Contacts of the helix formed by residues 265 - 271 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219A TYR* 3.9 4.2 + - - -
260A ILE 5.4 1.8 - - - -
261A SER* 3.7 11.2 - - - +
262A ASP* 3.2 21.6 + - + +
263A THR 4.2 0.9 - - - +
264A GLY* 1.3 78.5 - - - +
266A ILE* 1.3 73.9 + - + +
267A LEU* 3.3 40.4 - - + -
268A ASN* 2.9 27.5 + - - +
269A ILE 4.1 0.7 + - - -
311A ALA* 4.4 15.9 - - + -
337A VAL* 3.8 13.9 - - + -
338A GLY* 3.6 33.2 - - - -
364A THR* 5.1 2.0 - - - -
470A GLY* 4.3 22.7 - - - -
471A TYR* 6.2 1.1 - - + -
1570A AMP 2.9 39.2 + - - -
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Residues in contact with ILE 266 (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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219A TYR* 3.6 33.8 - - + -
233A HIS* 3.5 22.2 - - + +
238A LEU* 4.1 8.7 - - + -
264A GLY 3.8 0.4 + - - -
265A TRP* 1.3 86.5 - - + +
267A LEU* 1.3 66.0 + - + +
269A ILE* 3.0 20.6 + - + +
270A LEU* 3.1 29.4 + - + +
363A GLN 4.9 3.4 - - - +
364A THR* 3.5 49.6 + - + +
367A GLY* 5.2 0.9 - - - -
1570A AMP 4.6 1.8 - - - +
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Residues in contact with LEU 267 (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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259A THR* 4.0 8.4 - - + +
260A ILE 4.4 6.1 - - - +
261A SER* 3.9 12.8 - - - +
265A TRP* 3.0 49.1 - - + -
266A ILE* 1.3 83.5 - - + +
268A ASN* 1.3 56.9 + - - +
270A LEU* 4.6 4.0 - - + +
271A CYS* 2.9 55.6 + - + +
272A SER 3.6 0.9 + - - -
309A MET* 4.0 16.2 - - + -
310A GLY* 5.1 3.6 - - - -
311A ALA 5.1 0.2 - - - +
337A VAL* 3.8 24.0 - - + -
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Residues in contact with ASN 268 (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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115A ARG* 6.2 0.4 - - - +
119A TRP* 3.1 38.5 - - + -
120A TRP* 3.6 14.1 - - - -
259A THR* 4.9 3.4 + - - +
261A SER* 3.8 21.3 + - - +
262A ASP 3.8 11.2 - - - +
263A THR* 3.8 14.8 - - - +
265A TRP 2.9 14.4 + - - +
267A LEU* 1.3 80.3 - - - +
269A ILE* 1.3 60.9 + - - +
272A SER* 3.0 47.6 + - - -
273A LEU* 3.2 6.2 + - - +
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Residues in contact with ILE 269 (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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119A TRP* 4.2 7.7 - - + -
123A ILE* 3.4 33.4 - - + -
127A ILE* 4.8 1.6 - - + -
133A PHE* 4.1 15.5 - - + -
219A TYR* 3.5 21.3 - - + +
238A LEU* 4.2 13.2 - - + -
265A TRP 4.1 0.6 + - - -
266A ILE* 3.0 25.8 + - + +
268A ASN* 1.3 76.6 - - - +
270A LEU* 1.3 69.5 + - + +
273A LEU* 3.4 24.6 - - + +
274A MET* 3.0 47.5 + - + +
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Residues in contact with LEU 270 (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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237A SER 5.1 1.8 - - - +
238A LEU* 4.0 36.6 - - + +
241A LYS* 5.6 5.6 - - + -
242A ALA* 4.8 8.8 - - + +
266A ILE* 3.1 34.4 + - + +
267A LEU* 4.2 4.0 - - + +
269A ILE* 1.3 87.8 - - + +
271A CYS* 1.3 66.7 + - - +
274A MET* 3.7 8.4 + - - +
275A GLU* 3.0 26.3 + - - +
367A GLY* 3.9 28.3 - - - -
368A LEU* 4.5 10.1 - - + +
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Residues in contact with CYS 271 (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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248A TRP* 4.5 17.0 - - - -
249A THR* 5.4 0.4 - - - -
257A MET* 4.2 10.4 - - + +
259A THR* 3.2 24.8 + - + +
267A LEU* 2.9 32.9 + - + +
270A LEU* 1.3 85.2 - - - +
272A SER* 1.3 58.5 + - - +
273A LEU 3.3 1.1 - - - -
275A GLU* 3.9 7.7 - - - +
276A PRO* 3.0 23.8 - - - +
283A THR* 4.6 0.3 + - - -
309A MET* 4.0 19.3 - - + -
368A LEU* 5.2 5.2 - - - -
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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