Contacts of the helix formed by residues 259 - 270 (chain A) in PDB entry 2VQQ
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 GLY 259 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257A PRO 3.7 1.2 + - - -
258A MET* 1.3 75.4 - - - +
260A ASP* 1.3 66.8 + - - -
261A ALA 3.3 2.2 - - - -
262A GLU* 2.8 23.1 + - - +
263A TYR* 3.2 10.0 + - - -
303A ASN* 3.4 15.9 - - - -
304A LEU* 3.3 18.2 - - - +
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Residues in contact with ASP 260 (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 GLY* 1.3 70.3 - - - -
261A ALA* 1.3 58.6 + - - +
262A GLU 3.2 0.2 + - - -
263A TYR* 3.2 1.9 + - - +
264A LEU* 2.9 36.7 + - + +
303A ASN 4.7 2.1 + - - -
304A LEU* 3.3 7.7 - - - +
305A SER* 2.6 49.6 + - - -
308A CYS* 3.2 25.7 - - - +
356A LEU* 4.4 5.0 - - + +
357A PRO* 5.6 0.7 - - - +
360A VAL* 3.6 32.3 - - + +
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Residues in contact with ALA 261 (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 GLY 3.3 0.6 - - - -
260A ASP* 1.3 77.9 - - - +
262A GLU* 1.3 59.5 + - - +
264A LEU* 4.0 6.5 - - - +
265A ALA* 3.0 30.1 + - - +
360A VAL* 4.2 11.4 - - + +
363A GLN* 3.6 60.2 + - + +
365A PRO* 3.9 7.2 - - + +
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Residues in contact with GLU 262 (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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250A PHE* 4.1 6.5 - - + -
257A PRO 4.6 0.8 - - - +
258A MET* 3.8 12.3 - - + -
259A GLY* 2.8 37.1 + - - +
261A ALA* 1.3 78.2 + - - +
263A TYR* 1.3 60.9 + - + +
265A ALA* 3.5 3.5 + - - +
266A ALA* 3.0 26.5 + - - +
363A GLN* 3.2 22.1 + - - -
365A PRO* 3.5 8.3 - - + +
366A ASN* 2.9 43.1 + - - +
369A ALA* 3.3 31.2 - - + -
373A MET* 4.4 3.5 - - - +
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Residues in contact with TYR 263 (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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195A TRP* 4.8 14.3 + - + -
197A VAL* 4.3 6.2 - - - +
218A LEU* 4.0 31.5 + - + -
219A HIS* 4.6 8.0 + - - -
250A PHE* 3.5 26.8 - + - -
258A MET* 4.0 7.4 - - + -
259A GLY 3.2 6.0 + - - -
260A ASP 4.0 2.5 - - - +
262A GLU* 1.3 75.6 - - - +
264A LEU* 1.3 61.7 + - - +
266A ALA* 3.1 6.2 + - - +
267A PHE* 2.9 34.3 + - - +
291A ALA* 4.2 10.9 - - + +
302A TYR* 3.5 32.0 - + - -
304A LEU* 3.7 47.1 - - + -
308A CYS* 4.9 1.1 - - - -
309A PHE* 5.6 2.0 - + - -
312A LEU* 4.5 18.6 - - + -
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Residues in contact with LEU 264 (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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260A ASP* 2.9 23.9 + - + +
261A ALA* 4.0 5.6 - - - +
263A TYR* 1.3 74.3 - - - +
265A ALA* 1.3 57.7 + - - +
267A PHE* 3.3 7.2 + - - +
268A ARG* 2.9 28.0 + - - +
308A CYS* 4.1 11.2 - - - -
311A TYR* 4.8 8.3 - - + -
312A LEU* 4.0 21.1 - - + -
315A GLN* 4.2 13.8 + - - +
356A LEU* 3.6 30.5 - - + -
360A VAL* 4.0 17.0 - - + +
398A LEU* 3.7 36.2 - - + +
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Residues in contact with ALA 265 (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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261A ALA 3.0 20.1 + - - +
262A GLU 3.7 4.7 - - - +
264A LEU* 1.3 77.0 - - - +
266A ALA* 1.3 55.1 + - - +
268A ARG* 3.3 17.1 + - - +
269A THR* 2.8 35.0 + - - +
365A PRO* 3.4 25.1 - - + -
373A MET* 3.6 12.8 - - + -
394A ALA 4.1 5.2 - - - +
396A ARG 4.9 0.9 - - - +
398A LEU* 5.2 1.5 - - - +
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Residues in contact with ALA 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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218A LEU* 4.1 7.9 - - + -
248A MET* 4.0 21.3 - - + -
250A PHE* 4.0 21.1 - - + -
262A GLU 3.0 15.5 + - - +
263A TYR 3.1 8.2 + - - +
265A ALA* 1.3 76.1 - - - +
267A PHE* 1.3 56.7 + - - +
269A THR* 3.9 1.3 - - - -
270A VAL* 3.0 27.0 + - - +
271A VAL* 3.1 10.8 + - - +
373A MET* 3.6 12.0 - - - -
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Residues in contact with PHE 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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193A VAL* 4.6 3.4 - - + -
195A TRP* 4.1 21.1 - + - -
218A LEU* 4.0 27.4 - - + -
263A TYR 2.9 13.2 + - - +
264A LEU 3.3 8.5 + - - +
266A ALA* 1.3 73.8 - - - +
268A ARG* 1.3 64.8 + - - +
271A VAL* 3.9 22.0 - - + -
272A MET* 2.9 45.2 + - + +
273A PRO* 3.5 0.7 - - - +
312A LEU* 3.7 44.6 - - + -
315A GLN* 3.8 32.1 - - + +
316A LEU* 3.7 26.2 - - + -
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Residues in contact with ARG 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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264A LEU 2.9 16.2 + - - +
265A ALA* 3.3 11.7 + - - +
267A PHE* 1.3 78.4 - - - +
269A THR* 1.3 67.5 + - - +
272A MET* 5.1 1.9 - - - +
273A PRO* 3.1 20.6 - - - +
315A GLN* 5.0 3.3 + - - +
393A THR* 2.9 46.3 + - - -
394A ALA* 3.8 11.5 + - - +
396A ARG 3.3 19.8 + - - -
397A SER 4.8 0.4 + - - -
398A LEU* 4.0 22.5 - - + +
401A ALA* 3.5 33.3 - - - +
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Residues in contact with THR 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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265A ALA 2.8 20.6 + - - +
266A ALA 3.8 0.2 + - - -
268A ARG* 1.3 104.3 - - - +
270A VAL* 1.3 67.9 + - - +
273A PRO* 3.5 12.3 - - - +
373A MET* 3.5 14.7 - - - +
377A MET* 3.9 18.5 - - - +
387A LEU* 3.7 21.5 - - - +
393A THR* 4.7 2.9 - - - +
394A ALA* 3.9 23.3 - - + +
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Residues in contact with VAL 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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216A MET* 4.5 0.9 - - + -
246A VAL* 4.0 18.8 - - + -
248A MET* 3.9 29.6 - - + -
266A ALA 3.0 7.8 + - - +
269A THR* 1.3 91.2 - - - +
271A VAL* 1.3 70.3 + - + +
272A MET 3.6 0.7 - - - -
273A PRO* 3.7 1.6 - - - -
274A ILE* 3.3 39.4 + - + +
373A MET* 4.3 5.6 - - + +
376A VAL* 3.8 24.5 - - + -
377A MET* 3.9 20.2 - - + -
387A LEU* 5.4 1.3 - - + -
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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