Contacts of the helix formed by residues 196 - 215 (chain P) in PDB entry 1E33
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 196 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193P TRP* 2.8 28.2 + - - -
195P PRO* 1.3 78.3 - - - +
197P LEU* 1.3 62.8 + - - -
198P GLU 3.2 2.7 + - - -
199P ALA* 3.3 13.1 + - - +
200P ARG* 3.2 25.7 + - - +
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Residues in contact with LEU 197 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147P ILE* 3.8 15.7 - - + -
181P LEU* 4.3 23.3 - - + -
192P PRO* 4.5 11.2 - - + -
193P TRP 3.3 7.3 + - - +
194P LEU* 3.1 29.7 + - + +
196P GLY* 1.3 75.1 - - - +
198P GLU* 1.3 66.9 + - - +
200P ARG* 3.0 10.7 + - - +
201P TYR* 2.8 52.7 + - + +
226P HIS* 3.7 26.7 - - - +
233P PHE* 4.3 11.2 - - + -
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Residues in contact with GLU 198 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194P LEU 4.9 0.6 + - - -
195P PRO 5.2 2.4 + - - +
196P GLY 3.2 1.0 + - - -
197P LEU* 1.3 72.9 - - - +
199P ALA* 1.3 56.8 + - - +
201P TYR* 2.5 34.1 + - - +
202P MET* 2.7 30.9 + - + +
223P TYR* 4.6 6.3 - - - +
227P HIS* 5.6 1.8 - - + +
233P PHE* 5.6 0.4 - - - -
238P PHE* 4.6 8.6 - - - -
253P GLU* 3.6 40.7 + - + +
256P ALA* 4.1 2.3 - - - +
257P ALA* 3.2 43.1 + - + -
260P THR* 4.5 2.9 + - - -
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Residues in contact with ALA 199 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196P GLY* 3.3 12.9 + - - +
198P GLU* 1.3 77.0 + - - +
200P ARG* 1.3 70.9 + - + +
202P MET* 3.0 15.0 + - - +
203P ALA* 3.1 14.5 + - - +
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Residues in contact with ARG 200 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145P LEU* 4.2 17.8 - - + +
181P LEU* 3.5 25.0 - - - +
188P GLU* 2.5 46.9 + - - +
189P ALA* 4.6 10.7 - - - +
192P PRO* 5.4 4.3 - - - +
193P TRP 5.9 1.9 - - - +
196P GLY* 3.2 15.2 + - - +
197P LEU* 3.0 15.3 + - + +
199P ALA* 1.3 79.6 - - + +
201P TYR* 1.4 66.2 + - + +
203P ALA* 3.2 5.1 + - - +
204P PHE* 3.1 21.3 + - - +
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Residues in contact with TYR 201 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121P ALA* 4.2 11.2 - - + +
122P GLY* 3.8 11.4 - - - -
145P LEU* 3.4 35.4 - - + -
146P GLY* 3.6 15.5 - - - -
147P ILE* 3.6 7.3 - - - +
181P LEU* 4.1 5.3 - - + +
197P LEU* 2.8 40.4 + - + +
198P GLU* 2.5 18.4 + - - +
200P ARG* 1.4 73.5 - - - +
202P MET* 1.3 72.0 + - + +
204P PHE* 3.6 7.4 + - - +
205P ALA* 3.2 19.9 + - - +
223P TYR* 4.1 23.8 - + + +
224P ALA 5.3 0.9 - - - -
225P SER* 5.9 0.4 - - - -
226P HIS* 2.8 43.2 - + - -
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Residues in contact with MET 202 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198P GLU* 2.7 38.2 + - + +
199P ALA* 3.0 8.5 + - - +
201P TYR* 1.3 80.1 - - + +
203P ALA* 1.4 50.6 + - - +
205P ALA* 2.8 9.0 + - + +
206P HIS* 2.7 35.5 + - - +
223P TYR* 4.2 20.4 - - + +
257P ALA* 3.5 25.6 - - + +
260P THR* 3.4 31.6 - - + -
261P LEU* 3.3 34.3 - - + -
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Residues in contact with ALA 203 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199P ALA 3.1 11.1 + - - +
200P ARG* 3.6 9.6 - - - +
202P MET* 1.4 73.5 - - - +
204P PHE* 1.3 64.4 + - - +
205P ALA 3.1 0.3 + - - -
206P HIS* 3.2 8.1 + - - +
207P ASP* 2.9 32.9 + - - +
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Residues in contact with PHE 204 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A NAG 3.3 35.2 - - + -
119P GLY* 4.4 2.9 - - - -
120P MET 3.5 35.2 - - - -
121P ALA* 3.9 16.6 - - + -
143P ARG* 3.5 28.6 - - + -
145P LEU* 3.7 36.6 - - + -
200P ARG 3.1 15.5 + - - +
201P TYR* 3.8 3.8 - - - +
203P ALA* 1.3 76.3 - - - +
205P ALA* 1.3 66.6 + - + +
207P ASP* 3.7 7.5 + - - +
208P LEU* 3.1 24.7 + - + +
221P LEU* 4.4 9.6 - - + -
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Residues in contact with ALA 205 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201P TYR 3.2 10.2 + - - +
202P MET* 2.8 16.0 + - + +
204P PHE* 1.3 76.9 - - + +
