Contacts of the helix formed by residues 258 - 270 (chain A) in PDB entry 2C1H
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 TYR 258 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A TYR* 3.5 39.7 - + + +
203A SER* 4.4 0.5 + - - -
205A PHE* 5.5 2.9 - + - -
229A PRO* 3.4 21.7 - - - +
252A VAL* 4.2 5.8 - - + +
254A PRO* 3.2 56.8 - - + +
255A GLY 2.9 5.8 + - - +
257A ALA* 1.3 96.1 - - + +
259A LEU* 1.3 61.1 + - - +
260A ASP* 3.1 6.7 - - - -
261A ILE* 3.2 15.6 + - + +
262A VAL* 3.4 13.4 + - - +
302B GLU* 2.9 23.2 + - - -
306B CYS* 3.4 16.0 - - - -
309B ARG* 3.3 36.6 - - - +
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Residues in contact with LEU 259 (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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255A GLY 3.2 24.2 + - - +
256A LEU* 3.4 20.3 + - + +
257A ALA 3.7 0.8 - - - -
258A TYR* 1.3 76.5 - - - +
260A ASP* 1.3 59.8 + - - +
261A ILE 3.4 0.2 - - - -
262A VAL* 3.6 8.3 - - - +
263A TRP 3.2 13.3 + - - -
275A ILE* 4.0 5.4 - - + -
306A CYS* 3.2 28.0 - - + +
307A MET* 3.9 19.7 - - + -
309A ARG* 3.8 0.2 - - - +
310A ALA* 3.4 15.5 - - + +
257B ALA* 3.2 31.2 - - - +
259B LEU* 4.4 4.8 - - - +
260B ASP* 3.2 34.8 - - - +
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Residues in contact with ASP 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A THR* 4.0 5.5 - - - +
258A TYR* 3.6 3.3 - - - -
259A LEU* 1.3 77.5 - - - +
261A ILE* 1.3 75.4 + - - +
263A TRP* 3.4 4.2 + - - +
264A ARG* 3.2 28.0 + - - +
259B LEU* 3.2 27.4 - - - +
260B ASP* 3.8 7.1 - - - +
263B TRP* 3.9 15.4 - - + -
309B ARG* 2.9 45.2 + - - +
310B ALA* 3.3 23.2 - - + -
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Residues in contact with ILE 261 (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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199A ALA* 4.6 2.0 - - + -
201A TYR* 3.2 28.7 - - + +
232A THR* 3.5 28.7 - - + +
235A ALA* 3.8 22.7 - - + -
236A MET* 4.6 2.7 - - + -
252A VAL* 3.8 24.7 - - + -
258A TYR* 3.2 10.7 + - + +
260A ASP* 1.3 87.5 + - - +
262A VAL* 1.3 61.0 + - - +
264A ARG* 3.3 6.6 + - - +
265A THR* 2.7 37.1 + - - +
309B ARG* 3.4 26.0 - - - +
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Residues in contact with VAL 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A VAL* 4.1 22.7 - - + -
258A TYR 3.4 16.2 - - - +
259A LEU* 3.6 11.4 - - + +
261A ILE* 1.3 76.7 - - - +
263A TRP* 1.3 61.2 + - - +
265A THR* 3.3 4.2 + - - -
266A LYS* 3.1 22.3 + - - +
273A VAL* 3.8 15.7 - - + +
275A ILE* 3.7 26.7 - - + -
310A ALA* 3.8 11.2 - - + +
311A GLY 4.1 0.2 - - - -
312A ALA* 3.8 33.7 - - + +
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Residues in contact with TRP 263 (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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259A LEU 3.2 10.8 + - - +
260A ASP 3.6 7.9 - - - +
261A ILE 3.3 0.2 - - - -
262A VAL* 1.3 78.5 - - - +
264A ARG* 1.3 60.3 + - - +
266A LYS* 3.4 5.4 + - + +
267A GLU* 3.1 59.4 + - + +
309A ARG 4.0 14.8 - - - -
310A ALA* 3.3 37.6 + - - +
311A GLY* 4.9 3.4 - - - -
232B THR* 4.1 11.9 - - + -
233B GLU* 4.8 2.7 - - - -
260B ASP* 3.9 13.5 - - + -
