Contacts of the helix formed by residues 230 - 242 (chain B) in PDB entry 2G1O
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 230 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229B GLY* 1.3 74.4 - - - -
231B THR* 1.3 66.7 + - - +
232B SER* 3.2 10.8 + - - -
233B SER* 3.0 31.4 + - - -
234B ILE* 2.9 21.8 + - - +
297B ALA* 4.7 0.2 - - - -
298B MET 4.3 2.9 - - - -
299B ASP* 3.6 12.3 - - - +
306B PRO* 5.2 14.4 - - - -
307B THR 5.0 3.5 + - - -
308B TRP* 5.2 2.2 - - - +
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Residues in contact with THR 231 (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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229B GLY 3.9 0.8 + - - -
230B SER* 1.3 71.3 - - - +
232B SER* 1.3 63.7 + - - +
234B ILE* 3.5 2.1 + - - +
235B GLU* 3.0 48.0 + - + +
297B ALA* 3.9 22.6 - - + +
298B MET 5.0 0.2 + - - -
299B ASP* 2.6 37.6 + - - -
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Residues in contact with SER 232 (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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230B SER* 3.2 11.3 + - - -
231B THR* 1.3 78.7 - - - +
233B SER* 1.3 65.5 + - - +
235B GLU* 3.2 14.0 + - - +
236B LYS* 3.2 43.1 + - - +
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Residues in contact with SER 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B LEU* 4.1 12.9 - - - +
212B CYS 5.8 1.6 + - - -
230B SER* 3.0 29.4 + - - -
232B SER* 1.3 82.3 + - - +
234B ILE* 1.3 65.2 + - - +
236B LYS* 3.3 13.3 + - - +
237B LEU* 3.0 21.5 + - - +
308B TRP* 3.8 31.3 + - - -
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Residues in contact with ILE 234 (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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229B GLY* 3.7 17.3 - - - +
230B SER 2.9 18.3 + - - +
231B THR 4.0 3.6 - - - +
233B SER* 1.3 72.3 - - - +
235B GLU* 1.3 52.3 + - - +
237B LEU* 3.1 13.4 + - + +
238B MET* 2.7 48.9 + - + +
250B TYR* 3.8 27.4 - - + +
295B ILE* 3.7 20.9 - - + -
296B HIS 3.5 25.1 - - - +
297B ALA* 3.5 23.1 - - + +
308B TRP* 4.4 7.2 - - + -
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Residues in contact with GLU 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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231B THR* 3.0 41.8 + - + +
232B SER* 3.4 12.9 - - - +
233B SER 3.2 0.4 - - - -
234B ILE* 1.3 76.9 - - - +
236B LYS* 1.3 63.5 + - + +
238B MET* 3.4 2.3 + - - +
239B GLU* 3.0 25.7 + - - +
250B TYR* 3.9 20.0 - - - +
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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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210B LEU* 4.9 6.1 - - + +
211B LEU* 3.9 22.3 - - + +
232B SER* 3.2 37.2 + - - +
233B SER* 3.7 9.3 + - - +
235B GLU* 1.3 78.1 - - + +
237B LEU* 1.3 61.7 + - - +
239B GLU* 3.4 10.0 + - - +
240B ALA* 3.1 24.1 + - - +
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Residues in contact with LEU 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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203B VAL* 5.2 0.9 - - + -
205B VAL* 3.2 34.3 - - + -
210B LEU* 6.5 0.2 - - - -
211B LEU* 3.7 14.8 - - + +
233B SER 3.0 14.2 + - - +
234B ILE* 3.3 18.2 - - + +
236B LYS* 1.3 77.9 - - - +
238B MET* 1.3 62.5 + - + +
240B ALA* 3.3 5.0 + - - +
241B LEU* 2.9 35.6 + - + +
263B ILE* 4.2 19.1 - - + -
265B PHE* 6.3 0.7 - - + -
295B ILE* 4.2 35.2 - - + -
308B TRP* 4.5 14.1 - - + -
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Residues in contact with MET 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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234B ILE* 2.7 33.6 + - + +
235B GLU 4.0 3.1 - - - +
237B LEU* 1.3 73.2 - - + +
239B GLU* 1.3 61.7 + - - +
241B LEU* 3.0 7.2 + - + -
242B GLY 2.8 24.9 + - - -
243B ALA* 3.1 26.0 + - - +
250B TYR* 3.5 51.4 - - + -
293B LEU* 3.5 33.0 - - + -
295B ILE* 3.6 36.6 - - + +
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Residues in contact with GLU 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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235B GLU 3.0 18.8 + - - +
236B LYS* 3.8 8.6 - - - +
238B MET* 1.3 76.8 - - - +
240B ALA* 1.3 61.7 + - - +
242B GLY* 3.3 12.3 + - - -
243B ALA 4.8 3.6 - - - -
244B LYS* 6.0 5.6 - - - +
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Residues in contact with ALA 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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205B VAL* 4.4 15.3 - - + +
210B LEU* 3.9 27.6 - - + -
236B LYS 3.1 17.3 + - - +
237B LEU* 3.6 7.6 - - - +
238B MET 3.1 0.2 - - - -
239B GLU* 1.3 77.1 - - - +
241B LEU* 1.3 63.0 + - - +
242B GLY 3.7 0.2 + - - -
261B PRO* 4.9 4.2 - - - +
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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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205B VAL* 3.5 30.3 - - + -
237B LEU* 2.9 24.3 + - + +
238B MET* 3.0 11.2 + - - +
240B ALA* 1.3 79.8 - - - +
242B GLY* 1.3 57.6 + - - +
243B ALA* 3.2 8.1 + - + +
252B VAL* 5.7 0.7 - - - +
260B LEU* 3.3 33.6 - - + +
261B PRO* 3.6 15.2 - - + +
263B ILE* 4.1 16.2 - - + -
279B TYR* 3.5 37.5 - - + +
293B LEU* 4.0 16.8 - - + -
295B ILE* 5.0 2.0 - - + -
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Residues in contact with GLY 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 MET 2.8 4.7 + - - -
239B GLU* 3.3 11.4 + - - -
240B ALA 3.4 0.6 - - - -
241B LEU* 1.3 77.6 - - - +
243B ALA* 1.3 62.9 + - - +
244B LYS* 3.7 17.7 + - - +
252B VAL* 5.7 5.1 - - - +
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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