Contacts of the helix formed by residues 239 - 248 (chain C) in PDB entry 4HRE
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 239 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232C TYR* 3.9 0.7 - - - -
233C LYS* 3.6 35.5 + - - +
237C PRO 4.2 0.2 + - - -
238C TYR* 1.3 72.3 - - - +
240C MET* 1.3 61.0 + - - +
241C LEU* 4.1 12.8 - - - +
242C GLU* 2.9 34.0 + - - +
243C SER* 2.7 28.4 + - - -
264C GLN* 6.0 1.7 + - - +
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Residues in contact with MET 240 (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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198C LEU* 4.0 26.2 - - + -
213C TRP* 3.9 30.3 - - + +
217C MET* 4.0 12.3 - - + -
229C PHE* 3.9 35.6 + - + -
232C TYR* 3.7 27.3 - - + +
239C ASP* 1.3 72.2 - - - +
241C LEU* 1.3 64.2 + - - +
243C SER* 3.2 10.2 + - - -
244C ILE* 3.2 38.3 + - + +
260C VAL* 4.2 21.1 - - + -
264C GLN* 4.4 4.9 - - - +
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Residues in contact with LEU 241 (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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239C ASP* 3.4 13.2 + - - +
240C MET* 1.3 78.0 - - - +
242C GLU* 1.3 63.5 + - - +
244C ILE* 3.4 13.5 + - - +
245C LYS* 3.5 16.6 + - - +
257C LEU* 3.6 38.2 - - + +
260C VAL* 3.6 32.3 - - + +
261C GLN* 4.2 21.3 - - + +
264C GLN* 4.3 14.9 - - - +
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Residues in contact with GLU 242 (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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238C TYR* 3.8 28.3 - - + -
239C ASP* 2.9 24.0 + - - +
241C LEU* 1.3 74.3 - - - +
243C SER* 1.3 62.0 + - - +
245C LYS* 3.2 39.8 + - - +
246C LYS* 3.2 21.8 + - + +
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Residues in contact with SER 243 (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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203C VAL* 4.0 11.9 - - - -
213C TRP* 4.4 4.0 - - - -
232C TYR* 3.0 31.7 + - - -
236C SER* 3.8 1.6 + - - -
238C TYR* 3.5 18.0 + - - +
239C ASP 2.7 22.5 + - - -
240C MET* 3.2 12.8 + - - -
242C GLU* 1.3 75.1 - - - +
244C ILE* 1.3 52.7 + - - +
246C LYS* 3.1 3.7 + - - +
247C GLU* 2.7 40.8 + - - +
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Residues in contact with ILE 244 (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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213C TRP* 4.0 16.4 - - + -
217C MET* 5.2 0.7 - - + -
240C MET* 3.2 32.2 + - + +
241C LEU* 3.6 10.5 - - - +
242C GLU 3.3 0.2 - - - -
243C SER* 1.3 76.1 - - - +
245C LYS* 1.3 58.4 + - - +
248C VAL* 3.0 43.5 + - + +
253C GLU* 4.2 9.6 - - + +
256C PHE* 3.7 33.2 - - + +
257C LEU* 4.1 15.0 - - + -
260C VAL* 3.4 33.9 - - + -
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Residues in contact with LYS 245 (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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241C LEU* 3.5 16.5 + - - +
242C GLU* 3.2 35.4 + - - +
244C ILE* 1.3 78.6 - - - +
246C LYS* 1.3 60.8 + - - +
248C VAL 3.5 10.6 - - - +
253C GLU* 3.8 23.8 - - - +
257C LEU* 4.1 24.7 - - + -
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Residues in contact with LYS 246 (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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203C VAL* 5.2 5.6 - - + +
238C TYR* 3.2 46.3 + - + +
242C GLU* 3.2 19.9 + - - +
243C SER* 3.1 9.7 + - - +
245C LYS* 1.3 79.6 - - - +
247C GLU* 1.3 76.2 + - - +
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Residues in contact with GLU 247 (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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202C GLY* 3.3 8.8 - - - +
203C VAL* 3.6 37.6 - - + +
205C ARG 4.0 2.6 - - - +
207C GLY* 3.0 26.3 + - - +
208C THR* 3.3 22.0 + - - +
213C TRP* 3.6 27.6 - - + -
243C SER 2.7 22.6 + - - +
246C LYS* 1.3 94.0 - - - +
248C VAL* 1.3 61.2 + - + +
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Residues in contact with VAL 248 (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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208C THR* 4.3 21.1 - - + +
210C VAL* 4.6 5.4 - - + -
213C TRP* 4.5 11.4 - - + -
244C ILE* 3.0 42.8 + - + +
245C LYS 3.5 12.8 - - - +
247C GLU* 1.3 84.1 - - + +
249C LYS* 1.3 65.7 + - - +
252C LEU* 4.3 26.9 - - + -
253C GLU* 3.7 21.7 - - - +
256C PHE* 4.7 4.5 - - + -
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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