Contacts of the helix formed by residues 292 - 303 (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 ASP 292 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A LEU* 4.6 4.9 - - - +
290A LYS* 4.2 11.0 - - + +
291A PHE* 1.3 77.0 - - - +
293A PRO* 1.3 72.8 - - - +
294A LEU* 2.8 24.7 + - - +
295A VAL* 3.0 35.3 + - + +
296A ILE* 3.1 14.7 + - - +
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Residues in contact with PRO 293 (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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291A PHE 3.5 2.0 - - - +
292A ASP* 1.3 89.3 - - - +
294A LEU* 1.3 56.9 + - - +
296A ILE* 3.2 11.8 + - + +
297A LEU* 2.9 28.8 + - - +
317A MET* 3.3 48.2 - - + +
318A LEU* 3.6 5.4 - - + +
321A GLN* 3.7 30.5 - - + +
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Residues in contact with LEU 294 (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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292A ASP* 2.8 20.0 + - - +
293A PRO* 1.3 74.6 - - - +
295A VAL* 1.3 56.4 + - + +
297A LEU* 3.4 12.0 + - + -
298A LYS* 3.0 55.3 + - + +
321A GLN* 3.5 25.1 - - + +
326A TYR* 4.1 19.1 - - + -
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Residues in contact with VAL 295 (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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74A GLY* 5.6 1.6 - - - -
286A HIS* 3.4 36.6 - - + +
288A LEU* 3.7 11.0 - - + -
289A PRO* 6.4 0.2 - - + -
292A ASP* 3.0 32.1 + - + +
294A LEU* 1.3 75.1 - - + +
296A ILE* 1.3 60.7 + - - +
298A LYS* 3.3 9.3 + - + +
299A THR* 2.6 33.8 + - - +
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Residues in contact with ILE 296 (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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258A TRP* 3.7 23.7 - - + -
260A ILE* 4.1 14.8 - - + -
288A LEU* 4.0 29.8 - - + -
291A PHE* 4.8 14.1 - - + -
292A ASP 3.1 13.2 + - - +
293A PRO* 3.4 15.3 - - + +
295A VAL* 1.3 79.6 - - - +
297A LEU* 1.3 56.4 + - - +
299A THR* 3.3 2.9 + - - -
300A LEU* 3.0 31.9 + - + +
314A VAL* 4.3 18.2 - - + +
317A MET* 4.9 4.7 - - + -
318A LEU* 3.5 27.4 - - + -
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Residues in contact with LEU 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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293A PRO 2.9 16.9 + - - +
294A LEU* 3.6 12.1 - - + +
295A VAL 3.2 0.2 - - - -
296A ILE* 1.3 78.0 - - - +
298A LYS* 1.3 61.4 + - - +
300A LEU* 3.4 7.6 + - + +
301A SER* 3.0 23.9 + - - -
318A LEU* 4.2 18.4 - - + +
321A GLN* 4.2 13.7 - - + -
322A ASP* 3.6 28.9 - - + +
323A LEU* 3.2 28.5 - - + -
326A TYR* 3.7 26.7 - - + +
328A PHE* 3.9 19.6 - - + -
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Residues in contact with LYS 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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294A LEU* 3.0 47.5 + - + +
295A VAL* 3.9 7.9 - - + +
297A LEU* 1.3 76.3 - - - +
299A THR* 1.3 57.0 + - - +
301A SER* 3.4 6.3 + - - -
302A SER* 2.6 40.0 + - - +
326A TYR* 3.5 41.0 + - + -
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Residues in contact with THR 299 (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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258A TRP* 3.6 25.1 - - + -
284A PHE* 3.6 28.5 - - + -
286A HIS* 3.3 24.7 + - + -
295A VAL* 2.6 22.8 + - - +
296A ILE 3.4 5.2 - - - -
298A LYS* 1.3 74.4 - - - +
300A LEU* 1.3 64.8 + - - +
303A TYR* 3.1 41.9 + - + +
305A ILE* 4.5 1.8 - - + +
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Residues in contact with LEU 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A TRP* 3.6 24.7 - - + -
296A ILE* 3.0 19.5 + - + +
297A LEU* 3.6 9.0 - - - +
299A THR* 1.3 75.8 - - - +
301A SER* 1.3 53.2 + - - +
303A TYR 3.3 4.0 - - - +
305A ILE* 4.5 17.1 - - + +
308A MET* 4.0 33.4 - - + -
318A LEU* 4.1 21.1 - - + -
328A PHE* 3.6 31.8 - - + +
330A HIS* 2.7 32.7 + - - -
331A LEU* 4.5 14.1 - - + +
349A TRP* 5.0 0.7 - - + -
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Residues in contact with SER 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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297A LEU 3.0 17.4 + - - -
298A LYS 3.6 5.4 - - - -
300A LEU* 1.3 78.9 - - - +
302A SER* 1.3 61.7 + - - +
326A TYR* 3.7 25.8 - - - +
327A LYS 2.8 33.9 + - - +
328A PHE* 4.2 1.8 - - - -
330A HIS* 3.5 15.4 - - - -
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Residues in contact with SER 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 LYS* 2.6 26.7 + - - +
301A SER* 1.3 79.4 - - - +
303A TYR* 1.3 78.9 + - - +
304A PRO* 4.5 1.4 - - - +
326A TYR* 5.8 1.6 - - - -
330A HIS* 5.5 0.2 - - - -
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Residues in contact with TYR 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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70A TRP* 3.6 30.5 - + - -
72A VAL* 3.7 21.8 - - + +
78A GLU* 2.7 32.1 + - - -
284A PHE* 3.7 12.8 - + + -
286A HIS* 5.7 0.2 - + - -
299A THR* 3.1 35.4 + - + +
300A LEU 3.3 5.0 - - - +
302A SER* 1.3 93.9 - - - +
304A PRO* 1.4 59.1 - - + +
305A ILE* 2.7 34.3 + - + +
330A HIS* 3.0 18.1 + - - -
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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