Contacts of the helix formed by residues 305 - 313 (chain G) in PDB entry 2HOI
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 SER 305 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303G GLY 3.4 5.2 + - - -
304G VAL* 1.3 77.5 - - - +
306G ILE* 1.3 65.7 + - - +
307G PRO* 3.7 14.8 - - - -
308G GLU* 3.1 27.2 + - - -
309G ILE* 2.9 20.8 + - - +
300H ALA 4.5 4.3 - - - -
303H GLY* 3.6 24.0 - - - -
304H VAL 5.9 1.1 - - - -
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Residues in contact with ILE 306 (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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304G VAL 3.6 1.7 + - - +
305G SER* 1.3 70.1 - - - +
307G PRO* 1.4 65.5 - - + +
309G ILE* 3.2 14.9 + - + +
310G MET* 2.9 39.7 + - + +
318G VAL* 3.8 28.5 - - + -
321G VAL* 4.9 4.7 - - + -
322G MET* 3.8 15.9 - - + -
325G ILE* 3.8 28.9 - - + -
331G GLU* 4.3 9.6 - - - +
306H ILE* 6.0 3.8 - - + -
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Residues in contact with PRO 307 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305G SER* 3.5 13.5 - - - -
306G ILE* 1.4 95.4 - - + +
308G GLU* 1.3 54.7 + - + +
310G MET* 3.3 12.1 + - + +
311G GLN 3.0 21.8 + - - -
300H ALA* 5.0 11.4 - - + +
304H VAL 5.0 6.1 - - - +
306H ILE* 3.5 35.4 - - + +
309H ILE* 5.0 8.3 - - + -
321H VAL* 5.0 4.9 - - + -
322H MET* 3.9 3.6 - - - +
325H ILE* 3.5 26.1 - - + +
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Residues in contact with GLU 308 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299G MET* 4.8 0.9 - - - +
304G VAL* 3.7 16.3 - - + +
305G SER* 3.1 32.4 + - - +
307G PRO* 1.3 77.0 - - - +
309G ILE* 1.3 65.2 + - - +
310G MET 3.2 0.2 - - - -
311G GLN* 3.5 8.1 + - - +
312G ALA* 3.1 22.7 + - - +
300H ALA* 3.2 25.4 - - + +
301H ARG* 3.9 25.9 - - - +
325H ILE* 5.0 0.2 - - - -
328H LEU* 4.3 18.4 - - + -
334H ALA* 5.2 8.8 + - + +
337H ARG* 5.1 12.5 + - - -
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Residues in contact with ILE 309 (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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296G ALA* 4.3 11.2 - - + +
299G MET* 3.7 35.4 - - + -
300G ALA* 3.8 29.8 - - + +
304G VAL* 3.3 25.6 - - + +
305G SER 2.9 15.1 + - - +
306G ILE* 3.6 20.9 - - + +
308G GLU* 1.3 74.8 - - - +
310G MET* 1.3 62.3 + - - +
312G ALA* 3.4 10.7 + - - +
313G GLY 3.4 3.1 + - - -
315G TRP* 3.4 23.5 - - + -
321G VAL* 4.3 17.3 - - + -
325G ILE* 4.9 2.7 - - + -
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Residues in contact with MET 310 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306G ILE* 2.9 40.2 + - + +
307G PRO* 3.5 7.9 - - - +
309G ILE* 1.3 74.5 - - - +
311G GLN* 1.3 63.7 + - - +
313G GLY 3.5 1.0 + - - -
314G GLY 3.1 3.5 + - - -
315G TRP* 2.8 45.6 + - + +
316G THR* 3.4 37.5 - - - +
317G ASN 4.1 0.7 - - - -
318G VAL* 3.7 23.8 - - + +
321G VAL* 3.9 20.0 - - + -
306H ILE* 6.2 3.1 - - - -
322H MET* 3.6 19.1 - - + +
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Residues in contact with GLN 311 (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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206G THR 3.9 9.4 - - - +
207G ALA* 3.1 30.6 + - - +
208G GLY* 4.6 0.2 - - - -
211G LYS* 4.6 0.8 + - - +
307G PRO 3.0 16.2 + - - +
308G GLU 3.8 6.1 - - - +
309G ILE 3.4 0.2 - - - -
310G MET* 1.3 75.1 - - - +
312G ALA* 1.3 67.1 + - - +
313G GLY 3.3 0.5 + - - -
314G GLY 3.4 8.0 + - - -
322H MET* 3.5 7.6 - - + +
325H ILE* 3.3 37.0 - - + +
326H ARG* 3.1 20.9 + - - -
328H LEU* 3.7 32.9 + - + +
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Residues in contact with ALA 312 (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 THR 3.6 0.3 - - - +
171G LEU* 3.6 13.8 - - + +
211G LYS* 2.8 27.4 + - - +
299G MET* 3.9 26.0 - - + -
308G GLU 3.1 17.2 + - - +
309G ILE 3.5 7.2 - - - +
310G MET 3.3 0.4 - - - -
311G GLN* 1.3 84.1 + - - +
313G GLY* 1.3 54.3 + - - +
314G GLY 3.6 0.2 - - - -
334H ALA* 5.6 2.7 - - + -
335H MET* 4.7 9.9 - - + +
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Residues in contact with GLY 313 (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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171G LEU* 3.9 5.2 - - - -
173G ARG* 3.6 4.4 + - - -
207G ALA* 4.7 3.1 - - - -
211G LYS* 4.9 0.4 - - - -
292G ARG* 2.7 41.2 + - - -
309G ILE 3.4 7.3 + - - -
311G GLN 3.3 0.4 - - - -
312G ALA* 1.3 78.4 - - - +
314G GLY* 1.3 59.6 + - - +
315G TRP* 3.2 25.0 + - - -
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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