Contacts of the helix formed by residues 286 - 298 (chain G) in PDB entry 4U0Z
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 THR 286 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281G ARG* 4.6 2.2 + - - +
284G SER* 3.9 17.5 - - - +
285G VAL* 1.3 77.0 - - - +
287G ILE* 1.3 65.5 + - - +
288G SER* 3.8 10.4 + - - -
289G ASP* 2.6 50.3 + - - +
290G VAL* 3.6 11.3 + - - +
335G VAL* 4.0 8.7 - - - -
339G ASN* 5.5 1.3 - - - +
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Residues in contact with ILE 287 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286G THR* 1.3 74.7 - - - +
288G SER* 1.4 62.4 + - - +
290G VAL* 3.6 6.6 + - - +
291G LEU* 3.2 38.4 + - + +
309G PHE* 4.0 23.3 - - + -
328G GLU* 4.5 4.5 - - + +
331G MET* 3.7 43.7 - - + +
332G GLN* 3.9 19.5 - - + +
335G VAL* 3.8 19.8 - - + +
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Residues in contact with SER 288 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286G THR* 3.2 10.9 - - - -
287G ILE* 1.4 84.0 - - - +
289G ASP* 1.4 59.9 + - - +
291G LEU* 3.5 10.2 + - - +
292G GLU* 2.9 39.1 + - - +
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Residues in contact with ASP 289 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273G TYR* 4.5 3.5 + - - -
278G LEU* 3.5 26.8 - - + +
281G ARG* 2.7 37.7 + - - -
285G VAL* 3.7 9.8 - - + -
286G THR* 2.6 42.3 + - - +
288G SER* 1.4 75.9 - - - +
290G VAL* 1.4 56.5 + - + +
292G GLU* 3.2 8.6 + - - +
293G ILE* 3.0 35.5 + - + +
379G LEU* 6.1 0.4 - - + -
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Residues in contact with VAL 290 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285G VAL* 4.9 9.0 - - + -
286G THR 3.7 14.6 - - - +
287G ILE* 3.6 8.5 + - - +
288G SER 3.4 0.2 - - - -
289G ASP* 1.4 73.6 - - + +
291G LEU* 1.3 59.4 + - + +
293G ILE* 3.4 16.0 + - + +
294G HIS* 3.1 27.6 + - - +
309G PHE* 6.1 0.2 - - + -
331G MET* 4.2 25.6 - - + -
334G PHE* 5.1 3.6 - - + -
335G VAL* 4.9 5.8 - - + -
338G LEU* 5.6 0.4 - - + -
359G LEU* 4.3 20.9 - - + -
365G PHE* 4.2 15.5 - - + -
372G THR* 5.5 3.7 + - - -
376G LEU* 5.0 14.6 - - + -
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Residues in contact with LEU 291 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287G ILE* 3.2 30.1 + - + +
288G SER* 3.8 10.5 - - - +
289G ASP 3.4 0.2 - - - -
290G VAL* 1.3 76.7 - - + +
292G GLU* 1.4 52.8 + - - +
294G HIS* 3.6 4.2 + - - -
295G ARG* 2.9 32.3 + - - +
307G GLY* 3.3 35.6 - - - +
308G ARG* 4.2 3.8 - - - -
309G PHE* 3.7 44.0 - - + +
365G PHE* 4.1 6.3 - - + -
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Residues in contact with GLU 292 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273G TYR* 3.3 31.6 - - + +
288G SER* 2.9 27.5 + - - +
289G ASP 3.3 7.2 - - - +
290G VAL 3.2 0.2 - - - -
291G LEU* 1.4 76.5 - - - +
293G ILE* 1.4 64.2 + - - +
295G ARG* 3.4 19.7 - - - +
296G ARG* 2.9 49.3 + - - +
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Residues in contact with ILE 293 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270G ALA* 4.1 3.7 - - + +
