Contacts of the helix formed by residues 292 - 303 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288C LEU* 3.8 3.6 - - + +
290C LYS* 4.4 11.7 - - + +
291C PHE* 1.3 76.5 - - - +
293C PRO* 1.3 75.1 - - - +
294C LEU* 3.1 21.7 + - - +
295C VAL* 3.1 28.1 + - + +
296C ILE* 3.1 23.2 + - - +
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Residues in contact with PRO 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291C PHE 3.8 7.6 - - - +
292C ASP* 1.3 91.6 - - - +
294C LEU* 1.3 57.3 + - + +
296C ILE* 3.2 14.9 + - + +
297C LEU* 2.9 28.8 + - - +
317C MET* 4.0 38.4 - - + +
318C LEU* 3.8 5.8 - - + +
321C GLN* 3.7 28.2 - - + +
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Residues in contact with LEU 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292C ASP* 3.1 14.8 + - - +
293C PRO* 1.3 80.4 - - + +
295C VAL* 1.3 58.1 + - + +
297C LEU* 3.3 9.1 + - + +
298C LYS* 3.0 47.0 + - + +
321C GLN* 3.8 26.2 - - - +
326C TYR* 4.0 26.2 - - + -
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Residues in contact with VAL 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C GLY* 5.6 2.5 - - - -
286C HIS* 3.4 35.0 - - + +
288C LEU* 4.5 8.7 - - + -
292C ASP* 3.1 31.7 + - + +
294C LEU* 1.3 74.5 - - + +
296C ILE* 1.3 64.1 + - - +
298C LYS* 3.4 9.3 + - + +
299C THR* 2.8 31.7 + - - +
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Residues in contact with ILE 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258C TRP* 3.7 30.0 - - + -
260C ILE* 4.2 12.8 - - + -
288C LEU* 4.1 22.9 - - + -
291C PHE* 4.5 22.0 - - + -
292C ASP 3.1 19.5 + - - +
293C PRO* 3.5 13.2 - - + +
295C VAL* 1.3 75.9 - - - +
297C LEU* 1.3 62.4 + - - +
299C THR* 3.4 3.1 + - - -
300C LEU* 3.1 25.9 + - + +
314C VAL* 4.6 14.8 - - + +
317C MET* 5.6 4.0 - - + -
318C LEU* 3.7 24.7 - - + -
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Residues in contact with LEU 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293C PRO 2.9 16.1 + - - +
294C LEU* 3.7 10.1 - - + +
295C VAL 3.2 0.2 - - - -
296C ILE* 1.3 74.9 - - - +
298C LYS* 1.3 64.4 + - - +
300C LEU* 3.4 5.2 + - - +
301C SER* 3.1 21.1 + - - -
318C LEU* 4.0 13.0 - - + +
321C GLN* 4.0 19.5 - - + -
322C ASP 3.5 16.6 - - - +
323C LEU* 3.5 25.1 - - + -
326C TYR* 3.4 42.2 - - + +
328C PHE* 3.6 23.8 - - + -
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Residues in contact with LYS 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294C LEU* 3.0 38.0 + - + +
295C VAL* 3.8 8.3 - - + +
297C LEU* 1.3 75.3 - - - +
299C THR* 1.3 51.7 + - - +
301C SER* 3.2 6.7 + - - -
302C SER* 2.8 46.0 + - - +
326C TYR* 3.0 44.4 + - + -
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Residues in contact with THR 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258C TRP* 3.7 19.7 - - + -
284C PHE* 3.5 32.1 - - + -
286C HIS* 3.3 24.3 + - + -
295C VAL* 2.8 21.9 + - - +
296C ILE 3.6 4.9 - - - -
297C LEU 3.2 0.2 - - - -
298C LYS* 1.3 74.8 - - - +
300C LEU* 1.3 64.7 + - - +
302C SER* 4.6 0.2 - - - -
303C TYR* 3.2 41.7 + - + +
305C ILE* 4.4 1.9 - - + +
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Residues in contact with LEU 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258C TRP* 4.0 21.8 - - + -
296C ILE* 3.1 22.4 + - + +
297C LEU* 3.4 6.5 + - - +
299C THR* 1.3 75.7 - - - +
301C SER* 1.3 58.1 + - - +
303C TYR 3.3 4.5 - - - +
305C ILE* 4.4 17.7 - - + +
308C MET* 3.8 33.4 - - + -
318C LEU* 3.8 28.5 - - + -
328C PHE* 3.4 34.5 - - + +
330C HIS* 2.9 24.9 + - - -
331C LEU* 4.3 11.2 - - + +
349C TRP* 5.1 0.2 - - + -
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Residues in contact with SER 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297C LEU 3.1 12.8 + - - -
298C LYS* 3.4 9.4 - - - -
299C THR 3.2 0.2 - - - -
300C LEU* 1.3 78.9 - - - +
302C SER* 1.3 61.8 + - - +
303C TYR 3.6 0.2 - - - -
326C TYR* 3.9 22.5 - - - +
327C LYS 2.5 35.1 + - - +
328C PHE* 4.1 1.3 - - - -
330C HIS* 3.6 15.6 - - - -
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Residues in contact with SER 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298C LYS* 2.8 30.5 + - - +
301C SER* 1.3 76.7 - - - +
303C TYR* 1.3 76.4 + - - +
304C PRO* 4.6 2.1 - - - +
330C HIS* 5.4 0.7 - - - -
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Residues in contact with TYR 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C TRP* 3.4 27.8 - + + -
72C VAL* 3.6 22.0 - - + +
74C GLY* 6.1 0.5 - - - -
78C GLU* 2.6 41.5 + - - -
284C PHE* 3.8 12.3 - + + -
299C THR* 3.2 36.6 + - + +
300C LEU 3.3 5.9 - - - +
302C SER* 1.3 92.0 - - - +
304C PRO* 1.3 59.8 - - + +
305C ILE* 2.7 33.1 + - + +
330C HIS* 3.1 17.8 + - - -
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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
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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