Contacts of the helix formed by residues 284 - 296 (chain G) in PDB entry 40ER
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 284 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189G MET 3.9 10.3 - - - -
190G SER* 3.4 23.6 - - - +
191G LYS 3.5 7.2 - - - +
192G SER* 4.0 2.5 - - - +
282G HIS 5.1 2.7 - - - +
283G GLU* 1.3 78.4 - - - +
285G LEU* 1.3 63.9 + - - +
286G GLU* 3.9 5.5 + - - +
287G THR* 3.3 23.8 + - - -
288G ILE* 3.3 22.0 + - - +
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Residues in contact with LEU 285 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188G PHE* 4.0 22.4 - - + -
189G MET* 3.3 37.9 + - + +
191G LYS 3.2 7.3 + - - -
193G LEU* 4.4 15.6 - - + +
196G LEU* 3.7 24.5 - - + -
198G ILE* 4.1 23.8 - - + -
283G GLU 4.0 0.2 + - - -
284G THR* 1.3 71.0 - - - +
286G GLU* 1.3 66.1 + - - +
288G ILE* 3.1 9.7 + - + +
289G ILE* 3.1 50.3 + - + +
318G ILE* 5.1 8.1 - - + -
321G ALA* 6.4 0.2 - - + -
322G LEU* 6.2 0.2 - - + -
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Residues in contact with GLU 286 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177G LYS* 3.6 19.1 + - - -
185G LYS* 3.8 33.1 + - - +
189G MET* 3.2 35.7 + - + +
190G SER* 5.3 1.6 - - - -
284G THR* 4.1 7.0 - - - +
285G LEU* 1.3 81.4 - - - +
287G THR* 1.3 59.6 + - - +
289G ILE* 4.2 1.6 - - - +
290G ASN* 2.8 47.3 + - - +
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Residues in contact with THR 287 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283G GLU* 5.2 9.0 - - - -
284G THR* 3.3 22.2 + - - -
285G LEU 3.2 0.6 - - - -
286G GLU* 1.3 80.7 - - - +
288G ILE* 1.3 63.7 + - - +
290G ASN* 4.1 5.9 - - - +
291G ARG* 3.2 36.2 + - - +
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Residues in contact with ILE 288 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193G LEU* 3.6 49.1 - - + -
279G CYS* 4.4 18.8 - - + -
280G TYR 4.8 2.0 - - - +
283G GLU* 4.4 8.5 - - + +
284G THR 3.3 15.5 + - - +
285G LEU* 3.1 13.8 + - + +
287G THR* 1.3 75.3 - - - +
289G ILE* 1.3 69.7 + - + +
291G ARG* 3.2 7.0 + - - +
292G LEU* 2.8 39.8 + - + +
300G LEU* 4.1 19.5 - - + +
313G VAL* 4.8 9.6 - - + -
318G ILE* 5.3 3.6 - - + -
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Residues in contact with ILE 289 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173G LEU* 3.8 23.6 - - + -
177G LYS* 4.0 30.1 - - + -
189G MET* 4.2 14.1 - - + -
285G LEU* 3.1 45.6 + - + +
286G GLU* 4.2 2.5 - - - +
288G ILE* 1.3 82.9 - - + +
290G ASN* 1.3 64.8 + - - +
292G LEU* 3.2 6.0 + - - +
293G VAL* 3.0 26.6 + - + +
318G ILE* 3.9 37.0 - - + -
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Residues in contact with ASN 290 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177G LYS* 3.7 31.9 - - - +
286G GLU* 2.8 40.9 + - - +
287G THR* 4.1 6.2 - - - +
288G ILE 3.2 0.4 - - - -
289G ILE* 1.3 77.6 - - - +
291G ARG* 1.3 60.9 + - - +
293G VAL* 3.3 9.0 - - - +
294G GLU* 3.2 31.0 + - - +
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Residues in contact with ARG 291 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277G LEU* 5.3 12.3 - - + -
278G LYS 2.7 33.3 + - - -
279G CYS* 3.3 24.4 - - - +
280G TYR* 5.6 1.8 - - - -
283G GLU* 2.8 27.6 + - - -
287G THR* 3.2 25.0 + - - +
288G ILE* 3.2 5.9 + - - +
290G ASN* 1.3 78.6 - - - +
292G LEU* 1.3 58.1 + - - +
294G GLU* 4.0 6.3 - - - +
295G ALA* 3.0 32.1 + - + +
300G LEU* 4.7 14.5 - - + +
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Residues in contact with LEU 292 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173G LEU* 4.5 4.9 - - + -
288G ILE* 2.8 22.4 + - + +
289G ILE* 3.2 6.7 + - - +
291G ARG* 1.3 78.3 - - - +
293G VAL* 1.3 58.4 + - - +
295G ALA* 4.1 1.5 - - - -
296G GLU* 3.2 19.9 + - - -
297G VAL* 3.6 38.4 + - + +
299G ARG 4.1 6.7 - - - +
300G LEU* 3.7 26.9 - - + -
313G VAL 4.3 9.6 - - - +
315G LEU* 3.5 27.6 - - + +
318G ILE* 3.6 22.9 - - + -
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Residues in contact with VAL 293 (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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170G LYS 5.6 0.2 - - - +
173G LEU* 3.6 51.1 - - + +
174G LYS* 4.0 28.1 + - + +
177G LYS* 5.0 13.2 - - + -
289G ILE* 3.0 15.4 + - + +
290G ASN* 3.3 17.0 - - - +
292G LEU* 1.3 74.4 - - - +
294G GLU* 1.3 68.8 + - + +
296G GLU* 3.4 20.2 + - - +
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Residues in contact with GLU 294 (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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360A ARG* 5.6 3.6 + - - -
174G LYS* 5.7 1.6 - - - +
290G ASN* 3.2 19.6 + - - +
291G ARG* 4.0 5.7 - - - +
293G VAL* 1.3 84.5 - - + +
295G ALA* 1.3 59.0 + - - +
296G GLU* 3.7 9.2 - - - +
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Residues in contact with ALA 295 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A PRO* 3.8 9.4 - - - +
277G LEU* 3.9 32.8 - - + -
291G ARG* 3.0 20.4 + - + +
292G LEU* 4.1 3.6 - - - +
294G GLU* 1.3 75.0 - - - +
296G GLU* 1.3 71.1 + - - +
297G VAL* 3.3 19.0 + - + +
300G LEU* 5.7 0.4 - - + -
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Residues in contact with GLU 296 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A HIS* 3.2 31.7 + - - +
363A PRO* 3.1 21.6 - - + +
224B SER 4.2 9.0 - - - +
226B ASP* 5.5 0.9 + - - +
170G LYS* 2.5 33.6 + - - +
174G LYS* 3.9 22.3 + - + +
292G LEU 3.2 8.7 + - - -
293G VAL* 3.4 20.2 + - - +
294G GLU 3.3 8.6 - - - +
295G ALA* 1.3 81.5 - - - +
297G VAL* 1.3 54.8 + - - +
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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