Contacts of the helix formed by residues 198 - 218 (chain E) in PDB entry 2GER
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 PRO 198 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234B PRO* 3.8 12.8 - - + -
193E VAL* 4.3 0.4 - - - -
196E GLY 4.3 1.8 - - - +
197E LEU* 1.3 92.9 - - + +
199E ARG* 1.3 69.2 + - - +
200E ARG 5.1 0.7 - - - +
201E LEU* 3.4 34.1 - - + +
202E ALA* 3.1 17.3 + - - +
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Residues in contact with ARG 199 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B GLN* 5.6 2.2 - - - +
228B LYS* 3.6 7.3 - - - +
229B ASP* 3.4 52.8 + - + +
232B SER* 4.3 16.3 + - - +
234B PRO* 4.8 3.2 - - - +
239B ILE* 4.9 2.6 - - - +
242B LEU* 6.1 0.2 - - - +
186E ASP* 3.7 10.7 + - - -
189E ALA* 3.7 13.0 - - - +
190E ASP* 2.5 52.8 + - - +
193E VAL* 3.6 24.9 - - - +
197E LEU 4.0 0.8 + - - -
198E PRO* 1.3 70.9 - - - +
200E ARG* 1.3 72.5 + - + +
202E ALA* 2.8 16.3 + - - +
203E VAL* 3.0 19.1 + - + +
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Residues in contact with ARG 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198E PRO* 3.7 0.8 - - - +
199E ARG* 1.3 78.7 - - + +
201E LEU* 1.3 61.4 + - - +
203E VAL* 3.5 7.9 + - - +
204E ARG* 3.1 39.9 + - - +
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Residues in contact with LEU 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197E LEU* 3.1 26.2 - - + -
198E PRO* 3.4 30.1 + - + +
199E ARG 2.9 0.6 + - - -
200E ARG* 1.3 75.3 - - - +
202E ALA* 1.3 69.0 + - - +
204E ARG* 3.9 5.3 - - + +
205E LEU* 3.0 56.6 + - + +
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Residues in contact with ALA 202 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188E LEU 5.0 1.0 - - - +
189E ALA* 3.9 30.0 + - + +
192E GLY* 4.5 11.9 - - - -
193E VAL* 4.3 5.6 - - + -
197E LEU* 4.5 7.6 - - + +
198E PRO 3.1 9.2 + - - +
199E ARG 2.8 10.2 + - - +
201E LEU* 1.3 79.3 - - - +
203E VAL* 1.3 66.9 + - - +
205E LEU* 2.8 20.3 + - - +
206E GLY* 3.0 10.9 + - - -
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Residues in contact with VAL 203 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B ASP* 5.7 1.8 - - - +
185E LEU* 5.0 11.0 - - + +
186E ASP* 6.4 0.2 - - - -
189E ALA* 3.9 23.5 - - + +
199E ARG* 3.0 20.9 + - + +
200E ARG* 3.6 12.3 - - - +
202E ALA* 1.3 79.1 - - - +
204E ARG* 1.3 69.2 + - + +
205E LEU 3.1 0.2 + - - -
206E GLY* 3.3 1.4 + - - -
207E ALA* 3.2 23.1 + - + +
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Residues in contact with ARG 204 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200E ARG* 3.1 25.9 + - - +
201E LEU* 3.9 5.8 - - + +
203E VAL* 1.3 80.4 - - + +
205E LEU* 1.3 58.7 + - + +
207E ALA* 3.6 6.4 - - - +
208E GLN* 2.8 33.3 + - - +
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Residues in contact with LEU 205 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197E LEU* 4.2 15.0 - - + -
201E LEU* 3.0 47.0 + - + +
202E ALA* 2.8 12.7 + - - +
204E ARG* 1.3 75.6 - - + +
206E GLY* 1.3 66.1 + - - +
208E GLN* 3.3 8.2 + - + +
209E ALA* 3.0 21.0 + - - +
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Residues in contact with GLY 206 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185E LEU* 3.9 8.7 - - - -
188E LEU* 4.3 23.1 - - - -
202E ALA 3.0 12.0 + - - -
203E VAL* 3.9 2.0 - - - -
205E LEU* 1.3 72.5 - - - +
207E ALA* 1.3 68.5 + - - +
209E ALA* 2.6 26.7 + - - +
210E LEU* 3.0 7.4 + - - +
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Residues in contact with ALA 207 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185E LEU* 3.5 23.5 - - + +
203E VAL* 3.2 19.4 + - + +
204E ARG* 3.6 8.3 - - - +
206E GLY* 1.3 76.2 - - - +
208E GLN* 1.3 54.3 + - - +
210E LEU* 3.1 2.5 + - - +
211E LEU* 2.6 38.3 + - + +
