Contacts of the helix formed by residues 176 - 195 (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 SER 176 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171E THR* 2.6 13.3 + - - +
175E GLY* 1.3 72.5 - - - -
177E GLY* 1.3 70.5 + - - +
178E PRO 3.5 0.4 - - - -
179E ALA* 3.0 20.7 + - - +
180E TYR* 3.1 30.8 + - - -
261E SER* 2.6 30.3 + - - -
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Residues in contact with GLY 177 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173E LEU 2.6 28.1 + - - -
174E SER* 4.3 0.9 - - - -
176E SER* 1.3 69.6 - - - +
178E PRO* 1.3 60.6 - - - +
179E ALA 2.7 0.7 + - - -
180E TYR* 2.4 51.9 + - - +
181E ALA* 3.2 3.6 + - - -
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Residues in contact with PRO 178 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123E ASN* 3.4 31.9 - - + +
124E THR* 4.8 5.2 - - - +
125E PRO* 3.6 24.0 - - + -
174E SER* 3.3 15.0 - - - +
175E GLY 3.9 2.9 - - - +
176E SER 3.7 1.8 - - - -
177E GLY* 1.3 86.2 - - - +
179E ALA* 1.3 60.8 + - - +
181E ALA* 3.2 11.5 + - + +
182E PHE* 3.0 43.0 + - + -
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Residues in contact with ALA 179 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176E SER* 3.0 17.5 + - - +
177E GLY 2.7 3.8 + - - -
178E PRO* 1.3 73.1 - - - +
180E TYR* 1.3 69.9 + - + +
182E PHE* 3.1 25.1 + - - +
183E THR* 3.3 11.3 + - - -
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Residues in contact with TYR 180 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172E GLY 3.0 27.3 + - - -
173E LEU* 4.0 3.1 - - + -
176E SER* 3.6 15.0 - - - -
177E GLY* 2.4 44.5 + - - +
179E ALA* 1.3 71.5 - - + +
181E ALA* 1.3 63.4 + - - +
183E THR* 3.0 19.1 + - - +
184E ALA* 3.2 8.4 + - - +
254E LEU* 5.4 14.4 - - + -
257E ALA* 2.9 48.2 + - + -
258E VAL* 4.3 8.7 - - + -
261E SER* 3.3 9.1 - - - -
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Residues in contact with ALA 181 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177E GLY 3.2 2.0 + - - +
178E PRO* 3.2 18.3 + - + +
180E TYR* 1.3 77.9 - - - +
182E PHE* 1.3 60.6 - - + +
184E ALA* 2.5 41.5 + - - +
185E LEU* 3.1 15.2 + - + +
210E LEU* 5.5 4.5 - - + -
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Residues in contact with PHE 182 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124E THR* 5.6 8.5 - - + -
125E PRO* 5.7 4.9 - - + -
178E PRO* 3.0 31.6 + - + -
179E ALA* 3.1 11.6 + - - +
181E ALA* 1.3 81.5 - - + +
183E THR* 1.3 60.8 + - - +
185E LEU* 3.8 18.1 + - + +
186E ASP* 3.2 22.0 + - - +
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Residues in contact with THR 183 (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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179E ALA 3.3 6.1 + - - -
180E TYR* 3.0 12.6 + - - +
181E ALA 2.7 2.8 + - - -
182E PHE* 1.3 77.1 - - - +
184E ALA* 1.3 70.5 + - - +
186E ASP* 4.0 6.2 - - + +
187E ALA* 3.3 19.0 + - + +
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Residues in contact with ALA 184 (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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180E TYR 3.2 5.3 + - - +
181E ALA* 2.5 24.7 + - - +
183E THR* 1.3 76.9 - - - +
185E LEU* 1.3 57.3 + - + +
187E ALA* 2.9 7.6 + - - +
188E LEU* 2.8 39.5 + - + +
210E LEU* 4.4 12.6 - - + -
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Residues in contact with LEU 185 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181E ALA* 3.5 23.6 - - + +
182E PHE* 3.8 20.9 - - + +
184E ALA* 1.3 70.3 - - - +
186E ASP* 1.3 65.4 + - - +
188E LEU* 3.6 7.4 - - + +
189E ALA* 2.8 27.1 + - - +
203E VAL* 5.0 10.6 - - + +
206E GLY* 3.9 6.3 - - - -
207E ALA* 3.5 34.8 - - + +
210E LEU* 3.3 31.4 - - + -
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Residues in contact with ASP 186 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B GLY* 5.4 5.8 - - - -
228B LYS* 3.2 26.7 + - - -
229B ASP* 4.9 3.5 - - - +
246B GLU* 4.8 0.9 - - - +
