Contacts of the helix formed by residues 265 - 271 (chain C) in PDB entry 2VZE
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 TRP 265 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219C TYR* 3.9 3.7 + - - -
260C ILE 5.1 2.5 - - - -
261C SER* 3.5 20.2 - - - +
262C ASP* 3.2 22.0 + - + +
263C THR 4.3 0.7 - - - +
264C GLY* 1.3 79.0 - - - +
266C ILE* 1.3 82.4 + - + +
267C LEU* 3.5 34.6 - - + +
268C ASN* 2.9 21.0 + - - +
269C ILE 4.1 0.7 + - - -
311C ALA* 4.5 17.0 - - + -
337C VAL* 3.9 28.0 - - + -
338C GLY* 3.8 20.2 - - - -
364C THR* 5.2 2.5 - - - -
470C GLY* 4.5 17.3 - - - -
471C TYR* 6.4 1.1 - - + -
1571C AMP 3.2 32.0 + - - -
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Residues in contact with ILE 266 (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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219C TYR* 3.6 32.5 - - + -
233C HIS* 3.6 35.9 - - + +
238C LEU* 4.1 9.6 - - + -
264C GLY 3.9 0.4 + - - -
265C TRP* 1.3 86.9 - - + +
267C LEU* 1.3 66.1 + - - +
268C ASN 3.0 1.4 + - - -
269C ILE* 3.0 33.5 + - + +
270C LEU* 3.2 22.5 + - + +
363C GLN 4.9 4.7 - - - +
364C THR* 3.6 32.7 + - + +
367C GLY* 5.4 2.7 - - - -
1571C AMP 4.9 1.3 - - - +
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Residues in contact with LEU 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259C THR* 4.0 7.6 - - + +
260C ILE 4.3 5.2 - - - +
261C SER* 3.9 13.5 - - - +
265C TRP* 3.0 48.9 + - + -
266C ILE* 1.3 84.0 - - - +
268C ASN* 1.3 56.0 + - - +
270C LEU* 4.6 4.7 - - + +
271C CYS* 2.8 63.5 + - + +
272C SER 3.5 0.7 + - - -
309C MET* 3.8 20.6 - - + -
310C GLY* 5.0 3.1 - - - -
337C VAL* 3.7 23.1 - - + -
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Residues in contact with ASN 268 (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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115C ARG* 5.8 0.8 - - - +
119C TRP* 3.1 39.5 - - + -
120C TRP* 3.7 12.6 - - - -
259C THR* 4.9 2.4 + - - +
261C SER* 3.9 23.5 + - - +
262C ASP 3.8 10.5 - - - +
263C THR* 3.7 16.6 - - - +
265C TRP 2.9 14.1 + - - +
267C LEU* 1.3 78.6 - - - +
269C ILE* 1.3 58.5 + - - +
272C SER* 3.0 50.6 + - - -
273C LEU* 3.1 6.8 + - - +
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Residues in contact with ILE 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C TRP* 4.3 7.1 - - + -
123C ILE* 3.8 20.6 - - + -
127C ILE* 5.1 0.2 - - + -
133C PHE* 4.2 11.9 - - + -
219C TYR* 3.2 26.5 - - + +
238C LEU* 4.4 9.4 - - + -
265C TRP 4.1 0.4 + - - -
266C ILE* 3.0 33.3 + - + +
268C ASN* 1.3 80.3 - - - +
270C LEU* 1.3 63.7 + - + +
273C LEU* 3.5 37.5 - - + +
274C MET* 3.0 47.8 + - + +
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Residues in contact with LEU 270 (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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237C SER 5.1 1.8 - - - +
238C LEU* 4.0 39.5 - - + +
241C LYS* 5.6 5.2 - - + +
242C ALA* 4.7 9.2 - - + +
248C TRP* 5.8 0.3 + - - -
266C ILE* 3.2 29.2 + - + +
267C LEU* 4.2 3.6 - - + +
269C ILE* 1.3 85.1 - - + +
271C CYS* 1.3 66.5 + - - +
274C MET* 3.7 8.9 - - - +
275C GLU* 3.1 26.2 + - - +
367C GLY* 4.0 26.5 - - - -
368C LEU* 4.3 10.8 - - + +
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Residues in contact with CYS 271 (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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248C TRP* 3.9 21.5 - - - -
249C THR* 5.3 2.5 - - - -
257C MET* 4.6 6.1 - - + +
259C THR* 3.4 20.1 + - + +
267C LEU* 2.8 45.4 + - + +
270C LEU* 1.3 80.9 - - - +
272C SER* 1.3 59.5 + - - +
273C LEU 3.3 1.6 - - - -
275C GLU* 3.8 8.5 - - + +
276C PRO* 3.0 24.3 - - - +
309C MET* 3.8 19.1 - - + -
368C LEU* 6.0 0.2 - - - -
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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