Contacts of the helix formed by residues 176 - 195 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171D THR* 2.7 13.7 + - - +
172D GLY 3.9 0.2 - - - -
173D LEU 3.8 1.8 - - - -
175D GLY* 1.3 68.2 - - - -
177D GLY* 1.3 57.2 + - - +
179D ALA* 3.2 19.6 - - - +
180D TYR* 2.9 44.3 - - - -
261D SER* 2.8 27.4 + - - -
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Residues in contact with GLY 177 (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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173D LEU 3.0 19.2 + - - -
174D SER 4.8 0.2 - - - -
175D GLY 3.0 0.8 + - - -
176D SER* 1.3 74.3 - - - +
178D PRO* 1.3 73.2 - - - +
179D ALA 2.8 4.5 - - - -
180D TYR* 2.8 24.5 + - - +
181D ALA* 2.9 11.8 + - - +
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Residues in contact with PRO 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D ASN* 4.1 6.7 - - + +
124D THR* 4.8 3.8 - - - +
125D PRO* 3.3 40.4 - - + -
174D SER 3.9 7.2 - - - +
175D GLY 3.3 13.2 - - - +
177D GLY* 1.3 90.5 - - - +
179D ALA* 1.3 55.6 + - - +
181D ALA* 3.8 9.9 - - + -
182D PHE* 2.8 56.9 + - + -
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Residues in contact with ALA 179 (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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175D GLY 5.1 0.2 - - - +
176D SER* 3.2 30.1 - - - +
177D GLY 2.8 0.2 - - - -
178D PRO* 1.3 82.7 - - + +
180D TYR* 1.3 65.9 + - + +
182D PHE* 3.6 12.7 + - - +
183D THR* 3.3 15.8 + - - -
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Residues in contact with TYR 180 (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 GLY 3.1 20.0 + - - -
173D LEU* 4.7 0.4 - - - -
176D SER* 2.9 29.8 - - - -
177D GLY* 2.8 15.6 + - - +
179D ALA* 1.3 73.1 - - + +
181D ALA* 1.3 66.9 + - - +
183D THR* 3.0 18.7 + - - -
184D ALA* 3.0 12.5 + - - +
254D LEU* 5.1 17.3 - - + -
257D ALA* 2.9 32.5 + - + -
258D VAL* 2.9 35.7 + - + -
261D SER* 3.4 10.4 - - - -
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Residues in contact with ALA 181 (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 GLY 2.9 11.3 + - - +
178D PRO* 3.4 15.5 - - + +
180D TYR* 1.3 76.3 - - - +
182D PHE* 1.3 61.4 + - + +
184D ALA* 2.6 30.6 + - - +
185D LEU* 2.8 18.7 + - + +
210D LEU* 5.5 9.2 - - + -
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Residues in contact with PHE 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D THR* 5.3 8.3 - - - -
125D PRO* 5.7 3.8 - - + -
178D PRO* 2.8 43.4 + - + +
179D ALA* 4.0 7.9 - - - +
181D ALA* 1.3 77.4 - - + +
183D THR* 1.3 59.9 + - - +
185D LEU* 3.8 15.6 + - + +
186D ASP* 3.5 21.0 + - - +
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Residues in contact with THR 183 (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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179D ALA 3.3 13.4 + - - -
180D TYR* 3.0 12.0 + - - -
182D PHE* 1.3 77.0 - - - +
184D ALA* 1.3 62.2 + - - +
186D ASP* 4.0 4.8 - - - +
187D ALA* 3.4 21.0 + - - +
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Residues in contact with ALA 184 (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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180D TYR 3.0 9.3 + - - +
181D ALA* 2.6 20.0 + - - +
183D THR* 1.3 69.3 - - - +
185D LEU* 1.3 56.6 + - - +
186D ASP 3.0 5.0 + - - -
187D ALA* 3.1 6.1 + - - +
188D LEU* 3.0 39.8 + - + +
210D LEU* 5.2 7.2 - - + -
250D PHE* 6.3 4.3 - - + -
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Residues in contact with LEU 185 (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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181D ALA* 2.8 19.3 + - + +
182D PHE* 3.8 16.1 + - + +
184D ALA* 1.3 71.1 - - - +
186D ASP* 1.3 58.1 + - - +
188D LEU* 4.0 12.5 - - + +
189D ALA* 3.2 23.7 + - - +
203D VAL* 4.2 11.3 - - + +
206D GLY* 3.4 24.6 - - - +
207D ALA* 3.7 26.2 - - + -
210D LEU* 3.0 37.9 - - + -
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Residues in contact with ASP 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C GLY* 6.0 0.9 - - - -
228C LYS* 3.9 19.4 + - - -
229C ASP* 4.6 3.3 - - - +
251C ARG* 4.3 10.0 + - - -
182D PHE 3.5 16.1 + - - +
183D THR* 4.0 6.1 - - + +
184D ALA 3.0 1.0 - - - -
185D LEU* 1.3 78.4 - - - +