251B ARG* 4.0 15.2 + - - -
182E PHE 3.2 15.7 + - - +
183E THR* 4.0 6.7 - - + +
184E ALA 3.4 0.4 + - - -
185E LEU* 1.3 77.7 - - - +
187E ALA* 1.3 57.3 + - - +
189E ALA* 3.6 5.5 - - - +
190E ASP* 2.9 40.0 + - - +
199E ARG* 3.7 6.4 + - - -
203E VAL* 6.4 0.2 - - - -
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Residues in contact with ALA 187 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B GLU* 5.8 2.0 - - - +
183E THR* 3.3 10.7 + - + +
184E ALA* 2.9 13.9 + - - +
186E ASP* 1.3 78.5 + - - +
188E LEU* 1.3 59.2 + - + +
190E ASP* 3.1 11.4 + - - +
191E GLY* 2.9 26.9 + - - -
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Residues in contact with LEU 188 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184E ALA* 2.8 19.0 + - + +
185E LEU* 3.6 16.2 - - + +
187E ALA* 1.3 78.0 - - + +
189E ALA* 1.3 56.5 + - - +
191E GLY* 3.5 1.1 + - - +
192E GLY* 2.9 24.3 + - - -
202E ALA* 5.0 2.0 - - - +
206E GLY* 4.3 25.1 - - - -
209E ALA* 5.8 1.6 - - + -
210E LEU* 4.5 21.1 - - + -
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Residues in contact with ALA 189 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185E LEU 2.8 17.3 + - - +
186E ASP* 3.6 5.8 - - - +
188E LEU* 1.3 73.0 - - - +
190E ASP* 1.3 67.2 + - - +
191E GLY 3.1 1.1 - - - -
192E GLY* 3.7 0.3 - - - -
193E VAL* 2.9 30.8 + - - +
199E ARG* 3.7 15.5 - - - +
202E ALA* 3.9 12.3 - - + +
203E VAL* 3.9 33.9 - - + +
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Residues in contact with ASP 190 (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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228B LYS* 2.7 25.6 + - - -
239B ILE* 2.9 18.8 - - + +
242B LEU* 5.2 7.9 - - + +
246B GLU* 3.7 17.5 - - + +
186E ASP* 2.9 29.7 + - - +
187E ALA* 3.4 9.5 - - - +
189E ALA* 1.3 76.2 - - - +
191E GLY* 1.3 56.9 + - - +
194E LYS* 2.9 24.5 + - - +
199E ARG* 2.5 35.9 + - - +
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Residues in contact with GLY 191 (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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243B HIS* 6.3 0.9 - - - -
187E ALA 2.9 14.7 + - - -
188E LEU* 3.7 4.0 - - - -
190E ASP* 1.3 73.2 - - - +
192E GLY* 1.3 66.7 + - - +
194E LYS* 2.8 21.0 + - - +
195E MET* 2.9 15.5 + - - +
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Residues in contact with GLY 192 (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 2.9 16.5 + - - -
189E ALA 3.2 2.4 + - - -
191E GLY* 1.3 72.2 - - - +
193E VAL* 1.3 61.7 + - - +
195E MET* 3.2 13.9 + - - -
197E LEU* 3.0 42.5 + - - +
202E ALA* 4.5 7.0 - - - -
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Residues in contact with VAL 193 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B SER* 4.8 8.1 - - - +
233B SER 4.6 2.9 - - - -
234B PRO* 2.7 50.4 - - + +
239B ILE* 3.3 20.0 - - + -
189E ALA 2.9 22.0 + - - +
190E ASP 4.3 0.2 - - - -
192E GLY* 1.3 76.9 - - - +
194E LYS* 1.3 60.4 - - - +
196E GLY* 2.8 8.3 + - - -
197E LEU 3.5 14.1 + - - +
199E ARG* 3.6 42.8 - - - +
202E ALA* 4.3 4.5 - - + -
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Residues in contact with LYS 194 (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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234B PRO 4.4 0.7 - - - -
235B GLY 4.0 8.8 - - - +
239B ILE* 3.0 26.7 - - + +
240B HIS* 3.5 45.0 + - + +
243B HIS* 3.3 47.7 + - + +
190E ASP 2.9 9.5 + - - +
191E GLY* 2.8 17.5 + - - +
193E VAL* 1.3 71.4 - - - +
195E MET* 1.3 79.9 + - + +
196E GLY 3.2 3.0 + - - -
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Residues in contact with MET 195 (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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240B HIS* 5.5 3.1 - - + +
191E GLY 2.9 11.2 + - - +
192E GLY* 3.4 13.6 - - - +
193E VAL 2.9 0.6 + - - -
194E LYS* 1.3 100.6 - - + +
196E GLY* 1.3 55.7 + - - +
197E LEU* 3.5 10.1 + - + +
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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