Contacts of the helix formed by residues 203 - 215 (chain D) in PDB entry 1C2O
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 SER 203 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120D GLY* 4.4 11.7 - - - -
121D GLY* 5.2 0.6 - - - -
122D GLY* 4.5 9.4 + - - -
202D GLU* 1.3 92.5 + - - +
204D ALA* 1.4 65.7 + - - -
206D ALA* 3.0 5.0 + - - +
207D ALA* 3.0 16.8 + - - +
228D GLN 3.1 6.5 + - - -
229D SER 3.8 13.5 - - - -
230D GLY* 3.8 4.2 - - - -
236D TRP* 4.0 14.1 - - - -
295D PHE* 5.1 3.8 - - - -
297D PHE* 6.0 1.6 - - - -
338D PHE* 5.4 1.0 - - - -
447D HIS* 2.8 25.1 + - - -
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Residues in contact with ALA 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D TYR 4.6 0.4 - - - -
120D GLY* 3.9 2.8 - - - -
121D GLY 4.4 2.9 - - - +
122D GLY 4.2 4.7 - - - +
123D PHE* 3.5 54.2 - - + +
151D TYR* 4.8 1.8 - - - +
203D SER* 1.4 81.5 + - - +
205D GLY* 1.3 48.6 + - - +
207D ALA* 3.2 7.3 - - - +
208D SER* 2.6 42.5 + - - -
236D TRP* 3.8 9.6 - - + -
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Residues in contact with GLY 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D ILE* 3.2 33.9 - - - +
119D TYR 3.4 7.6 - - - -
120D GLY* 3.5 7.1 - - - -
201D GLY* 4.0 4.3 - - - -
202D GLU 2.6 14.5 + - - -
204D ALA* 1.3 70.7 - - - +
206D ALA* 1.3 49.5 + - - -
208D SER* 2.9 5.9 + - - -
209D VAL* 2.6 37.1 + - - +
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Residues in contact with ALA 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D GLY 3.1 24.8 - - - +
202D GLU 2.7 9.3 + - - -
203D SER 3.1 10.3 - - - +
205D GLY* 1.3 69.6 - - - +
207D ALA* 1.4 52.1 + - - +
209D VAL* 2.9 8.1 + - - +
210D GLY* 2.7 32.7 + - - -
227D LEU* 3.8 11.3 - - - +
228D GLN 3.4 20.4 - - - +
230D GLY 3.3 22.0 - - - +
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Residues in contact with ALA 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D PHE* 4.0 6.3 - - + -
203D SER 3.0 7.9 + - - +
204D ALA* 3.2 20.6 - - - +
206D ALA* 1.4 76.9 - - - +
208D SER* 1.3 56.9 + - - +
210D GLY* 3.3 2.9 + - - -
211D MET* 3.0 31.7 + - + +
230D GLY 4.1 0.8 - - - -
231D THR 3.4 29.2 - - - +
232D PRO* 3.7 3.1 - - - +
236D TRP* 4.0 3.8 - - + -
237D ALA* 3.9 18.8 - - + -
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Residues in contact with SER 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D ILE* 4.2 3.8 - - - -
123D PHE* 3.5 15.9 - - - -
151D TYR* 4.8 0.7 + - - -
173D LEU* 3.8 9.2 - - - +
176D GLN* 3.2 35.8 + - - -
204D ALA 2.6 23.2 + - - -
205D GLY* 2.9 14.2 + - - -
207D ALA* 1.3 70.5 - - - +
209D VAL* 1.4 56.9 + - - +
210D GLY 2.9 0.9 - - - -
211D MET* 2.5 27.9 + - - +
212D HIS* 2.8 16.8 + - - -
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Residues in contact with VAL 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D ILE* 4.4 8.9 - - + +
199D LEU* 4.0 27.5 - - + +
200D PHE 4.1 1.6 - - - +
201D GLY* 3.7 16.2 - - - +
205D GLY 2.6 20.6 + - - +
206D ALA* 3.3 7.2 - - - +
208D SER* 1.4 71.9 - - - +
210D GLY* 1.4 65.7 + - - +
212D HIS* 2.9 21.6 + - - +
213D ILE* 3.1 12.9 + - + +