263B TRP* 3.9 24.0 - + - -
264B ARG* 3.3 56.4 - - + +
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Residues in contact with ARG 264 (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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232A THR* 3.3 46.0 - - - +
233A GLU* 2.8 33.7 + - - +
236A MET* 3.5 39.0 - - + +
260A ASP 3.2 15.4 + - - +
261A ILE* 3.6 5.4 - - - +
263A TRP* 1.3 78.2 - - - +
265A THR* 1.3 60.3 + - - +
267A GLU* 3.7 4.1 + - - +
268A ARG* 3.2 33.4 + - - +
263B TRP* 3.4 46.4 - - - +
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Residues in contact with THR 265 (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 MET* 3.6 11.9 - - - +
239A VAL* 3.9 32.7 - - + +
250A VAL* 4.1 18.2 - - + +
252A VAL* 3.9 15.1 - - + +
261A ILE* 2.7 24.2 + - - +
262A VAL* 3.7 7.2 - - - -
263A TRP 3.3 0.2 - - - -
264A ARG* 1.3 77.1 - - - +
266A LYS* 1.3 61.9 + - - +
269A PHE* 3.4 31.3 + - + +
271A VAL 5.2 0.5 - - - +
273A VAL* 4.1 15.4 - - + +
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Residues in contact with LYS 266 (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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262A VAL 3.1 17.1 + - - +
263A TRP* 3.9 7.2 - - + +
264A ARG 3.4 0.2 - - - -
265A THR* 1.3 72.9 - - - +
267A GLU* 1.3 65.8 + - - +
268A ARG 3.2 6.0 + - - -
269A PHE 4.2 3.6 + - - -
270A ASP* 4.5 8.0 + - - +
271A VAL 4.5 8.5 + - - +
272A PRO* 5.7 0.4 - - - -
273A VAL* 3.7 17.5 - - + +
310A ALA 4.7 0.4 - - - +
311A GLY* 3.3 33.2 - - - +
313A ASP* 3.6 23.1 - - - +
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Residues in contact with GLU 267 (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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263A TRP* 3.1 59.3 + - + +
264A ARG* 4.3 5.4 - - - +
265A THR 3.4 0.6 - - - -
266A LYS* 1.3 81.1 - - - +
268A ARG* 1.3 57.7 + - + +
269A PHE 3.9 0.2 - - - -
270A ASP* 5.5 1.0 - - - +
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Residues in contact with ARG 268 (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 MET* 3.3 41.7 - - - +
240A GLU* 5.4 6.7 + - - -
264A ARG* 3.2 26.2 + - - +
266A LYS 3.2 0.4 - - - -
267A GLU* 1.3 81.1 - - + +
269A PHE* 1.3 86.9 + - + +
270A ASP* 4.0 7.8 - - - +
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Residues in contact with PHE 269 (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 MET* 3.5 38.6 - - + -
239A VAL* 3.7 20.9 - - + -
240A GLU* 3.6 38.1 - - + -
243A ILE* 3.6 30.9 - - + +
250A VAL* 5.7 0.7 - - + -
265A THR* 3.4 29.8 + - + +
266A LYS 4.2 0.2 + - - -
268A ARG* 1.3 109.2 - - + +
270A ASP* 1.3 73.5 + - - +
271A VAL* 3.0 15.2 + - + +
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Residues in contact with ASP 270 (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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265A THR 4.9 0.4 + - - -
266A LYS* 4.5 10.7 + - - +
267A GLU 5.5 0.9 - - - +
268A ARG* 4.1 5.4 + - - +
269A PHE* 1.3 82.1 + - - +
271A VAL* 1.3 61.1 + - - +
272A PRO* 4.7 1.0 - - - +
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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