Contacts of the helix formed by residues 258 - 267 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302A GLU* 2.8 24.6 + - - -
306A CYS* 3.5 16.3 - - - -
309A ARG* 3.3 37.0 - - - +
201B TYR* 3.5 41.0 - + + +
205B PHE* 5.6 2.7 - + - -
229B PRO* 3.5 19.3 - - + +
252B VAL* 4.0 6.0 - - + +
254B PRO* 3.2 58.1 - - + +
255B GLY 2.9 5.8 + - - +
257B ALA* 1.3 95.1 - - + +
259B LEU* 1.3 63.1 + - - +
260B ASP* 3.2 4.3 - - - -
261B ILE* 3.2 15.1 + - + +
262B VAL* 3.3 14.5 + - - +
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Residues in contact with LEU 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A ALA* 3.4 28.0 - - + +
259A LEU* 4.4 4.3 - - - +
260A ASP* 3.2 26.1 - - + +
255B GLY 3.5 8.8 + - - +
256B LEU* 3.4 22.4 + - + +
257B ALA 3.8 0.6 - - - -
258B TYR* 1.3 74.7 - - - +
260B ASP* 1.3 59.1 + - - +
262B VAL* 3.5 7.4 + - + +
263B TRP 3.1 21.0 + - - -
275B ILE* 3.5 32.3 - - + -
306B CYS* 4.0 18.2 - - + +
307B MET* 4.0 11.0 - - + +
309B ARG* 5.0 0.7 - - - +
310B ALA* 3.4 26.1 - - + +
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Residues in contact with ASP 260 (chain B).
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 28.6 - - - +
260A ASP* 3.8 8.0 - - - +
263A TRP* 3.9 18.1 - - + -
309A ARG* 2.8 43.6 + - - -
310A ALA* 3.6 20.3 + - + -
232B THR* 3.9 8.5 - - - +
258B TYR 3.5 4.0 - - - -
259B LEU* 1.3 78.2 - - - +
261B ILE* 1.3 67.4 + - - +
263B TRP* 3.3 4.3 + - - +
264B ARG* 3.0 33.1 + - - +
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Residues in contact with ILE 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A ARG* 3.6 23.3 - - - +
199B ALA* 4.5 3.6 - - + -
201B TYR* 3.3 27.4 - - + +
232B THR* 3.5 36.6 - - + +
235B ALA* 3.7 24.7 - - + -
236B MET* 4.8 1.3 - - + -
252B VAL* 3.8 24.5 - - + -
258B TYR* 3.2 9.8 + - + +
260B ASP* 1.3 77.0 - - - +
262B VAL* 1.3 59.5 + - - +
264B ARG* 3.3 7.1 + - - +
265B THR* 2.9 37.7 + - - +
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Residues in contact with VAL 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B VAL* 3.8 24.7 - - + -
258B TYR 3.4 15.3 - - - +
259B LEU* 3.6 11.9 - - + +
261B ILE* 1.3 77.0 - - - +
263B TRP* 1.3 59.9 + - - +
265B THR* 3.4 3.8 + - - -
266B LYS* 3.1 23.0 + - - +
273B VAL* 4.1 12.0 - - + +
275B ILE* 3.7 26.9 - - + -
310B ALA* 3.7 17.7 - - + +
311B GLY 4.3 0.2 - - - -
312B ALA* 4.0 30.1 - - + +
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Residues in contact with TRP 263 (chain B).
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* 4.4 10.1 - - + -
233A GLU* 4.9 3.4 - - - -
260A ASP* 3.9 13.0 - - + -
263A TRP* 3.9 21.7 - + - -
264A ARG* 3.4 61.6 - - + +
259B LEU 3.1 14.0 + - - +
260B ASP* 3.3 7.6 + - - +
262B VAL* 1.3 74.1 - - - +
264B ARG* 1.3 63.6 + - - +
266B LYS* 3.4 5.7 + - + +
267B GLU* 3.1 60.1 + - + +
309B ARG 4.1 13.7 - - - -
310B ALA* 3.3 31.4 + - - +
311B GLY* 4.8 3.6 - - - -
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Residues in contact with ARG 264 (chain B).
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* 3.3 44.1 - - + +
232B THR* 3.3 49.9 + - - +
233B GLU* 2.8 33.5 + - - +
236B MET* 3.6 37.1 - - + +
260B ASP 3.0 18.3 + - - +
261B ILE* 3.6 7.2 - - - +
263B TRP* 1.3 78.0 - - - +
265B THR* 1.3 60.8 + - - +
267B GLU* 3.6 3.9 + - - +
268B ARG* 3.2 35.2 + - - +
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Residues in contact with THR 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B MET* 3.5 13.2 - - - +
239B VAL* 4.1 22.2 - - + +
250B VAL* 3.9 21.8 - - + -
252B VAL* 4.0 11.8 - - + +
261B ILE* 2.9 20.9 + - - +
262B VAL* 3.7 6.5 - - - -
263B TRP 3.3 0.2 - - - -
264B ARG* 1.3 77.3 - - - +
266B LYS* 1.3 59.5 + - - +
269B PHE* 3.3 33.2 + - + +
270B ASP 4.7 0.2 + - - -
271B VAL 5.3 0.3 - - - +
273B VAL* 3.8 22.4 - - + +
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Residues in contact with LYS 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B VAL 3.1 17.3 + - - +
263B TRP* 3.9 6.5 - - + +
264B ARG 3.4 0.2 - - - -
265B THR* 1.3 77.4 - - - +
267B GLU* 1.3 66.4 + - - +
268B ARG 3.2 2.8 + - - -
269B PHE 4.4 2.8 + - - -
270B ASP* 4.6 13.9 + - - +
271B VAL 4.9 6.7 - - - +
272B PRO* 6.1 0.4 - - - -
273B VAL* 4.0 15.9 - - + -
310B ALA 4.6 0.7 - - - +
311B GLY* 3.2 37.0 - - - +
313B ASP* 4.0 17.9 - - - +
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Residues in contact with GLU 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B TRP* 3.1 60.7 + - + +
264B ARG* 4.3 4.9 - - - +
265B THR 3.4 0.4 - - - -
266B LYS* 1.3 80.4 - - - +
268B ARG* 1.3 58.9 + - + +
270B ASP* 5.4 2.3 - - - +
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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