Contacts of the helix formed by residues 305 - 309 (chain C) in PDB entry 2ZV6
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 VAL 305 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A LYS* 4.0 17.7 - - + -
201A TRP* 3.4 28.0 - - + -
207A TYR* 4.5 17.5 - - + +
52C GLN* 3.3 15.9 + - - +
300C ARG* 4.3 19.4 + - + +
303C GLY 4.3 1.3 - - - +
304C MET* 1.3 73.9 - - - +
306C ASP* 1.3 67.4 + - - +
307C ILE 3.4 0.7 - - - -
308C PHE* 3.0 18.2 + - - +
309C ASN* 3.2 25.8 - - - +
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Residues in contact with ASP 306 (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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199A LYS* 2.6 33.4 + - - +
48C ASN* 3.3 29.6 - - - +
49C THR* 3.7 18.2 - - - +
52C GLN* 2.9 30.4 + - - +
305C VAL* 1.3 71.9 - - - +
307C ILE* 1.3 54.0 + - - +
308C PHE 2.7 10.9 + - - -
309C ASN* 2.4 33.8 + - - +
311C ASP* 3.3 21.3 - - - +
312C ALA* 3.3 5.1 + - - +
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Residues in contact with ILE 307 (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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41C VAL* 4.4 14.8 - - + -
49C THR* 3.3 42.8 - - + +
52C GLN* 3.7 20.0 - - + -
53C ILE* 4.0 20.9 - - + -
304C MET* 4.0 13.5 - - + +
306C ASP* 1.3 71.1 - - + +
308C PHE* 1.3 83.5 + - + +
309C ASN 3.5 0.4 - - - -
312C ALA* 3.7 9.4 - - - +
314C LEU* 4.5 11.2 - - + -
324C VAL* 3.8 2.6 - - - +
325C LEU* 3.0 39.4 + - + +
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Residues in contact with PHE 308 (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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296C LYS* 3.5 50.3 + - + +
299C LEU* 4.1 12.1 - - + -
300C ARG* 3.9 33.2 + - + +
304C MET* 3.1 57.7 - - + -
305C VAL 3.0 6.7 + - - +
306C ASP 2.7 7.5 + - - -
307C ILE* 1.3 87.3 - - + +
309C ASN* 1.3 57.4 + - - +
324C VAL* 4.6 5.9 - - - +
325C LEU* 3.6 25.1 - - + +
327C GLY 4.6 2.2 - - - -
328C VAL* 4.2 20.9 - - + -
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Residues in contact with ASN 309 (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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199A LYS* 4.7 3.8 - - - +
207A TYR* 5.5 1.2 + - - -
300C ARG* 5.8 1.8 - - - +
305C VAL* 3.2 32.2 + - - +
306C ASP* 2.4 35.5 + - - +
308C PHE* 1.3 81.4 - - - +
310C GLY* 1.3 55.5 + - - +
311C ASP* 2.8 29.6 + - - +
312C ALA 2.9 14.2 + - - -
324C VAL* 2.9 17.4 - - - +
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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