Contacts of the helix formed by residues 296 - 305 (chain A) in PDB entry 2VR1
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 GLU 296 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211A GLU* 2.7 35.1 - - - +
228A ARG* 3.3 12.2 - - - +
230A CYS* 4.2 0.9 - - - -
238A LYS* 3.5 24.5 + - - +
241A GLU* 3.4 24.2 - - + -
294A GLN* 3.1 16.6 + - - +
295A VAL* 1.3 78.8 + - - +
297A HIS* 1.3 60.8 + - - +
298A PRO* 3.3 3.1 - - - -
299A VAL* 3.3 20.5 - - - +
336A GLU* 3.2 22.0 - - - +
338A ARG* 3.3 16.6 + - - -
1447A CL 4.1 3.1 - - - +
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Residues in contact with HIS 297 (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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13A ILE* 4.1 12.3 - - + -
16A ARG* 3.2 35.8 + - + +
213A GLN* 4.6 1.1 - - - +
228A ARG* 3.6 13.4 - - - +
293A ILE* 3.8 21.3 - - + +
294A GLN* 2.8 27.5 + - - +
295A VAL 3.8 0.4 + - - -
296A GLU* 1.3 75.0 - - - +
298A PRO* 1.3 85.0 - - + +
299A VAL 3.1 1.0 + - - -
300A THR* 3.2 13.7 + - - -
301A GLU* 3.2 37.0 + - + +
308A LEU* 3.8 15.2 - - + +
309A ILE* 4.0 8.2 - - + +
387A LYS* 3.8 14.6 - - - -
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Residues in contact with PRO 298 (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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295A VAL 3.4 8.1 - - - +
296A GLU 3.3 5.8 - - - -
297A HIS* 1.3 108.7 - - + +
299A VAL* 1.3 60.8 + - - +
301A GLU* 3.2 13.4 + - - +
302A MET* 3.1 28.3 + - - +
336A GLU* 3.7 7.9 - - - +
366A ARG* 3.6 22.5 + - - +
368A GLU* 4.6 2.2 - - + -
387A LYS* 3.7 20.6 - - - +
389A ILE* 3.8 22.2 - - + -
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Residues in contact with VAL 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A ARG* 3.4 24.0 - - + -
241A GLU* 3.9 9.9 - - + +
242A GLU* 4.4 4.0 - - - +
243A ALA* 3.8 17.3 - - + +
296A GLU 3.3 18.5 + - - +
298A PRO* 1.3 73.4 - - - +
300A THR* 1.3 69.8 + - - +
302A MET* 3.2 13.4 + - - +
303A ILE* 3.4 17.7 + - - +
334A ALA* 3.9 13.5 - - + +
335A VAL 4.1 5.2 - - - -
336A GLU* 3.6 40.6 - - + +
389A ILE* 4.2 6.3 - - + -
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Residues in contact with THR 300 (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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213A GLN* 4.2 11.3 - - + +
225A LEU* 3.2 42.3 + - + +
227A GLU 4.9 1.0 + - - -
228A ARG* 2.8 43.5 + - - +
243A ALA* 4.6 2.8 - - - +
297A HIS 3.2 5.2 + - - -
299A VAL* 1.3 80.6 - - - +
301A GLU* 1.3 54.5 + - - +
303A ILE* 3.5 7.9 - - + +
304A THR* 2.7 38.6 + - + +
308A LEU* 4.3 7.4 - - + -
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Residues in contact with GLU 301 (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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16A ARG* 2.9 19.4 + - - -
297A HIS* 3.2 26.6 + - - +
298A PRO* 3.4 9.9 - - - +
299A VAL 3.1 0.6 - - - -
300A THR* 1.3 77.7 - - - +
302A MET* 1.3 56.5 + - - +
304A THR* 3.8 0.2 - - - -
305A GLY* 2.9 32.1 + - - -
306A VAL 3.2 21.5 - - - +
307A ASP* 3.6 3.1 - - - -
308A LEU* 2.8 32.5 + - + +
366A ARG* 2.8 37.9 + - - +
363B PHE* 3.5 14.3 - - + -
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Residues in contact with MET 302 (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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298A PRO 3.1 15.1 + - - +
299A VAL 3.2 0.8 + - - +
301A GLU* 1.3 77.3 - - - +
303A ILE* 1.3 59.4 + - - +
304A THR 3.8 0.2 + - - -
305A GLY* 4.5 2.6 + - - -
331A ARG 4.4 0.2 - - - +
334A ALA* 3.7 20.4 - - + -
364A GLY* 4.1 14.4 - - - +
365A VAL 5.3 0.2 - - - -
366A ARG* 3.7 46.0 - - + -
389A ILE* 3.8 17.3 - - + -
391A TYR* 3.4 44.6 - - + +
363B PHE* 4.1 14.1 - - - -
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Residues in contact with ILE 303 (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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226A ALA* 4.2 20.6 - - + -
227A GLU 4.7 0.2 - - - +
243A ALA* 3.5 40.6 - - + +
244A PRO* 3.8 14.4 - - + -
299A VAL 3.6 10.1 - - - +
300A THR* 3.5 16.4 - - - +
302A MET* 1.3 79.0 - - - +
304A THR* 1.3 59.9 + - + +
329A HIS 3.1 5.7 - - - +
330A VAL* 3.6 13.7 - - + -
331A ARG* 2.9 45.6 + - - +
332A GLY 3.9 2.2 - - - +
333A HIS* 3.7 20.4 - - - +
334A ALA* 3.7 6.3 - - + +
391A TYR* 4.3 0.4 - - + -
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Residues in contact with THR 304 (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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225A LEU* 4.3 17.5 - - + +
226A ALA* 5.1 2.2 - - + -
300A THR* 2.7 37.8 + - + +
301A GLU* 3.5 1.6 + - - -
303A ILE* 1.3 89.1 - - + +
305A GLY* 1.3 60.8 + - - +
306A VAL* 3.1 31.4 + - - +
308A LEU* 6.2 0.2 - - - +
327A GLU 5.8 0.3 - - - +
328A VAL* 4.3 17.0 - - + -
329A HIS 3.8 14.5 + - - +
330A VAL* 5.4 0.7 - - - -
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Residues in contact with GLY 305 (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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301A GLU 2.9 13.5 + - - -
302A MET 4.4 3.1 + - - -
303A ILE 3.8 0.4 - - - -
304A THR* 1.3 77.0 - - - +
306A VAL* 1.3 61.1 + - - +
307A ASP* 3.8 2.1 + - - +
363B PHE* 4.0 15.5 - - - -
391B TYR* 6.0 6.4 - - - -
393B GLU* 4.7 16.5 - - - +
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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