225D ALA* 3.7 25.4 - - + -
226D VAL 3.6 26.7 - - - +
227D LEU* 4.1 6.3 - - + -
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Residues in contact with GLY 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206D ALA 2.7 13.8 + - - -
207D ALA 3.5 5.6 - - - -
208D SER 2.9 0.4 - - - -
209D VAL* 1.4 79.1 - - - +
211D MET* 1.3 56.4 + - - +
213D ILE* 3.1 11.8 + - - +
214D LEU* 2.9 36.6 + - - +
227D LEU* 3.9 13.0 - - - -
232D PRO* 3.9 14.8 - - - -
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Residues in contact with MET 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D PHE* 3.8 8.1 - - + -
173D LEU* 4.0 19.3 - - + -
207D ALA* 3.0 33.8 + - + +
208D SER* 2.5 15.5 + - - +
210D GLY* 1.3 68.7 - - - +
212D HIS* 1.4 66.7 + - + +
214D LEU* 3.5 5.4 - - + -
215D SER* 2.7 29.2 + - - -
232D PRO* 3.8 18.8 - - + +
237D ALA* 3.8 11.7 - - + +
238D THR* 4.1 4.3 - - + -
301D PRO* 3.7 39.7 - - + -
307D PHE* 4.2 3.1 - - + -
308D LEU* 3.5 33.5 - - + +
312D PRO* 5.5 0.9 - - + -
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Residues in contact with HIS 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D ILE* 4.1 14.3 - - + +
173D LEU* 3.7 13.7 + - + +
176D GLN* 3.1 42.3 + - + -
177D ARG* 3.9 5.7 + - - +
180D LEU* 4.1 17.1 - - + +
199D LEU* 3.9 17.3 - - + +
208D SER 2.8 18.0 + - - -
209D VAL 2.9 6.2 + - - +
211D MET* 1.4 76.7 - - + +
213D ILE* 1.3 58.7 + - - +
215D SER 2.9 29.3 + - - +
218D SER* 2.7 38.6 - - - -
219D ARG* 4.1 2.3 - - - -
222D PHE* 4.1 4.9 - - + -
307D PHE* 3.7 15.5 - + - -
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Residues in contact with ILE 213 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209D VAL 3.1 16.7 + - - +
210D GLY* 3.4 10.8 - - - +
212D HIS* 1.3 77.2 - - - +
214D LEU* 1.3 65.2 + - + +
215D SER 3.4 0.5 + - - -
216D LEU* 5.3 2.1 - - - +
219D ARG* 3.2 35.1 + - - +
222D PHE* 3.8 21.9 - - + -
225D ALA* 3.9 21.1 - - + -
227D LEU* 4.6 11.7 - - + -
321D PHE* 4.1 19.2 - - + -
324D LEU* 3.5 26.5 - - + -
326D VAL* 4.4 7.0 - - + -
414D LEU* 6.4 0.2 - - + -
418D LEU* 5.3 8.3 - - + -
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Residues in contact with LEU 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210D GLY 2.9 24.4 + - - +
211D MET* 3.1 7.8 + - + +
213D ILE* 1.3 80.3 - - + +
215D SER* 1.3 57.3 + - - +
216D LEU* 3.9 5.6 + - - +
232D PRO* 3.3 32.3 - - + -
307D PHE 4.8 2.1 - - - +
308D LEU* 4.4 8.1 - - + -
309D SER* 4.9 3.1 + - - -
312D PRO* 4.5 8.1 - - + -
315D LEU* 3.4 54.6 - - + +
316D ILE* 4.1 14.4 - - + +
321D PHE* 4.0 28.0 - - + -
414D LEU* 5.5 0.7 - - + -
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Residues in contact with SER 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D ARG* 3.0 26.7 + - - -
211D MET 2.7 16.8 + - - -
212D HIS 2.9 18.4 + - - +
214D LEU* 1.3 79.2 - - - +
216D LEU* 1.3 72.6 + - - +
217D PRO* 4.5 2.4 - - - +
218D SER* 3.1 4.7 + - - -
219D ARG* 3.5 5.4 - - - +
306D ASP 4.9 0.3 + - - -
307D PHE* 2.6 40.3 + - - -
308D LEU* 5.1 0.2 - - - -
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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