Contacts of the helix formed by residues 234 - 246 (chain A) in PDB entry 3ITX
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 ASP 234 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220A HIS* 3.4 21.2 - - + +
232A VAL 3.6 0.8 - - - -
233A GLN* 1.3 102.1 + - + +
235A TRP* 1.3 67.8 + - + +
236A GLY* 3.0 13.3 + - - -
237A THR* 3.1 11.4 + - - -
238A ASN 3.0 21.7 + - - -
258A HIS* 6.2 2.0 - - + -
235C TRP* 2.8 28.0 + - - -
262C THR* 6.0 1.6 - - - +
267C ILE* 5.0 2.1 - - - +
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Residues in contact with TRP 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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220A HIS* 3.6 19.1 - - + +
234A ASP* 1.3 79.2 - - + +
236A GLY* 1.3 62.1 + - - +
238A ASN* 3.6 9.7 - - + +
239A TYR* 2.8 40.2 + + + +
258A HIS* 5.7 0.4 - - - -
267A ILE* 3.4 47.4 - - + +
270A ARG* 3.6 30.1 - - + -
271A LEU* 3.9 28.5 - - + +
233C GLN* 4.1 4.5 - - - -
234C ASP* 2.8 28.8 + - - -
236C GLY* 3.7 11.1 - - - -
237C THR* 3.4 38.6 - - - -
240C LEU* 3.9 16.2 - - + -
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Residues in contact with GLY 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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234A ASP* 3.0 8.6 + - - -
235A TRP* 1.3 85.1 - - - +
237A THR* 1.3 61.6 + - - +
239A TYR* 3.2 7.6 + - - +
240A LEU* 3.1 24.4 + - - +
235C TRP* 3.7 18.6 - - - -
236C GLY* 4.0 21.8 - - - -
239C TYR* 6.0 0.3 - - - -
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Residues in contact with THR 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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196A PHE* 3.5 26.5 - - + -
231A VAL 3.5 21.3 - - - +
232A VAL* 4.1 3.1 - - - -
233A GLN* 2.6 29.7 + - - -
234A ASP* 3.1 8.8 + - - -
236A GLY* 1.3 74.9 - - - +
238A ASN* 1.3 63.9 + - - +
240A LEU* 3.1 13.6 + - - +
241A ILE* 3.0 28.4 + - + +
235C TRP* 3.5 3.5 - - - -
270C ARG* 3.1 20.1 + - - +
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Residues in contact with ASN 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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218A SER* 2.6 50.9 + - - +
220A HIS* 2.9 31.9 + - + +
232A VAL* 4.4 2.9 - - - +
234A ASP 3.0 17.5 + - - +
235A TRP* 3.6 9.4 - - - +
236A GLY 3.2 0.2 - - - -
237A THR* 1.3 77.4 - - - +
239A TYR* 1.3 61.3 + - - +
241A ILE* 3.1 9.2 + - - +
242A ALA 3.0 19.4 + - - -
251A CYS* 3.3 26.3 - - - +
252A LEU 3.8 2.2 + - - -
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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
----------------------------------------------------------
235A TRP* 2.8 33.5 + + + +
236A GLY* 3.5 6.5 - - - +
238A ASN* 1.3 73.7 - - - +
240A LEU* 1.3 68.0 + - - +
242A ALA* 3.3 0.7 + - - -
243A GLN* 2.8 61.2 + - + +
251A CYS* 3.8 8.2 - - - -
271A LEU* 4.6 7.9 - - + -
274A PHE* 3.9 30.4 - - + +
276A LYS* 3.8 32.3 - - + -
236C GLY 6.0 0.2 - - - -
239C TYR* 4.3 23.3 - + - -
240C LEU* 3.4 29.8 - - + +
243C GLN* 6.4 0.2 - - + -
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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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196A PHE* 4.3 10.8 - - + -
236A GLY 3.1 13.8 + - - +
237A THR* 3.1 10.5 + - - +
239A TYR* 1.3 77.6 - - + +
241A ILE* 1.3 54.5 + - - +
243A GLN* 4.1 3.2 - - + +
244A THR* 2.6 38.4 + - - -
235C TRP* 3.8 31.2 - - + -
239C TYR* 3.5 47.1 - - + +
270C ARG* 4.5 4.0 - - + +
274C PHE* 3.7 44.0 - - + -
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Residues in contact with ILE 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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196A PHE* 3.5 22.4 - - + -
199A TYR* 3.3 39.0 - - + +
200A LEU* 3.9 10.8 - - + -
203A MET* 4.7 0.2 - - + -
218A SER* 3.8 14.1 - - - +
232A VAL* 3.7 28.0 - - + -
237A THR* 3.0 20.6 + - + +
238A ASN* 3.3 10.8 - - - +
240A LEU* 1.3 74.0 - - - +
242A ALA* 1.3 60.9 + - - +
244A THR* 3.2 2.6 + - - -
245A LEU* 2.9 55.1 + - + +
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Residues in contact with ALA 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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218A SER* 5.1 0.9 - - - +
238A ASN 3.0 15.8 + - - +
239A TYR 3.9 1.6 - - - +
241A ILE* 1.3 78.2 - - - +
243A GLN* 1.3 63.3 + - - +
245A LEU 3.4 0.2 + - - -
246A GLY 3.2 17.3 + - - +
249A ALA* 3.4 32.2 - - - +
250A GLN* 3.9 4.0 - - - +
251A CYS* 3.8 15.9 - - - -
276A LYS* 3.2 29.0 + - + -
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Residues in contact with GLN 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* 2.8 55.6 + - + +
240A LEU* 4.1 4.3 - - + +
242A ALA* 1.3 75.2 - - - +
244A THR* 1.3 62.1 + - - +
246A GLY* 4.0 6.8 + - - -
274A PHE 5.0 2.4 - - - +
276A LYS* 3.7 19.8 + - - +
239C TYR* 6.4 0.4 - - + -
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Residues in contact with THR 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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200A LEU* 4.5 23.2 - - + +
240A LEU 2.6 23.2 + - - -
241A ILE* 3.2 5.8 + - - -
243A GLN* 1.3 80.1 - - - +
245A LEU* 1.3 67.4 + - + +
246A GLY* 4.6 0.2 - - - -
274C PHE* 4.4 16.6 - - - -
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Residues in contact with LEU 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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200A LEU* 4.0 9.9 - - + +
203A MET* 3.9 17.7 - - + +
204A ALA* 3.7 35.0 - - + +
207A TYR* 3.5 27.2 - - + -
216A LEU* 4.0 26.5 - - + -
218A SER* 5.7 0.7 - - - +
241A ILE* 2.9 38.2 + - + +
242A ALA 3.4 0.2 + - - -
244A THR* 1.3 85.6 - - + +
246A GLY* 1.3 57.3 + - - +
249A ALA* 3.5 20.6 - - + -
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Residues in contact with GLY 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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207A TYR* 3.4 4.3 - - - -
242A ALA 3.2 6.4 + - - +
243A GLN 4.0 5.3 + - - -
244A THR 3.5 2.4 - - - -
245A LEU* 1.3 80.6 - - - +
247A PRO* 1.3 70.0 - - - +
248A LYS 3.2 2.9 - - - -
249A ALA 3.0 13.9 + - - -
276A LYS* 2.9 21.6 + - - -
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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