
371C SER 3.3 1.8 + - - -
372C ALA 3.9 10.4 - - - +
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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
------------------------------------------------------------
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