Contacts of the helix formed by residues 239 - 248 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232B TYR* 4.7 0.7 - - - -
233B LYS* 4.4 30.0 - - + -
237B PRO 4.3 0.4 + - - -
238B TYR* 1.3 72.8 - - - +
240B MET* 1.3 59.2 + - - +
241B LEU* 3.9 14.1 - - - +
242B GLU* 2.8 30.2 + - - +
243B SER* 2.8 24.1 + - - -
264B GLN* 5.9 0.7 + - - -
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Residues in contact with MET 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B LEU* 3.9 21.3 - - - -
213B TRP* 3.8 35.4 - - + -
217B MET* 3.7 22.2 - - + -
229B PHE* 4.0 33.2 + - + +
232B TYR* 3.9 35.9 - - + +
239B ASP* 1.3 72.4 - - - +
241B LEU* 1.3 61.9 + - - +
243B SER* 4.0 2.9 - - - -
244B ILE* 3.2 31.3 + - + +
260B VAL* 4.2 20.9 - - + -
264B GLN* 5.0 2.9 - - - +
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Residues in contact with LEU 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B ASP* 3.2 15.0 + - - +
240B MET* 1.3 78.8 - - - +
242B GLU* 1.3 62.6 + - - +
244B ILE* 3.2 19.4 + - + +
245B LYS* 3.5 9.3 + - + +
257B LEU* 3.6 37.1 - - + +
260B VAL* 3.5 37.0 - - + -
261B GLN* 4.4 15.7 - - + +
264B GLN* 4.1 18.7 - - - +
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Residues in contact with GLU 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238B TYR* 4.0 22.7 - - + -
239B ASP* 2.8 26.0 + - - +
241B LEU* 1.3 73.2 - - - +
243B SER* 1.3 62.1 + - - +
245B LYS* 3.3 37.0 + - - +
246B LYS* 3.4 26.8 + - + +
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Residues in contact with SER 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B VAL* 3.8 12.6 - - - +
213B TRP* 4.6 2.7 - - - -
232B TYR* 3.2 22.2 + - - -
236B SER* 3.8 1.9 + - - -
238B TYR* 3.2 24.7 + - - +
239B ASP 2.8 16.5 + - - -
240B MET* 3.7 12.3 - - - -
242B GLU* 1.3 75.3 - - - +
244B ILE* 1.3 60.2 + - - +
246B LYS* 3.0 8.2 + - - +
247B GLU* 2.9 32.7 + - - +
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Residues in contact with ILE 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B TRP* 4.0 23.8 - - + -
217B MET* 5.0 1.3 - - + -
240B MET* 3.2 27.3 + - + +
241B LEU* 3.2 14.8 + - + +
243B SER* 1.3 76.7 - - - +
245B LYS* 1.3 57.7 + - - +
248B VAL* 3.0 43.8 + - + +
253B GLU* 3.8 11.9 - - + +
256B PHE* 3.9 21.3 - - + +
257B LEU* 3.8 21.5 - - + +
260B VAL* 3.6 30.5 - - + -
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Residues in contact with LYS 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241B LEU* 3.5 14.7 + - - +
242B GLU* 3.3 34.1 + - - +
243B SER 3.1 0.6 - - - -
244B ILE* 1.3 76.6 - - - +
246B LYS* 1.3 60.9 + - - +
248B VAL 3.8 6.9 - - - +
249B LYS* 6.0 0.2 - - - +
253B GLU* 3.4 24.9 - - - +
257B LEU* 4.2 22.2 - - + +
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Residues in contact with LYS 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B VAL* 5.8 0.7 - - + -
206B LYS* 5.0 4.2 + - - -
238B TYR* 3.8 47.7 + - + +
242B GLU* 3.4 25.7 + - - +
243B SER* 3.0 10.6 + - - +
245B LYS* 1.3 81.7 - - - +
247B GLU* 1.3 73.3 + - + +
248B VAL 3.8 0.7 + - - -
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Residues in contact with GLU 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B GLY* 3.6 7.4 - - - +
203B VAL* 3.3 44.0 - - + +
205B ARG 4.0 3.9 - - - +
206B LYS* 3.2 31.5 + - - +
207B GLY 3.2 17.8 - - - +
208B THR* 3.5 27.8 + - + +
213B TRP* 4.0 11.0 - - + -
243B SER 2.9 17.1 + - - +
246B LYS* 1.3 84.8 - - + +
248B VAL* 1.3 61.8 + - + +
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Residues in contact with VAL 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B THR* 4.4 6.3 - - + +
210B VAL* 4.4 22.2 - - + -
213B TRP* 4.5 12.6 - - + -
244B ILE* 3.0 37.2 + - + +
245B LYS 3.8 7.6 - - - +
246B LYS 3.6 0.6 - - - -
247B GLU* 1.3 87.4 - - + +
249B LYS* 1.3 62.5 + - - +
252B LEU* 4.5 15.9 - - + -
253B GLU* 3.3 33.2 - - - +
256B PHE* 4.5 11.4 - - + -
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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