Contacts of the helix formed by residues 234 - 242 (chain A) in PDB entry 4ORA
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 GLY 234 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214A GLU* 3.6 14.8 + - - -
231A PRO* 5.5 0.9 - - - -
233A PHE* 1.3 84.0 - - - +
235A PRO* 1.3 71.4 - - - +
236A MET 3.5 1.8 - - - -
237A CYS* 3.4 2.9 + - - +
238A ASP* 2.9 38.5 + - - -
267A TYR* 6.1 1.4 - - - -
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Residues in contact with PRO 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A SER* 3.7 13.2 - - - +
214A GLU* 4.0 27.3 - - + +
215A ILE* 3.6 27.9 - - + +
220A ASP 5.6 0.2 - - - +
224A LEU* 3.8 22.2 - - + -
231A PRO* 6.4 0.4 - - + -
234A GLY* 1.3 83.7 - - - +
236A MET* 1.3 60.9 + - + +
238A ASP* 2.9 4.5 + - - +
239A LEU* 2.8 31.5 + - - +
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Residues in contact with MET 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A ARG* 3.4 20.0 - - - +
196A LEU* 3.7 23.8 - - + -
224A LEU* 4.3 11.7 - - + +
225A ASP 3.9 9.2 - - - +
226A ARG* 3.3 44.6 - - + +
228A LYS* 3.8 18.6 - - + +
230A PRO* 4.3 13.5 - - + -
231A PRO* 4.4 17.3 - - + -
234A GLY 3.5 0.2 - - - -
235A PRO* 1.3 81.6 - - + +
237A CYS* 1.3 64.5 + - - +
239A LEU* 3.4 11.5 + - - +
240A LEU* 3.4 28.5 + - + +
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Residues in contact with CYS 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A PRO* 5.1 4.7 - - - -
231A PRO* 3.3 25.8 + - - +
232A ALA* 3.6 22.2 - - - -
233A PHE* 3.8 13.7 - - - +
234A GLY 3.4 9.5 + - - +
235A PRO 3.3 0.4 - - - -
236A MET* 1.3 76.6 - - - +
238A ASP* 1.3 59.0 + - - +
240A LEU* 3.2 2.7 + - - -
241A TRP* 2.8 53.3 + - - +
265A CYS* 4.2 13.2 - - - -
266A SER* 4.4 9.4 - - - -
492A MET* 4.7 0.7 - - - -
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Residues in contact with ASP 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A GLY 4.3 0.9 - - - -
211A LEU 3.8 5.2 - - - +
212A SER* 2.4 36.0 + - - -
213A PRO* 3.6 0.9 - - - +
214A GLU* 4.7 2.3 - - - +
233A PHE* 5.6 0.3 - - - -
234A GLY* 2.9 21.5 + - - +
235A PRO 2.9 8.3 + - - +
237A CYS* 1.3 74.5 - - - +
239A LEU* 1.3 65.0 + - - +
242A SER* 2.8 34.7 + - - -
266A SER* 2.6 34.9 + - - +
267A TYR* 3.5 28.6 - - - -
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Residues in contact with LEU 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A LEU* 4.1 24.9 - - + +
205A LEU* 5.7 1.3 - - + -
207A VAL* 3.9 24.2 - - + +
208A HIS 4.2 3.6 + - - -
209A GLY 2.7 30.8 + - - -
210A GLY 3.0 24.8 + - - +
211A LEU* 5.4 0.9 - - + -
215A ILE* 3.7 19.3 - - + -
221A ILE* 4.4 20.0 - - + -
224A LEU* 3.6 31.0 - - + -
235A PRO 2.8 16.4 + - - +
236A MET* 3.6 6.7 - - - +
238A ASP* 1.3 72.5 - - - +
240A LEU* 1.3 58.6 + - + +
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Residues in contact with LEU 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A ARG* 3.3 36.6 - - - +
158A GLY 4.1 13.9 - - - +
159A ASN* 3.5 17.7 - - + +
196A LEU* 4.5 18.4 - - + +
208A HIS* 3.3 27.0 - - + +
209A GLY* 3.7 6.0 - - - +
230A PRO* 3.7 33.4 - - + -
236A MET* 3.4 19.7 - - + +
237A CYS* 3.2 6.0 + - - +
238A ASP 3.1 0.8 - - - -
239A LEU* 1.3 83.6 - - + +
241A TRP* 1.3 67.9 + - + +
290A HIS* 3.8 3.1 - - - -
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Residues in contact with TRP 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A ASN* 3.5 40.8 + - + +
165A LEU* 3.8 33.0 - - + -
230A PRO* 5.4 6.2 - - + +
231A PRO 5.7 0.2 - - - -
237A CYS* 2.8 38.7 + - - +
238A ASP 3.0 0.2 + - - -
240A LEU* 1.3 90.4 - - + +
242A SER* 1.3 66.3 + - - +
243A ASP 3.7 0.9 + - - -
260A ASN* 4.2 0.3 + - - -
263A ARG* 3.8 49.4 - - + +
265A CYS* 3.8 9.2 - - - +
266A SER* 3.6 19.0 - - - -
290A HIS* 3.2 15.1 + - - -
490A GLU 4.0 6.3 - - - -
491A ARG 4.3 2.5 - - - -
492A MET* 3.9 49.2 - - + +
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Residues in contact with SER 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A GLY* 3.0 24.4 - - - +
210A GLY* 3.2 15.3 - - - +
211A LEU 2.8 27.2 + - - -
238A ASP 2.8 19.1 + - - -
240A LEU 4.0 0.4 - - - -
241A TRP* 1.3 75.1 - - - +
243A ASP* 1.3 60.2 + - - +
266A SER* 3.6 11.1 + - - -
267A TYR* 3.2 20.9 - - - +
269A TYR* 3.2 10.3 - - - -
288A ARG* 3.2 5.0 + - - -
290A HIS* 3.8 0.2 - - - -
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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