Contacts of the helix formed by residues 235 - 243 (chain B) in PDB entry 1AHF
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 GLU 235 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230B ARG* 3.3 52.7 + - + +
231B GLY* 3.2 37.6 - - - +
233B LEU 4.4 0.3 + - - -
234B GLU* 1.3 79.3 + - - +
236B ASP* 1.3 62.0 + - - +
237B ALA 3.0 6.3 + - - -
238B GLU* 3.4 22.5 + - - +
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Residues in contact with ASP 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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190B GLY 3.8 12.1 - - - +
191B CYS* 3.8 18.6 - - - +
223B PHE* 3.1 22.6 - - + -
226B GLN* 4.5 0.2 - - + -
227B GLY 3.2 16.4 + - - +
228B PHE 3.4 0.5 + - - -
229B ALA* 3.0 35.5 + - - +
230B ARG* 2.9 26.1 + - - +
231B GLY 2.8 23.2 + - - +
233B LEU 4.1 2.7 - - - +
235B GLU* 1.3 81.0 - - - +
237B ALA* 1.3 56.6 + - - +
238B GLU 3.4 2.0 - - - -
239B GLY 5.0 1.7 + - - -
240B LEU* 5.6 0.5 + - - +
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Residues in contact with ALA 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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87B LEU 3.5 7.6 - - - +
223B PHE* 4.1 9.6 - - + -
226B GLN* 3.9 15.9 - - - +
233B LEU 3.8 1.7 + - - +
234B GLU 3.5 3.8 + - - +
235B GLU 3.0 1.2 - - - -
236B ASP* 1.3 76.1 - - - +
238B GLU* 1.3 55.7 + - - +
239B GLY 3.4 2.0 - - - -
240B LEU* 3.2 5.8 + - + +
241B ARG* 2.8 75.7 + - - +
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Residues in contact with GLU 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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202B LEU* 3.5 43.3 - - + +
205B TRP* 5.7 1.3 - - + -
230B ARG* 3.2 33.4 + - - +
234B GLU 4.0 6.1 + - - +
235B GLU* 3.5 27.7 - - - +
236B ASP 3.4 1.0 - - - -
237B ALA* 1.3 77.8 - - - +
239B GLY* 1.3 58.2 + - - +
241B ARG* 3.7 9.2 - - - +
242B ALA* 3.0 26.3 + - - +
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Residues in contact with GLY 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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190B GLY 5.5 2.3 + - - -
205B TRP* 3.6 42.9 - - - +
221B PHE* 4.2 6.7 - - - -
236B ASP 5.0 2.4 + - - -
237B ALA 3.4 0.6 - - - -
238B GLU* 1.3 76.9 - - - +
240B LEU* 1.3 66.4 + - - +
242B ALA* 3.3 1.5 + - - +
243B PHE* 3.1 30.7 + - - -
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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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87B LEU* 3.7 37.0 - - + +
88B PHE* 3.8 29.4 - - + -
190B GLY* 5.7 2.3 + - - -
221B PHE* 3.8 38.5 - - + -
223B PHE* 4.6 17.3 - - + -
236B ASP 5.6 0.4 + - - +
237B ALA* 3.2 12.3 + - - +
239B GLY* 1.3 75.3 - - - +
241B ARG* 1.3 53.1 + - - +
243B PHE* 2.8 6.6 + - - +
244B ALA* 2.7 34.7 + - + -
250B LEU* 4.6 7.0 - - + -
252B VAL* 4.2 17.5 - - + -
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Residues in contact with ARG 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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86B LEU 4.0 3.2 + - - -
87B LEU 2.3 40.5 + - - +
88B PHE* 2.8 39.2 + - - +
89B GLY* 3.3 5.7 - - - +
234B GLU* 2.7 51.5 + - - +
237B ALA* 2.8 40.7 + - - +
238B GLU* 3.7 8.9 - - - +
240B LEU* 1.3 78.0 - - + +
242B ALA* 1.3 59.5 + - - +
244B ALA* 3.7 10.7 - - - +
245B ALA* 3.4 20.3 + - - +
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Residues in contact with ALA 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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202B LEU* 4.9 7.2 - - + -
205B TRP 4.9 3.8 - - - +
206B GLN* 4.7 29.2 - - + +
209B ALA* 4.2 3.0 - - + +
238B GLU 3.0 18.8 + - - +
239B GLY* 3.8 6.7 - - - +
240B LEU 3.1 0.2 - - - -
241B ARG* 1.3 74.1 - - - +
243B PHE* 1.3 66.6 + - - +
245B ALA* 3.4 10.6 + - - +
246B MET* 3.2 22.3 - - - +
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Residues in contact with PHE 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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188B PHE* 3.8 37.0 - + - -
205B TRP* 3.6 38.6 - + - -
208B LEU* 3.9 8.1 - - + -
209B ALA* 3.8 21.5 - - + -
212B SER* 3.4 18.6 - - - -
219B PRO* 3.6 27.1 - - + -
221B PHE* 3.7 15.5 - + + -
239B GLY 3.1 22.1 + - - +
240B LEU 2.8 8.6 + - - +
242B ALA* 1.3 77.7 - - - +
244B ALA* 1.3 56.6 + - - +
245B ALA 2.9 6.6 + - - -
246B MET 2.9 13.5 + - - -
247B HIS* 3.0 27.5 + - - +
250B LEU* 4.1 7.4 - - + -
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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