Contacts of the helix formed by residues 265 - 274 (chain B) in PDB entry 2VRW
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 THR 265 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257B ALA* 3.5 23.3 + - - +
263B ALA 3.2 0.8 - - - -
264B THR* 1.3 91.0 - - + +
266B LEU* 1.3 66.7 + - - +
267B TYR 3.3 2.7 - - - -
268B GLN* 3.0 44.5 + - - +
269B VAL* 3.4 8.4 + - - +
272B LYS* 6.0 1.6 - - - -
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Residues in contact with LEU 266 (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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199B LEU* 3.7 18.4 - - + -
202B ILE* 4.4 8.5 - - + -
254B LEU* 3.3 33.4 - - + -
257B ALA* 3.9 13.5 - - + +
258B LEU* 3.8 17.7 - - + -
263B ALA 3.2 17.7 + - - +
264B THR 3.4 0.4 - - - -
265B THR* 1.3 77.7 + - - +
267B TYR* 1.3 65.0 + - - +
269B VAL* 3.2 14.6 + - + +
270B PHE* 3.5 24.7 + - + -
343B LEU* 3.7 30.5 - - + -
352B GLU* 6.0 0.9 - - - +
356B LEU* 4.3 9.6 - - + -
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Residues in contact with TYR 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B THR 3.3 24.0 - - - -
266B LEU* 1.3 78.1 - - - +
268B GLN* 1.3 97.6 + - + +
270B PHE* 3.4 6.0 + - - +
271B ILE* 3.1 41.4 + - + +
355B ASN* 3.3 66.8 + - + +
356B LEU* 4.1 12.5 - - + +
358B LEU* 4.2 13.5 - - + -
359B ALA* 3.7 15.5 - - + +
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Residues in contact with GLN 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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265B THR* 3.0 32.7 + - - +
267B TYR* 1.3 116.5 + - + +
269B VAL* 1.3 56.4 + - - +
271B ILE* 3.3 7.0 + - + +
272B LYS* 2.8 52.5 + - - +
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Residues in contact with VAL 269 (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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250B PHE* 3.7 26.5 - - + -
253B GLU* 3.8 19.7 - - + +
254B LEU* 4.0 22.4 - - + +
257B ALA* 3.7 30.3 - - + -
265B THR* 3.7 6.5 - - - +
266B LEU* 3.2 7.5 + - + +
268B GLN* 1.3 76.7 - - - +
270B PHE* 1.3 63.6 + - + +
272B LYS* 3.4 20.6 - - - +
273B TYR* 3.1 27.0 + - + +
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Residues in contact with PHE 270 (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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202B ILE* 4.3 21.5 - - + -
250B PHE* 3.8 29.4 - + - -
254B LEU* 4.3 2.9 - - + -
266B LEU* 3.5 39.3 - - + -
267B TYR 3.4 6.8 + - - +
268B GLN 3.3 0.2 - - - -
269B VAL* 1.3 78.0 - - + +
271B ILE* 1.3 61.6 - - - +
273B TYR* 3.2 2.8 + - - +
274B LYS 3.0 18.7 + - - -
277B PHE* 5.4 0.4 - + - -
336B TYR* 3.8 23.3 - + + -
339B LEU* 6.2 1.6 - - + -
340B LEU* 4.0 34.5 - - + -
359B ALA* 3.9 12.8 - - + -
362B ALA* 5.1 0.2 - - - -
363B MET* 3.7 40.2 - - + +
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Residues in contact with ILE 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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267B TYR* 3.1 43.5 + - + +
268B GLN* 3.8 6.3 - - - +
270B PHE* 1.3 74.7 - - - +
272B LYS* 1.3 63.2 + - - +
273B TYR 3.3 0.7 + - - -
274B LYS* 3.4 21.7 + - + +
275B GLU* 4.8 0.9 + - - +
358B LEU* 3.9 26.7 - - + +
359B ALA* 4.2 12.1 - - - -
362B ALA* 4.2 9.4 - - + -
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Residues in contact with LYS 272 (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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253B GLU* 3.3 26.2 + - - +
265B THR* 5.3 1.8 + - - -
268B GLN* 2.8 35.3 + - - +
269B VAL* 3.4 26.1 - - - +
271B ILE* 1.3 75.1 - - - +
273B TYR* 1.3 64.1 + - + +
274B LYS 3.9 0.2 + - - -
275B GLU* 4.8 2.9 + - - +
276B ARG* 4.1 25.2 + - - +
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Residues in contact with TYR 273 (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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246B VAL* 3.8 32.5 - - + -
249B HIS* 3.4 21.0 - - + +
250B PHE* 3.7 31.6 - + + -
253B GLU* 2.5 42.9 + - + -
269B VAL* 3.1 25.4 + - + +
270B PHE 3.2 1.8 + - - +
272B LYS* 1.3 78.9 - - + +
274B LYS* 1.3 66.4 + - - +
275B GLU 3.3 2.7 - - - -
276B ARG* 3.0 46.2 + - + +
277B PHE* 2.9 42.2 + + + -
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Residues in contact with LYS 274 (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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270B PHE 3.0 11.3 + - - +
271B ILE* 3.4 17.5 + - + +
273B TYR* 1.3 77.5 - - - +
275B GLU* 1.3 65.9 + - + +
277B PHE* 3.3 15.1 + - - +
278B LEU* 3.7 2.6 + - - +
362B ALA* 3.8 33.3 - - + +
363B MET* 4.0 12.3 - - + -
365B ASP* 2.6 37.5 + - - +
366B LEU* 3.6 16.1 - - + +
528B SER* 5.8 0.2 + - - -
533B GLN 4.5 3.4 + - - -
534B MET* 4.0 18.8 - - - +
535B LEU* 3.6 29.0 - - + +
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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