Contacts of the helix formed by residues 236 - 249 (chain A) in PDB entry 4OI0
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 236 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233A TRP* 5.6 0.4 - - - -
234A VAL 4.2 0.2 + - - -
235A ASP* 1.3 71.7 - - - +
237A GLU* 1.3 58.8 + - - -
239A TYR* 3.1 26.9 + - - +
240A LYS* 3.9 4.5 + - - +
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Residues in contact with GLU 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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194A SER* 5.1 3.8 - - - -
197A LEU* 3.7 28.0 - - + +
233A TRP* 3.7 26.5 - - + -
235A ASP 3.1 1.0 + - - -
236A GLY* 1.3 69.4 - - - -
238A GLY* 1.3 62.5 + - - +
239A TYR 3.3 0.2 - - - -
240A LYS* 3.5 10.7 + - - +
241A CYS* 3.3 23.6 + - - -
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Residues in contact with GLY 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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233A TRP* 3.3 47.8 - - - +
234A VAL 4.2 0.2 - - - -
235A ASP 2.8 11.3 + - - -
237A GLU* 1.3 76.5 - - - +
239A TYR* 1.3 64.3 + - - +
241A CYS* 3.2 16.5 + - - +
242A ILE* 3.3 13.5 + - - +
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Residues in contact with TYR 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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234A VAL 3.3 18.2 + - - +
235A ASP 4.6 0.9 - - - -
236A GLY 3.1 14.4 + - - +
238A GLY* 1.3 77.4 - - - +
240A LYS* 1.3 74.5 + - + +
242A ILE* 3.1 18.1 + - + +
243A VAL* 3.2 20.5 + - + +
261A ARG* 6.4 0.2 - - - -
262A LEU* 3.6 24.7 - - + -
265A ASP* 3.4 43.3 + - + +
266A LEU* 3.7 21.7 + - + +
269A GLU* 2.8 31.7 + - - +
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Residues in contact with LYS 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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197A LEU* 6.1 0.9 - - + -
201A GLU* 4.5 4.5 - - - +
236A GLY 3.9 4.6 + - - +
237A GLU* 3.5 11.9 + - - +
238A GLY 3.3 0.4 - - - -
239A TYR* 1.3 90.4 - - + +
241A CYS* 1.3 64.4 + - - +
243A VAL* 3.4 9.5 + - + +
244A LYS* 3.0 47.0 + - - +
269A GLU* 5.4 7.2 - - - -
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Residues in contact with CYS 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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193A PRO* 4.6 2.9 - - - -
197A LEU* 3.6 31.2 - - - -
200A TYR* 3.8 29.8 - - + -
201A GLU* 4.0 14.5 + - - -
204A PHE* 3.8 6.3 - - + -
233A TRP* 4.9 1.6 - - - -
237A GLU 3.3 12.9 + - - -
238A GLY* 3.2 14.5 + - - +
239A TYR 3.2 0.4 - - - -
240A LYS* 1.3 74.9 - - - +
242A ILE* 1.3 54.6 + - + +
244A LYS* 3.4 2.9 + - - -
245A ALA* 2.7 36.9 + - - +
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Residues in contact with ILE 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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118A LEU* 3.9 5.6 - - + +
120A VAL* 3.8 40.2 - - + -
230A THR* 5.2 11.4 - - + +
231A CYS 5.7 1.6 - - - +
233A TRP 4.4 2.9 - - - +
234A VAL* 4.1 27.1 - - + -
238A GLY 3.5 12.6 - - - +
239A TYR* 3.1 9.8 + - + +
241A CYS* 1.3 77.4 - - + +
243A VAL* 1.3 57.1 + - - +
245A ALA* 3.3 6.2 + - - +
246A ALA* 2.9 30.0 + - + +
254A VAL* 6.3 0.2 - - + -
262A LEU* 4.1 16.6 - - + -
266A LEU* 4.0 27.4 - - + -
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Residues in contact with VAL 243 (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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239A TYR* 3.2 27.2 + - + +
240A LYS* 3.8 11.9 - - + +
241A CYS 3.4 0.2 - - - -
242A ILE* 1.3 76.4 - - - +
244A LYS* 1.3 63.1 + - + +
246A ALA* 3.4 8.2 + - - +
247A SER* 3.0 28.2 + - - -
266A LEU* 4.1 11.9 - - + -
269A GLU* 3.6 38.6 - - + +
270A LEU* 5.0 10.7 - - + +
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Residues in contact with LYS 244 (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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201A GLU* 3.4 38.1 + - + +
204A PHE* 3.7 13.4 - - + -
240A LYS* 3.0 34.3 + - + +
241A CYS 3.8 2.9 - - - +
243A VAL* 1.3 79.5 - - + +
245A ALA* 1.3 59.7 + - - +
247A SER* 3.7 6.3 - - - -
248A ALA* 2.9 32.1 + - - +
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Residues in contact with ALA 245 (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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118A LEU* 4.4 13.9 - - + -
150A LEU* 4.2 26.0 - - + -
204A PHE* 3.7 17.6 - - + -
230A THR* 5.0 2.9 - - + -
241A CYS 2.7 22.0 + - - +
242A ILE* 3.6 7.2 - - - +
244A LYS* 1.3 69.1 - - - +
246A ALA* 1.3 65.5 + - - +
249A PHE* 3.1 31.4 + - + +
251A VAL* 4.6 0.3 - - - +
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Residues in contact with ALA 246 (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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118A LEU* 4.0 10.9 - - + +
242A ILE* 2.9 18.0 + - + +
243A VAL 3.5 5.4 - - - +
245A ALA* 1.3 74.0 - - - +
247A SER* 1.3 63.0 + - - +
250A GLU* 3.1 3.5 + - - -
251A VAL* 3.1 50.0 + - + +
254A VAL* 4.8 1.8 - - + -
270A LEU* 3.9 26.0 - - + -
271A PRO* 6.2 0.7 - - + -
274A VAL* 6.1 0.7 - - + -
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Residues in contact with SER 247 (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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243A VAL* 3.0 18.8 + - - -
244A LYS* 3.7 7.6 - - - -
246A ALA* 1.3 76.9 - - - +
248A ALA* 1.3 64.4 + - - +
250A GLU* 3.1 21.1 + - - +
271A PRO* 6.6 0.2 - - - -
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Residues in contact with ALA 248 (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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204A PHE* 4.1 14.1 - - + -
205A LYS* 4.1 26.7 - - + -
208A ALA* 3.4 20.8 - - + +
212A ASN* 5.0 4.2 + - - -
244A LYS 2.9 21.7 + - - +
245A ALA 4.0 2.5 - - - +
247A SER* 1.3 74.5 + - - +
249A PHE* 1.3 61.8 + - + +
250A GLU* 3.3 7.7 + - - +
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Residues in contact with PHE 249 (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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116A ARG* 2.8 31.7 + - - +
148A VAL* 3.9 22.7 - - + -
150A LEU* 4.3 11.7 - - + -
204A PHE* 3.5 44.2 - + + -
207A MET* 3.8 18.2 - - + -
208A ALA* 3.7 21.5 - - + -
211A LEU* 4.1 7.0 - - + -
226A MET* 4.0 20.0 - - + -
228A ILE* 3.6 26.5 - - + -
245A ALA* 3.1 23.9 + - + +
248A ALA* 1.3 77.4 - - + +
250A GLU* 1.3 68.5 + - - +
251A VAL* 3.3 2.6 + - + -
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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