Contacts of the helix formed by residues 234 - 246 (chain B) in PDB entry 2H1R
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 PRO 234 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232B ASN 4.6 0.4 - - - +
233B PHE* 1.4 88.7 - - + +
235B PHE* 1.3 66.6 + - - +
236B LYS* 4.4 9.4 - - + +
237B LYS* 3.2 23.1 + - + +
238B TYR* 3.2 10.4 + - - +
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Residues in contact with PHE 235 (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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212B LEU* 3.7 17.5 - - + -
215B LEU* 3.6 27.8 - - + -
216B GLU* 3.5 53.3 + - + +
219B TYR* 3.6 40.4 - + + -
220B LYS* 5.5 0.7 - - - +
231B VAL* 5.8 0.9 - - - -
233B PHE 3.6 2.9 + - - -
234B PRO* 1.3 69.5 - - - +
236B LYS* 1.3 59.6 + - - +
238B TYR* 3.1 14.2 + + - -
239B CYS* 2.7 51.2 + - + +
273B ILE* 3.9 27.1 - - + -
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Residues in contact with LYS 236 (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 HIS* 5.8 0.9 - - - -
207B LYS* 4.5 18.1 + - - +
212B LEU* 3.9 34.0 - - + +
234B PRO* 3.2 7.7 - - + +
235B PHE* 1.3 78.7 - - - +
237B LYS* 1.3 57.9 + - - +
239B CYS* 3.8 0.5 - - - +
240B LEU* 2.8 62.0 + - + +
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Residues in contact with LYS 237 (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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233B PHE* 5.4 4.0 - - + -
234B PRO* 3.2 21.8 + - + +
236B LYS* 1.3 77.6 - - - +
238B TYR* 1.3 60.9 + - - +
240B LEU* 4.9 2.9 - - - -
241B ASP* 2.9 45.7 + - - +
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Residues in contact with TYR 238 (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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219B TYR* 3.7 20.2 + + - -
231B VAL* 3.6 41.7 - - + +
233B PHE* 5.4 5.0 - - + +
234B PRO 3.2 10.5 + - - +
235B PHE* 3.1 23.1 + + - +
237B LYS* 1.3 79.2 - - - +
239B CYS* 1.3 63.2 + - - +
241B ASP* 3.8 3.6 - - - +
242B VAL 4.1 0.2 + - - -
271B LYS* 2.7 99.8 + - + +
273B ILE* 4.0 14.8 - - + -
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Residues in contact with CYS 239 (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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206B PHE* 4.2 12.3 - - - -
212B LEU* 4.1 15.9 - - + -
215B LEU* 4.0 23.6 - - - -
235B PHE* 2.7 39.7 + - + +
236B LYS 3.9 2.5 - - - +
238B TYR* 1.3 74.3 - - - +
240B LEU* 1.3 63.4 + - - +
242B VAL* 3.2 21.8 + - - +
243B LEU* 4.2 1.6 + - - +
268B PHE* 3.8 21.3 - - - -
273B ILE* 4.2 9.0 - - - -
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Residues in contact with LEU 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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203B HIS* 3.8 30.1 - - + +
206B PHE* 3.6 41.7 - - + +
207B LYS* 4.0 7.6 - - + +
212B LEU* 5.0 3.1 - - + -
236B LYS* 2.8 55.9 + - + +
237B LYS* 4.5 3.1 - - - +
239B CYS* 1.3 69.5 - - - +
241B ASP* 1.3 64.6 + - - +
243B LEU* 3.1 28.0 + - + +
244B GLU* 3.3 12.4 + - - +
249B CYS* 4.8 2.1 - - - -
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Residues in contact with ASP 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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237B LYS* 2.9 34.0 + - - +
238B TYR* 4.6 1.2 + - - -
239B CYS 3.3 0.2 - - - -
240B LEU* 1.3 75.6 - - - +
242B VAL* 1.3 57.3 + - - +
244B GLU* 3.8 20.9 - - - +
245B HIS* 2.9 31.0 + - - +
271B LYS* 3.6 20.8 + - - +
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Residues in contact with VAL 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 4.1 1.1 - - - +
239B CYS* 3.2 15.0 + - - +
240B LEU 3.1 1.2 - - - -
241B ASP* 1.3 76.8 - - - +
243B LEU* 1.3 66.5 + - - +
245B HIS* 3.3 8.0 + - - +
246B LEU* 3.1 29.7 + - + +
264B LEU* 4.5 2.0 - - + -
267B GLU* 3.7 33.0 - - + +
268B PHE* 3.7 40.6 - - + +
271B LYS* 3.6 31.0 - - + +
273B ILE* 4.9 0.7 - - + -
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Residues in contact with LEU 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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202B LEU* 3.7 48.2 - - + +
203B HIS* 3.7 13.0 - - + +
206B PHE* 4.1 9.9 - - + -
239B CYS 4.8 0.2 - - - +
240B LEU* 3.1 29.3 + - + +
242B VAL* 1.3 77.4 - - - +
244B GLU* 1.3 57.0 + - - +
246B LEU* 3.2 3.0 + - - -
247B ASP 2.9 8.8 + - - -
248B MET* 2.9 29.3 + - + +
249B CYS* 3.8 18.4 - - - +
264B LEU* 3.7 25.8 - - + -
268B PHE* 4.1 16.4 - - + -
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Residues in contact with GLU 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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240B LEU 3.3 9.4 + - - +
241B ASP* 3.8 21.5 - - - +
243B LEU* 1.3 75.7 - - - +
245B HIS* 1.3 65.6 + - - +
247B ASP* 3.1 21.4 + - - +
249B CYS* 3.7 18.1 - - - -
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Residues in contact with HIS 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 ASP 2.9 20.0 + - - +
242B VAL* 3.6 6.2 + - - +
244B GLU* 1.3 77.5 - - - +
246B LEU* 1.3 76.5 + - + +
247B ASP* 3.5 7.3 + - - +
267B GLU* 4.0 29.7 + - - +
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Residues in contact with LEU 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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242B VAL* 3.1 16.3 + - + +
243B LEU 4.0 1.3 - - - +
245B HIS* 1.3 93.0 - - + +
247B ASP* 1.3 72.3 + - - +
248B MET* 3.3 23.7 - - + +
251B LYS* 5.5 0.2 + - - -
263B LYS* 3.8 31.1 + - + +
264B LEU* 3.8 34.8 - - + +
267B GLU* 3.8 33.0 - - + +
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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