187D ALA* 1.3 62.9 + - - +
188D LEU 3.2 0.4 - - - -
189D ALA* 3.4 1.9 + - - -
190D ASP* 2.8 40.2 + - - +
199D ARG* 3.1 19.0 + - - -
203D VAL* 5.5 2.3 - - - +
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Residues in contact with ALA 187 (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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183D THR 3.4 11.5 + - - +
184D ALA* 3.1 10.4 + - - +
186D ASP* 1.3 81.8 - - - +
188D LEU* 1.3 56.1 + - + +
190D ASP* 3.0 10.7 - - - +
191D GLY* 2.9 24.8 + - - -
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Residues in contact with LEU 188 (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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184D ALA* 3.0 24.5 + - + +
185D LEU* 4.0 24.0 - - + +
187D ALA* 1.3 73.3 - - + +
189D ALA* 1.3 52.3 + - - +
190D ASP 2.9 4.5 - - - -
191D GLY* 2.9 2.9 + - - +
192D GLY* 2.5 36.0 + - - -
202D ALA 5.4 0.9 - - - +
206D GLY* 4.9 14.6 - - - -
209D ALA* 6.5 0.2 - - + -
210D LEU* 4.7 15.5 - - + -
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Residues in contact with ALA 189 (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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185D LEU 3.2 19.3 + - - +
186D ASP 3.4 0.6 + - - +
188D LEU* 1.3 78.9 - - - +
190D ASP* 1.3 57.9 + - - +
192D GLY 3.9 0.2 - - - -
193D VAL* 2.9 33.8 + - - +
199D ARG* 3.5 18.2 - - - +
202D ALA* 3.7 17.1 + - + +
203D VAL* 3.3 34.1 - - + +
206D GLY* 5.9 0.2 - - - -
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Residues in contact with ASP 190 (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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228C LYS* 3.4 25.8 + - - -
239C ILE* 3.1 17.2 - - + +
242C LEU* 5.7 4.4 - - - +
246C GLU* 4.1 16.6 - - - +
186D ASP* 2.8 17.2 + - - +
187D ALA* 3.0 15.6 - - - +
189D ALA* 1.3 75.5 - - - +
191D GLY* 1.3 66.4 + - - +
193D VAL 3.0 2.6 + - - -
194D LYS* 2.9 19.2 + - - +
199D ARG* 2.6 39.1 + - - +
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Residues in contact with GLY 191 (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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243C HIS* 6.0 3.1 - - - -
187D ALA 2.9 14.4 + - - -
188D LEU* 2.9 2.4 + - - -
190D ASP* 1.3 72.7 - - - +
192D GLY* 1.3 69.0 + - - +
194D LYS* 2.8 21.8 + - - +
195D MET* 3.1 18.1 + - - +
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Residues in contact with GLY 192 (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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188D LEU 2.5 20.6 + - - -
189D ALA 4.0 2.0 - - - -
191D GLY* 1.3 70.7 - - - +
193D VAL* 1.3 61.2 + - - +
195D MET* 3.1 14.4 + - - +
197D LEU* 2.9 41.4 + - - +
202D ALA* 4.4 4.3 - - - -
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Residues in contact with VAL 193 (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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232C SER* 5.0 8.1 - - - +
233C SER 4.5 2.2 - - - -
234C PRO* 2.9 36.5 - - + +
239C ILE* 3.1 23.6 - - + -
189D ALA 2.9 21.3 + - - +
190D ASP 3.0 2.1 + - - +
191D GLY 3.0 1.0 - - - -
192D GLY* 1.3 73.0 - - - +
194D LYS* 1.3 52.9 + - - +
195D MET 2.6 16.8 + - - -
196D GLY 2.6 14.2 + - - -
197D LEU 3.3 17.0 - - - +
199D ARG* 3.7 35.9 - - + +
202D ALA* 4.1 2.9 - - + -
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Residues in contact with LYS 194 (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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234C PRO 3.8 4.9 - - - +
235C GLY 4.0 1.7 - - - +
239C ILE* 3.1 35.1 - - + +
240C HIS* 3.1 50.9 + - + +
243C HIS* 3.8 45.5 + - + +
190D ASP 2.9 8.3 + - - +
191D GLY* 2.8 16.6 + - - +
193D VAL* 1.3 71.0 - - - +
195D MET* 1.3 83.7 + - + +
196D GLY 3.3 1.7 + - - -
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Residues in contact with MET 195 (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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240C HIS* 5.4 2.2 - - + -
191D GLY* 3.3 14.8 - - - +
192D GLY* 3.5 9.4 - - - +
193D VAL 2.6 4.2 + - - -
194D LYS* 1.3 121.3 - - + +
196D GLY* 1.3 59.2 + - - +
197D LEU* 3.4 6.9 + - + +
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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