Contacts of the helix formed by residues 265 - 272 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B TYR* 4.0 3.1 + - - -
260B ILE 5.3 1.6 - - - -
261B SER* 3.5 19.5 - - - +
262B ASP* 3.2 20.3 + - + +
263B THR 4.2 1.2 - - - +
264B GLY* 1.3 79.2 - - - +
266B ILE* 1.3 75.5 + - + +
267B LEU* 3.3 31.9 - - + -
268B ASN* 2.8 27.9 + - - +
269B ILE 4.1 0.9 + - - -
311B ALA* 4.5 13.5 - - + -
337B VAL* 3.8 14.6 - - + -
338B GLY* 3.7 31.9 - - - -
364B THR* 5.0 2.5 - - - -
470B GLY* 4.2 26.6 + - - -
471B TYR* 6.2 2.7 - + + -
1570B AMP 3.0 36.1 + - - -
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Residues in contact with ILE 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B TYR* 3.7 29.7 - - + -
233B HIS* 3.4 22.9 - - + +
238B LEU* 4.2 9.6 - - + -
264B GLY 3.9 0.4 + - - -
265B TRP* 1.3 83.6 - - + +
267B LEU* 1.3 65.9 + - - +
269B ILE* 3.0 38.2 - - + +
270B LEU* 3.1 21.1 + - + +
363B GLN 4.8 4.0 - - - +
364B THR* 3.4 52.9 + - + +
367B GLY* 5.3 1.6 - - - -
1570B AMP 4.7 1.6 - - - +
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Residues in contact with LEU 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B THR* 4.0 12.7 - - + +
260B ILE 4.2 6.5 - - - +
261B SER* 3.8 15.3 - - - +
265B TRP* 3.0 48.3 - - + -
266B ILE* 1.3 82.0 - - - +
268B ASN* 1.3 57.7 + - - +
270B LEU* 4.6 5.4 - - + +
271B CYS* 2.8 54.9 + - + +
309B MET* 4.1 12.1 - - + -
310B GLY* 5.0 3.6 - - - -
337B VAL* 3.6 24.7 - - + -
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Residues in contact with ASN 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B TRP* 3.6 15.7 - - + -
120B TRP* 3.5 25.1 - - - -
259B THR* 4.6 3.8 + - - +
261B SER* 3.9 21.0 + - - +
262B ASP 3.8 9.9 - - - +
263B THR* 3.5 32.6 - - - +
265B TRP 2.8 17.6 + - - +
267B LEU* 1.3 74.6 - - - +
269B ILE* 1.3 58.3 + - - +
272B SER* 3.0 49.0 + - - -
273B LEU* 3.2 5.5 + - - +
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Residues in contact with ILE 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B TRP* 4.4 7.2 - - + -
123B ILE* 3.6 30.5 - - + -
127B ILE* 5.0 0.4 - - + -
133B PHE* 4.2 15.3 - - + -
219B TYR* 3.5 21.3 - - + +
238B LEU* 4.3 11.7 - - + -
265B TRP 4.1 0.6 + - - -
266B ILE* 3.0 36.2 + - + +
268B ASN* 1.3 77.0 - - - +
270B LEU* 1.3 65.6 + - + +
273B LEU* 3.4 24.5 - - + +
274B MET* 3.0 47.5 + - + +
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Residues in contact with LEU 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B SER 5.2 1.8 - - - +
238B LEU* 3.9 38.6 - - + +
241B LYS* 5.8 4.9 - - + -
242B ALA* 4.9 8.7 - - + +
266B ILE* 3.1 28.8 + - + +
267B LEU* 4.2 4.5 - - + +
269B ILE* 1.3 86.5 - - + +
271B CYS* 1.3 67.1 + - - +
274B MET* 3.6 8.2 - - - +
275B GLU* 3.1 26.7 + - - +
367B GLY* 3.8 29.4 - - - -
368B LEU* 4.1 11.7 - - + +
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Residues in contact with CYS 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B TRP* 4.5 16.6 - - - -
249B THR* 5.4 0.4 - - - -
257B MET* 4.3 10.8 - - + +
259B THR* 3.4 19.2 + - + +
267B LEU* 2.8 34.0 + - + +
270B LEU* 1.3 85.5 - - - +
272B SER* 1.3 60.8 + - - +
273B LEU 3.3 1.6 - - - -
275B GLU* 3.7 8.6 - - - +
276B PRO* 3.0 24.8 - - - +
283B THR* 4.8 0.2 + - - -
309B MET* 3.9 20.4 - - + -
368B LEU* 5.7 4.3 - - - -
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Residues in contact with SER 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B TRP* 3.1 24.8 + - - -
259B THR* 3.5 22.6 + - - -
267B LEU 3.6 1.2 + - - -
268B ASN* 3.0 35.2 + - - -
271B CYS* 1.3 80.0 - - - +
273B LEU* 1.3 57.0 + - - +
276B PRO* 3.5 1.8 - - - +
283B THR* 2.5 40.3 + - - +
284B PHE 5.0 1.0 + - - -
285B VAL* 4.5 3.8 - - - +
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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
------------------------------------------------------------
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