Contacts of the helix formed by residues 292 - 306 (chain G) in PDB entry 4ZZ7
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 ALA 292 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257G PRO* 6.1 6.1 - - + -
289G VAL 5.1 0.4 - - - +
290G GLY* 3.9 6.3 - - - -
291G ASP 1.3 72.6 + - - +
293G ALA* 1.3 65.8 + - + +
295G ASP* 4.0 5.6 + - - +
296G ALA* 3.6 21.0 + - - +
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Residues in contact with ALA 293 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255G VAL* 4.3 17.9 - - + +
256G MET 4.8 3.6 - - - +
257G PRO* 5.0 6.7 - - + -
261G MET* 4.4 19.3 - - + +
288G ALA* 4.3 4.0 - - + -
289G VAL 3.9 17.9 - - - +
290G GLY 4.6 0.2 - - - +
291G ASP* 3.4 1.8 - - - +
292G ALA* 1.3 78.2 - - + +
294G GLY* 1.3 57.5 + - - +
295G ASP 3.3 0.7 - - - -
296G ALA* 4.1 4.9 - - - +
297G LEU* 2.8 37.7 + - - +
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Residues in contact with GLY 294 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288G ALA* 3.6 21.4 - - - +
290G GLY 3.4 8.7 + - - -
291G ASP* 3.6 2.0 - - - +
292G ALA 3.6 0.6 - - - -
293G ALA* 1.3 77.9 - - - +
295G ASP* 1.3 55.1 + - - +
297G LEU* 4.0 2.0 - - - +
298G VAL* 3.2 21.8 + - - +
390G VAL* 5.5 0.7 - - - -
392G ARG* 2.7 38.4 + - - -
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Residues in contact with ASP 295 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291G ASP* 3.9 18.6 - - - +
292G ALA 4.0 7.8 + - - +
293G ALA 3.3 0.2 - - - -
294G GLY* 1.3 72.2 - - - +
296G ALA* 1.3 62.0 + - - +
298G VAL* 3.4 3.2 + - - +
299G SER* 2.9 32.6 + - - -
392G ARG* 3.4 20.1 + - - +
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Residues in contact with ALA 296 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261G MET* 4.2 15.4 - - + +
292G ALA 3.6 16.1 + - - +
293G ALA* 3.4 6.1 + - - +
295G ASP* 1.3 75.9 - - - +
297G LEU* 1.3 62.5 - - - +
299G SER* 3.9 5.8 - - - -
300G LYS* 3.3 37.8 + - - +
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Residues in contact with LEU 297 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255G VAL* 4.6 15.3 - - + -
261G MET* 4.7 13.2 - - - +
264G ALA* 5.6 0.7 - - + -
265G VAL* 3.8 23.7 - - + +
268G LEU* 4.1 19.7 - - + -
286G ALA* 3.9 19.1 - - + -
288G ALA* 4.5 11.4 - - + -
293G ALA 2.8 22.1 + - - +
294G GLY 4.0 2.9 - - - +
296G ALA* 1.3 69.6 - - - +
298G VAL* 1.3 62.9 + - + +
299G SER 3.0 1.6 + - - -
300G LYS* 3.1 2.9 + - - +
301G MET* 2.8 39.2 + - + +
388G LEU* 6.0 1.8 - - + -
390G VAL* 3.8 31.9 - - + -
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Residues in contact with VAL 298 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294G GLY 3.2 17.0 + - - +
295G ASP* 3.4 4.1 + - - +
297G LEU* 1.3 80.4 - - + +
299G SER* 1.3 60.8 + - - +
301G MET* 4.0 5.7 - - - +
302G THR* 2.6 39.6 + - - +
347G VAL* 3.9 24.9 - - + -
368G LEU* 4.2 6.1 - - + -
370G ASP* 3.1 35.7 - - + +
390G VAL* 4.4 21.1 - - + -
392G ARG* 3.9 1.6 - - - +
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Residues in contact with SER 299 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295G ASP 2.9 18.7 + - - -
296G ALA* 3.9 9.0 - - - -
298G VAL* 1.3 81.8 - - - +
300G LYS* 1.3 66.5 + - - +
302G THR* 3.0 12.0 + - - -
303G GLN* 3.2 16.8 + - - +
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Residues in contact with LYS 300 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261G MET* 4.1 25.5 - - + +
262G ASP* 2.7 33.1 + - - +
265G VAL* 3.7 21.7 - - + +
296G ALA* 3.3 22.2 + - - +
297G LEU 3.1 3.3 + - - +
299G SER* 1.3 82.1 - - - +
301G MET* 1.3 60.5 + - - +
303G GLN* 3.6 10.6 + - - +
304G ALA* 3.2 19.9 + - - +
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Residues in contact with MET 301 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265G VAL* 3.8 25.5 - - + +
268G LEU* 4.5 10.1 - - - -
269G LEU* 3.3 40.8 - - + -
273G PHE* 4.1 5.8 - - + -
297G LEU* 2.8 27.6 + - + +
298G VAL* 4.3 0.7 - - - -
300G LYS* 1.3 71.5 - - - +
302G THR* 1.3 60.0 + - - +
304G ALA* 4.7 0.2 - - + -
305G MET* 2.9 56.9 + - + +
368G LEU* 3.7 14.6 - - + -
388G LEU* 3.7 27.6 - - + -
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Residues in contact with THR 302 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298G VAL* 2.6 23.1 + - - +
299G SER* 3.0 6.3 + - - -
301G MET* 1.3 78.3 - - - +
303G GLN* 1.3 58.6 + - - +
305G MET* 3.5 6.5 + - - +
306G GLN* 2.8 41.8 + - - +
347G VAL* 3.3 25.1 - - + +
348G VAL* 3.7 21.1 - - + -
368G LEU* 3.7 3.7 - - - +
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Residues in contact with GLN 303 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299G SER* 3.2 15.4 + - - +
300G LYS* 3.7 12.8 - - - +
301G MET 3.3 0.4 - - - -
302G THR* 1.3 75.0 - - + +
304G ALA* 1.3 66.4 + - - +
306G GLN* 3.2 21.5 + - - +
307G LYS* 4.2 7.6 + - - +
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Residues in contact with ALA 304 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265G VAL* 4.3 11.0 - - + -
266G ASN* 6.0 0.2 - - - -
269G LEU* 3.8 33.5 - - + +
300G LYS 3.2 14.5 + - - +
301G MET 4.2 2.0 - - - +
303G GLN* 1.3 78.9 - - - +
305G MET* 1.3 60.1 + - - +
307G LYS* 3.4 28.8 + - + +
308G LEU* 4.2 3.1 + - - +
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Residues in contact with MET 305 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269G LEU* 4.4 2.6 - - - +
273G PHE* 3.8 22.0 - - + -
301G MET* 2.9 49.1 + - + +
302G THR* 3.7 7.2 - - - +
303G GLN 3.2 0.2 - - - -
304G ALA* 1.3 78.1 - - - +
306G GLN* 1.3 62.5 + - - +
307G LYS 3.2 0.4 - - - -
308G LEU* 3.4 43.6 - - + +
348G VAL* 4.0 15.3 - - + +
366G GLY 3.8 21.5 - - - +
367G THR 3.9 8.3 - - - +
368G LEU* 3.6 25.6 - - + -
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Residues in contact with GLN 306 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302G THR* 2.8 35.4 + - - +
303G GLN* 3.2 13.4 + - - +
305G MET* 1.3 77.7 - - - +
307G LYS* 1.3 59.1 + - + +
308G LEU 3.3 8.7 + - - +
348G VAL* 4.5 22.6 - - - +
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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