273G TYR* 4.6 6.3 - - + -
274G ILE* 3.9 19.5 - - + -
278G LEU* 3.9 25.6 - - + -
289G ASP* 3.0 18.2 + - + +
290G VAL* 3.4 19.0 + - + +
292G GLU* 1.4 70.2 - - - +
294G HIS* 1.4 61.1 + - - +
296G ARG* 3.1 6.7 + - - +
297G VAL* 2.9 33.7 + - + +
372G THR* 4.7 11.0 - - - +
375G LEU* 3.6 33.9 - - + -
376G LEU* 5.2 15.3 - - + -
379G LEU* 4.7 9.6 - - + -
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Residues in contact with HIS 294 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290G VAL 3.1 16.5 + - - +
291G LEU 3.9 4.0 - - - +
293G ILE* 1.4 73.1 - - - +
295G ARG* 1.3 65.4 + - - +
297G VAL* 4.2 3.8 - - + -
298G LEU* 3.2 37.7 + - + +
305G GLU* 3.7 15.0 - - + -
306G ALA* 3.7 7.6 - - - +
307G GLY 2.9 27.5 + - - -
365G PHE* 3.4 51.9 - + + +
366G ILE 5.6 0.4 - - - -
367G ASP 2.8 27.4 + - - -
368G GLY* 4.0 3.6 - - - -
372G THR* 3.7 17.7 + - - +
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Residues in contact with ARG 295 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291G LEU 2.9 19.9 + - - +
292G GLU* 3.4 26.0 - - - +
293G ILE 3.2 0.2 - - - -
294G HIS* 1.3 76.4 - - - +
296G ARG* 1.3 63.4 + - + +
299G GLY* 3.3 27.6 - - - -
303G PRO* 2.7 37.6 + - - +
304G VAL 5.4 0.8 + - - -
306G ALA* 2.7 35.9 + - - +
307G GLY* 3.7 11.6 - - - +
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Residues in contact with ARG 296 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266G GLY* 3.2 21.0 - - - +
269G ALA* 3.5 29.5 + - + +
270G ALA* 3.6 19.7 - - - +
273G TYR* 3.4 44.2 - - - +
292G GLU* 2.9 48.0 + - - +
293G ILE 3.1 5.1 + - - +
295G ARG* 1.3 86.3 - - + +
297G VAL* 1.4 64.8 + - - +
298G LEU 3.4 0.8 + - - -
299G GLY* 3.7 5.8 + - - -
300G TYR* 3.9 9.4 - - + +
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Residues in contact with VAL 297 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262G ASN 5.0 2.1 - - - +
263G GLU* 4.5 5.9 - - - +
266G GLY* 3.8 20.6 + - - -
267G MET* 4.4 6.2 + - - -
270G ALA* 3.7 16.4 - - + -
293G ILE* 2.9 28.1 + - + +
294G HIS* 3.4 6.9 + - + +
296G ARG* 1.4 76.3 - - - +
298G LEU* 1.3 60.3 + - + +
300G TYR 5.1 0.5 + - - -
301G VAL* 5.4 1.6 - - - +
368G GLY* 4.5 7.6 - - - +
371G ARG* 3.8 45.7 + - + +
372G THR* 4.0 13.7 - - - +
375G LEU* 3.8 17.0 - - + -
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Residues in contact with LEU 298 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294G HIS* 3.2 40.5 + - + +
297G VAL* 1.3 75.7 - - + +
299G GLY* 1.3 56.0 + - - +
300G TYR 3.3 2.9 - - - -
301G VAL* 3.2 26.7 + - + +
302G ASP* 2.8 61.2 + - + +
305G GLU* 4.6 4.3 - - + -
306G ALA* 3.5 8.1 - - + +
366G ILE* 6.2 0.2 - - + -
367G ASP* 4.0 33.7 - - + +
368G GLY* 4.7 1.8 - - - +
371G ARG* 4.4 16.8 - - - +
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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
------------------------------------------------------------
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