Contacts of the helix formed by residues 203 - 215 (chain D) in PDB entry 5CEV
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 MET 203 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121D TYR* 3.7 20.4 - - + +
172D ILE* 4.6 6.1 - - + -
198D VAL* 4.0 10.9 + - + +
202D GLY* 1.3 70.6 - - - -
204D THR* 1.3 63.3 + - - +
206D VAL* 4.3 14.4 - - - -
207D MET* 2.9 48.4 + - + +
246D LEU* 3.3 36.8 - - + -
250D GLU* 3.7 43.9 + - + +
253D LEU* 4.2 14.4 - - + -
254D ALA* 4.2 4.5 - - + -
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Residues in contact with THR 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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202D GLY* 3.3 1.4 - - - -
203D MET* 1.3 78.4 - - - +
205D ARG* 1.3 57.9 + - - +
208D GLU* 2.9 53.8 + - - +
253D LEU* 3.4 13.1 - - - +
257D MET* 3.7 11.0 - - + +
199E ASP 3.6 2.6 + - - -
200E ARG* 2.8 54.6 + - + +
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Residues in contact with ARG 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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201D LEU* 3.5 45.0 + - + +
202D GLY 3.3 1.6 + - - -
204D THR* 1.3 75.8 - - - +
206D VAL* 1.3 61.2 - - - +
208D GLU* 3.3 24.4 + - - +
209D GLU* 2.8 77.5 + - - +
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Residues in contact with VAL 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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172D ILE* 4.2 24.7 - - + -
193D TYR* 3.7 49.8 - - + -
197D GLU 4.0 17.7 - - - +
198D VAL* 4.2 11.9 - - + +
201D LEU* 4.3 4.9 - - + -
202D GLY 3.2 13.3 + - - +
203D MET* 3.7 15.5 - - - +
205D ARG* 1.3 77.4 - - - +
207D MET* 1.3 58.1 + - - +
209D GLU* 3.4 2.1 + - - +
210D THR* 2.9 32.6 + - - -
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Residues in contact with MET 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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119D ILE* 5.1 1.8 - - + -
121D TYR* 5.3 1.1 - - - -
172D ILE* 3.9 26.5 - - + -
203D MET* 2.9 33.3 + - + +
206D VAL* 1.3 76.7 - - - +
208D GLU* 1.3 58.0 + - - +
210D THR* 3.3 5.2 + - + -
211D ILE* 2.9 43.7 + - + +
254D ALA* 3.7 38.1 - - + +
257D MET* 3.7 22.2 - - + -
258D LEU* 3.6 39.5 - - + -
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Residues in contact with GLU 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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204D THR* 2.9 34.9 + - - +
205D ARG* 3.6 30.0 + - - +
207D MET* 1.3 77.1 - - - +
209D GLU* 1.3 61.8 + - - +
211D ILE* 3.9 4.6 - - - +
212D ALA* 3.0 26.2 + - - +
257D MET* 3.7 16.1 - - + +
200E ARG* 4.9 7.5 + - - +
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Residues in contact with GLU 209 (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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191D LYS* 4.7 4.1 + - - -
193D TYR* 2.6 42.8 + - - +
201D LEU* 4.2 7.0 - - - +
205D ARG* 2.8 72.8 + - - +
206D VAL 3.7 1.3 - - - +
208D GLU* 1.3 76.2 - - - +
210D THR* 1.3 55.8 + - - +
212D ALA* 3.8 4.2 - - - +
213D TYR* 2.9 30.9 + - - +
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Residues in contact with THR 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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119D ILE* 3.7 31.2 - - + -
170D VAL* 3.3 36.9 - - + +
172D ILE* 3.7 14.6 - - + +
191D LYS* 5.3 0.4 - - - +
193D TYR* 3.4 10.1 + - - -
206D VAL 2.9 19.7 + - - -
207D MET* 3.3 10.3 + - + -
209D GLU* 1.3 73.7 - - - +
211D ILE* 1.3 65.8 + - - +
213D TYR* 3.3 6.1 + - - +
214D LEU* 3.0 25.3 + - + +
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Residues in contact with ILE 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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207D MET* 2.9 28.3 + - + +
208D GLU* 4.0 5.4 - - - +
210D THR* 1.3 73.4 - - + +
212D ALA* 1.3 58.6 + - - +
214D LEU* 4.3 0.2 - - - +
215D LYS* 2.9 51.5 + - - +
257D MET* 3.7 41.7 - - + +
258D LEU* 4.0 22.2 - - + -
261D ALA* 3.6 24.0 - - + -
263D ILE* 4.1 14.7 - - + +
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Residues in contact with ALA 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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208D GLU 3.0 18.1 + - - +
209D GLU* 3.9 4.9 - - - +
211D ILE* 1.3 78.1 - - - +
213D TYR* 1.3 63.5 + - - +
215D LYS* 4.1 6.0 - - - +
216D GLU* 3.1 29.8 + - - +
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Residues in contact with TYR 213 (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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167D GLU* 2.7 40.7 + - - +
169D VAL 4.5 0.7 - - - -
170D VAL* 3.7 25.6 - - + -
189D GLY 5.3 2.8 + - - -
191D LYS* 3.7 40.5 + - + +
209D GLU 2.9 21.0 + - - +
210D THR* 3.5 4.5 - - - +
212D ALA* 1.3 78.8 - - - +
214D LEU* 1.3 71.3 + - + +
216D GLU* 3.5 9.1 - - - +
217D ARG* 2.9 62.6 + - - +
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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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117D GLY* 4.4 1.3 - - - -
118D VAL 4.3 3.6 - - - +
119D ILE* 3.5 37.5 - - + -
168D HIS* 3.4 32.8 - - - +
170D VAL* 4.0 14.6 - - + -
210D THR* 3.0 16.0 + - + +
211D ILE 4.3 0.7 - - - +
213D TYR* 1.3 87.9 - - + +
215D LYS* 1.3 63.7 + - - +
216D GLU 3.0 5.4 - - - -
217D ARG* 3.0 13.4 + - + -
218D THR* 2.8 35.3 + - + +
221D VAL* 4.0 20.4 - - + -
263D ILE* 4.9 3.6 - - + -
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Residues in contact with LYS 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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211D ILE* 2.9 38.3 + - - +
212D ALA* 4.1 5.6 - - - +
214D LEU* 1.3 76.6 - - - +
216D GLU* 1.3 58.8 + - - +
217D ARG 3.5 0.5 + - - -
218D THR* 4.4 10.0 - - - +
221D VAL* 6.0 0.4 - - - -
261D ALA* 3.2 28.2 + - - +
263D ILE* 3.7 21.5 - - + +
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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