Contacts of the helix formed by residues 231 - 243 (chain A) in PDB entry 4I6J
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 231 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A LEU 5.5 0.2 - - - -
72A PHE* 4.3 1.0 - - - -
76A SER* 3.3 29.1 + - - -
79A ASP* 3.7 8.5 - - - -
229A GLN 4.1 0.4 + - - -
230A GLY* 1.3 74.7 - - - -
232A GLU* 1.3 64.9 + - - -
233A THR 3.4 2.9 + - - -
234A GLU* 3.6 3.8 + - - +
235A ALA* 3.2 20.1 + - - +
272A TYR* 3.9 1.9 - - - -
277A CYS* 3.7 15.8 - - - +
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Residues in contact with GLU 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU 4.0 12.2 + - - +
32A ARG* 3.4 2.8 - - - -
33A LEU* 2.9 34.4 + - - +
34A HIS* 2.9 46.1 + - + +
76A SER 5.2 0.6 + - - -
79A ASP* 3.4 7.9 + - - +
80A LEU* 4.2 7.1 - - + +
83A SER* 4.4 9.3 + - - -
231A GLY* 1.3 70.1 - - - -
233A THR* 1.3 58.5 + - - +
235A ALA* 3.0 1.6 + - - +
236A LEU* 2.7 46.2 + - + +
277A CYS* 3.5 18.3 - - - +
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Residues in contact with THR 233 (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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79A ASP* 2.6 33.4 + - - -
83A SER* 4.4 4.7 + - - -
232A GLU* 1.3 80.0 - - - +
234A GLU* 1.3 62.1 + - - +
236A LEU* 3.3 7.0 + - - +
237A ALA* 3.2 21.4 + - + +
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Residues in contact with GLU 234 (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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79A ASP* 4.2 1.0 + - - -
229A GLN* 3.4 40.3 - - + +
230A GLY 4.5 2.9 - - - +
231A GLY 3.6 7.0 + - - +
233A THR* 1.3 78.4 - - - +
235A ALA* 1.3 58.6 + - - +
237A ALA* 3.1 9.2 + - - +
238A ARG* 2.8 64.0 + - - +
272A TYR* 3.4 22.7 - - + +
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Residues in contact with ALA 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A GLY 3.2 9.1 + - - +
232A GLU 3.0 8.6 + - - +
234A GLU* 1.3 77.7 - - - +
236A LEU* 1.3 61.4 + - - +
238A ARG* 3.5 3.5 + - - +
239A LEU* 3.1 22.2 + - - +
269A LEU* 4.4 2.8 - - - +
272A TYR* 3.5 44.2 - - + -
277A CYS 3.6 18.2 - - - +
278A LEU* 4.0 9.8 - - + +
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Residues in contact with LEU 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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34A HIS* 3.7 33.4 - - + +
232A GLU* 2.7 30.4 + - + +
233A THR* 3.8 6.3 - - - +
235A ALA* 1.3 78.3 - - - +
237A ALA* 1.3 57.0 - - - +
239A LEU* 3.5 7.5 - - + +
240A ASP* 2.9 30.5 + - - +
278A LEU* 4.0 8.5 - - + -
282A LEU* 3.8 28.7 - - + -
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Residues in contact with ALA 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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233A THR 3.2 11.2 + - - +
234A GLU* 3.1 12.6 + - - +
236A LEU* 1.3 76.2 - - - +
238A ARG* 1.3 67.3 + - + +
239A LEU 3.1 0.2 - - - -
240A ASP* 3.2 8.8 + - - +
241A LYS* 3.1 37.4 + - - +
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Residues in contact with ARG 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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227A VAL 4.0 15.2 + - - -
228A TRP* 3.6 19.4 - - - +
229A GLN 5.1 0.2 - - - +
234A GLU* 2.8 43.9 + - - +
235A ALA 3.8 2.2 - - - +
237A ALA* 1.3 77.4 - - + +
239A LEU* 1.3 56.1 + - - +
241A LYS* 3.4 6.9 + - + +
242A HIS* 2.8 32.9 + - - +
265A SER 3.6 5.7 + - - -
266A PRO* 3.2 50.4 - - - +
267A THR* 4.2 2.8 - - - +
268A GLY 3.0 22.1 + - - +
269A LEU* 3.6 18.1 - - + +
272A TYR* 3.0 37.9 + - - -
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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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235A ALA 3.1 13.8 + - - +
236A LEU* 3.5 13.7 - - + +
238A ARG* 1.3 75.2 - - - +
240A ASP* 1.3 57.1 + - - +
242A HIS* 3.1 5.5 + - + +
243A LEU* 2.9 41.9 + - + +
269A LEU* 3.8 15.0 - - + +
278A LEU* 3.9 18.6 - - + -
282A LEU* 3.9 31.2 - - + -
283A PHE* 3.7 34.1 - - + +
286A ARG* 4.2 24.2 - - + +
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Residues in contact with ASP 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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236A LEU* 2.9 19.0 + - - +
237A ALA* 3.2 8.9 + - - +
239A LEU* 1.3 77.2 - - - +
241A LYS* 1.3 57.7 + - + +
243A LEU* 3.3 3.5 + - - +
244A GLU* 3.0 25.6 + - - +
286A ARG* 2.7 34.4 + - - +
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Residues in contact with LYS 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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237A ALA* 3.1 27.8 + - - +
238A ARG* 3.9 5.3 - - - +
240A ASP* 1.3 73.5 - - + +
242A HIS* 1.3 67.5 + - - +
244A GLU* 3.1 22.1 + - - +
247A ALA* 4.8 5.7 - - - +
266A PRO* 4.3 23.6 + - + +
267A THR* 4.0 16.0 - - + +
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Residues in contact with HIS 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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238A ARG 2.8 19.6 + - - +
239A LEU* 3.1 9.2 + - - +
241A LYS* 1.3 78.3 - - - +
243A LEU* 1.3 76.9 + - + +
247A ALA* 5.5 0.5 - - - +
248A TRP* 3.5 32.6 + + - +
267A THR* 2.9 39.7 + - - +
268A GLY* 5.4 2.2 - - - -
269A LEU* 4.2 8.7 - - + -
283A PHE* 4.0 25.9 - + - -
287A LEU* 5.6 1.0 - - - +
307A GLN* 5.2 6.0 + - - -
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Residues in contact with LEU 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 LEU* 2.9 28.7 + - + +
240A ASP 3.6 3.8 - - - +
241A LYS 3.1 0.2 - - - -
242A HIS* 1.3 90.4 - - + +
244A GLU* 1.3 67.0 + - - +
245A ARG* 2.8 4.7 + - - -
248A TRP* 4.3 4.3 - - + -
283A PHE* 4.8 2.5 - - + +
286A ARG* 3.3 63.7 - - + +
287A LEU* 3.5 29.6 - - + +
290A LEU* 3.4 32.4 - - + +
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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