206P HIS* 1.3 65.5 + - - +
208P LEU* 3.0 16.1 + - - +
209P MET* 3.1 21.4 + - + +
221P LEU* 3.7 31.0 - - + -
223P TYR* 6.5 0.7 - - + -
261P LEU* 3.9 18.8 - - + -
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Residues in contact with HIS 206 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202P MET 2.7 16.0 + - - +
203P ALA* 3.5 11.7 - - - +
205P ALA* 1.3 70.7 - - - +
207P ASP* 1.3 73.8 + - - +
209P MET* 3.1 14.4 + - + +
210P ALA* 3.1 35.8 + - + +
264P ALA* 4.2 22.4 - - + -
267P ASP* 5.8 3.5 + - - +
268P LEU* 4.6 13.0 - - + +
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Residues in contact with ASP 207 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A NAG 5.6 0.8 + - - +
143P ARG* 3.9 10.5 - - - +
203P ALA* 2.9 28.0 + - - +
204P PHE* 3.9 7.1 - - - +
206P HIS* 1.3 84.6 + - - +
208P LEU* 1.3 57.1 + - - +
210P ALA* 4.8 2.2 - - - -
211P ASP* 2.8 40.3 + - - +
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Residues in contact with LEU 208 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117P LEU* 3.5 29.9 - - + +
118P THR 4.2 1.3 - - - -
119P GLY* 3.9 31.6 - - - +
143P ARG* 3.6 41.7 - - + +
204P PHE* 3.1 13.8 + - + +
205P ALA* 3.0 9.6 + - - +
207P ASP* 1.3 78.6 - - - +
209P MET* 1.3 65.1 + - + +
212P ALA* 3.3 15.8 + - - +
219P PHE* 4.5 13.4 - - + +
220P PHE 4.2 6.7 - - - +
221P LEU* 4.1 25.4 - - + -
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Residues in contact with MET 209 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24P VAL* 6.1 1.1 - - - -
205P ALA* 3.1 21.4 + - + +
206P HIS* 3.6 12.6 - - + +
207P ASP 3.1 0.2 - - - -
208P LEU* 1.3 78.9 - - + +
210P ALA* 1.3 55.7 + - - +
212P ALA* 2.8 27.2 + - - +
213P GLN* 2.9 10.4 + - - +
219P PHE* 3.6 49.2 - - + -
221P LEU* 5.2 9.4 - - + -
261P LEU* 4.3 14.8 - - + +
264P ALA* 3.4 35.4 - - + +
265P ILE* 4.0 16.4 - - + -
268P LEU* 4.0 17.0 - - + -
270P LEU* 5.6 0.6 - - - +
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Residues in contact with ALA 210 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206P HIS* 3.1 31.3 + - + +
207P ASP* 4.0 2.5 - - - +
209P MET* 1.3 73.4 - - - +
211P ASP* 1.3 71.3 + - - +
213P GLN* 2.8 16.3 + - - +
214P ARG* 3.0 9.3 + - - -
268P LEU* 3.7 20.7 - - + +
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Residues in contact with ASP 211 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A NAG 3.0 19.6 + - - -
117P LEU* 4.2 5.6 - - + -
143P ARG* 2.6 36.9 + - - +
207P ASP* 2.8 25.8 + - - +
210P ALA* 1.3 74.3 - - - +
212P ALA* 1.3 58.9 + - - +
214P ARG* 3.1 3.8 + - - +
215P GLU* 3.0 30.9 + - + +
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Residues in contact with ALA 212 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117P LEU* 3.6 17.0 - - + +
208P LEU 3.3 14.6 + - - +
209P MET 2.8 16.8 + - - +
211P ASP* 1.3 66.2 - - - +
213P GLN* 1.3 67.7 + - - +
215P GLU* 3.5 0.9 + - - -
216P ASP 3.4 1.2 + - - -
217P ARG* 2.8 48.3 + - - +
219P PHE* 3.7 24.9 - - + -
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Residues in contact with GLN 213 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209P MET 2.9 8.8 + - - +
210P ALA* 2.8 16.5 + - - +
212P ALA* 1.3 68.7 - - - +
214P ARG* 1.3 67.5 + - - +
216P ASP* 2.5 22.5 + - - +
217P ARG 4.9 0.4 - - - -
219P PHE* 5.6 0.6 - - - -
268P LEU* 2.7 56.6 + - + +
270P LEU* 4.0 18.6 - - + +
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Residues in contact with ARG 214 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210P ALA 3.0 7.9 + - - -
211P ASP* 3.3 6.5 - - - +
213P GLN* 1.3 82.1 - - - +
215P GLU* 1.3 54.4 + - - +
216P ASP 3.1 2.8 + - - -
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Residues in contact with GLU 215 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A NAG 4.8 10.2 + - - +
117P LEU* 4.7 5.8 - - - +
143P ARG* 4.9 0.9 + - - -
211P ASP* 3.0 26.6 + - - +
212P ALA 3.5 0.2 + - - -
213P GLN 2.7 3.2 + - - -
214P ARG* 1.3 69.0 - - - +
216P ASP* 1.3 63.3 + - - +
217P ARG* 3.0 44.8 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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