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Residues in contact with GLN 208 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204E ARG 2.8 22.6 + - - +
205E LEU* 3.6 9.2 - - + +
207E ALA* 1.3 72.2 - - - +
209E ALA* 1.3 55.9 + - - +
211E LEU* 4.0 23.7 - - - +
212E GLY* 2.9 26.6 + - - +
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Residues in contact with ALA 209 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188E LEU* 5.8 1.6 - - + -
205E LEU 3.0 11.7 + - - +
206E GLY* 2.6 24.2 + - - +
208E GLN* 1.3 67.5 - - - +
210E LEU* 1.3 59.2 + - + +
212E GLY* 2.9 2.8 + - - -
213E ALA* 2.5 40.8 + - + +
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Residues in contact with LEU 210 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181E ALA* 5.3 5.8 - - + +
184E ALA* 4.4 13.9 - - + -
185E LEU* 3.3 39.0 - - + -
188E LEU* 4.5 13.9 - - + -
206E GLY 3.0 11.8 + - - +
207E ALA* 3.9 2.0 - - - +
209E ALA* 1.3 75.3 - - + +
211E LEU* 1.3 69.6 + - - +
213E ALA* 4.1 8.7 - - + -
214E ALA* 2.9 28.8 + - + +
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Residues in contact with LEU 211 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E GLU* 6.5 0.4 - - + -
207E ALA* 2.6 27.0 + - + +
208E GLN* 3.8 22.9 - - - +
210E LEU* 1.3 75.7 - - - +
212E GLY* 1.3 64.0 + - - +
214E ALA* 3.9 2.9 - - - +
215E LYS* 3.1 35.7 + - + +
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Residues in contact with GLY 212 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208E GLN* 2.9 15.4 + - - -
209E ALA 2.9 5.8 + - - -
211E LEU* 1.3 82.7 - - - +
213E ALA* 1.3 66.1 + - - +
215E LYS* 3.4 6.2 + - - +
216E MET* 2.9 27.6 + - - +
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Residues in contact with ALA 213 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209E ALA 2.5 27.7 + - - +
210E LEU* 4.0 9.9 - - + +
212E GLY* 1.3 71.6 - - - +
214E ALA* 1.3 56.8 + - - +
216E MET* 2.9 30.2 - - - +
217E LEU* 3.0 11.3 + - - +
227E LEU* 5.3 1.4 - - - +
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Residues in contact with ALA 214 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210E LEU* 2.9 18.1 + - + +
211E LEU* 3.9 3.4 - - - +
213E ALA* 1.3 72.8 - - - +
215E LYS* 1.3 68.8 + - - +
216E MET 2.8 1.3 - - - -
217E LEU* 2.7 20.1 + - - +
218E LEU* 2.8 26.7 + - + +
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Residues in contact with LYS 215 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211E LEU* 3.1 28.3 + - + +
212E GLY* 3.8 5.6 - - - +
214E ALA* 1.3 79.6 - - - +
216E MET* 1.3 62.0 + - - +
218E LEU* 3.5 14.3 + - + +
219E HIS* 3.1 44.1 - - + +
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Residues in contact with MET 216 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212E GLY 2.9 14.7 + - - +
213E ALA* 2.9 19.7 - - - +
214E ALA 2.8 1.2 + - - -
215E LYS* 1.3 76.4 - - - +
217E LEU* 1.3 62.6 + - - +
219E HIS* 3.2 16.6 + - - +
220E SER* 3.6 12.3 + - - -
227E LEU* 4.4 28.1 - - + +
230E ASN* 6.4 0.9 - - + -
231E VAL* 5.0 16.6 - - + -
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Residues in contact with LEU 217 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213E ALA 3.0 10.4 + - - +
214E ALA* 2.7 12.9 + - - +
216E MET* 1.3 68.6 - - - +
218E LEU* 1.3 56.0 + - + +
219E HIS 2.4 18.6 + - - -
220E SER* 3.0 12.1 + - - +
221E GLU* 3.2 31.8 + - - +
224E PRO* 3.4 44.9 - - + -
227E LEU* 4.1 17.4 - - + +
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Residues in contact with LEU 218 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214E ALA* 2.8 31.6 + - + +
215E LYS* 3.7 11.2 - - - +
216E MET 3.3 0.2 - - - -
217E LEU* 1.3 73.6 - - + +
219E HIS* 1.3 68.3 + - + +
221E GLU 5.5 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
------------------------------------------------------------
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