Contacts of the helix formed by residues 176 - 195 (chain C) in PDB entry 2GRA
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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C THR* 2.7 11.2 + - - +
175C GLY* 1.3 73.5 - - - +
177C GLY* 1.3 67.5 + - - +
178C PRO* 3.3 3.4 - - - -
179C ALA* 2.9 26.5 + - - +
180C TYR* 3.1 32.3 + - - -
261C SER* 2.8 23.4 + - - -
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Residues in contact with GLY 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C LEU 2.7 20.1 + - - -
174C SER* 4.1 2.0 - - - -
176C SER* 1.3 74.4 - - - +
178C PRO* 1.3 59.8 - - - +
180C TYR* 2.6 50.6 + - - +
181C ALA* 3.1 5.2 + - - +
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Residues in contact with PRO 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C ASN* 4.4 5.8 - - + +
124C THR* 5.5 3.6 - - - +
125C PRO* 4.1 31.4 - - + -
174C SER* 3.2 18.8 - - - +
175C GLY 4.2 3.1 - - - +
176C SER 3.4 3.1 - - - -
177C GLY* 1.3 87.3 - - - +
179C ALA* 1.3 51.6 + - - +
181C ALA* 3.0 11.2 + - + +
182C PHE* 2.7 60.4 + - + -
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Residues in contact with ALA 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C SER* 2.9 16.2 + - - +
178C PRO* 1.3 78.6 - - - +
180C TYR* 1.3 59.3 + - + +
182C PHE* 3.8 14.6 - - + +
183C THR* 2.7 34.0 + - - -
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Residues in contact with TYR 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C GLY 2.7 24.7 + - - -
173C LEU* 4.1 0.4 - - + -
176C SER* 3.1 28.0 - - - -
177C GLY* 2.6 34.8 + - - +
179C ALA* 1.3 74.5 - - + +
181C ALA* 1.3 51.0 + - - +
183C THR* 2.7 12.1 + - - -
184C ALA* 2.6 35.9 + - - +
254C LEU* 5.1 18.4 - - + -
257C ALA* 3.7 28.4 + - + -
258C VAL* 3.8 14.1 - - + -
261C SER* 3.5 11.8 - - - -
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Residues in contact with ALA 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C GLY 3.1 3.5 + - - +
178C PRO* 3.0 16.1 + - + +
180C TYR* 1.3 79.1 - - - +
182C PHE* 1.3 58.1 + - + +
184C ALA* 3.1 8.7 + - - +
185C LEU* 2.7 46.9 + - + +
210C LEU* 5.2 7.6 - - + -
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Residues in contact with PHE 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C THR* 6.1 4.0 - - - -
125C PRO* 6.0 3.6 - - + -
178C PRO* 2.7 44.8 + - + +
179C ALA* 3.8 11.2 - - + +
181C ALA* 1.3 76.6 - - + +
183C THR* 1.3 57.2 + - - +
185C LEU* 3.5 12.7 - - + +
186C ASP* 3.0 30.1 + - - +
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Residues in contact with THR 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C ALA 2.7 18.8 + - - -
180C TYR* 2.7 15.3 + - - -
182C PHE* 1.3 72.8 - - - +
184C ALA* 1.3 66.2 + - - +
185C LEU 2.8 3.0 + - - -
186C ASP* 3.1 6.0 + - - +
187C ALA* 3.0 23.8 + - + +
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Residues in contact with ALA 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C TYR 2.6 15.4 + - - +
181C ALA* 3.6 12.1 - - - +
183C THR* 1.3 74.2 - - - +
185C LEU* 1.3 56.8 + - - +
187C ALA* 3.2 7.4 - - - +
188C LEU* 3.0 37.7 + - + +
210C LEU* 5.2 9.4 - - + -
250C PHE* 6.1 7.4 - - + -
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Residues in contact with LEU 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C ALA* 2.7 25.6 + - + +
182C PHE* 3.5 13.9 - - + +
183C THR 2.8 1.4 + - - -
184C ALA* 1.3 69.9 - - - +
186C ASP* 1.3 64.0 + - - +
187C ALA 2.8 6.3 + - - -
188C LEU* 3.1 7.4 + - + +
189C ALA* 2.9 27.0 + - - +
203C VAL* 4.3 12.8 - - + +
206C GLY* 3.5 9.4 - - - -
207C ALA* 3.4 39.9 - - + +
210C LEU* 3.3 30.7 - - + -
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Residues in contact with ASP 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A GLY* 5.7 4.8 - - - +
228A LYS* 3.2 18.7 + - - +
229A ASP* 4.9 0.5 - - - +
251A ARG* 4.8 13.7 + - - -
182C PHE 3.0 20.0 + - - +
183C THR* 3.9 4.7 - - - +
185C LEU* 1.3 72.7 - - - +
187C ALA* 1.3 57.0 + - - +
189C ALA* 3.1 22.3 - - - +
190C ASP* 3.2 16.3 - - - +
199C ARG* 2.9 26.5 + - - +
203C VAL* 6.4 0.9 - - - -
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Residues in contact with ALA 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C THR* 3.0 12.4 + - + +
184C ALA* 3.2 15.0 - - - +
185C LEU 2.8 0.8 + - - -
186C ASP* 1.3 76.0 - - - +
188C LEU* 1.3 64.0 + - + +
190C ASP* 2.7 30.0 - - - +
191C GLY* 3.2 3.6 + - - -
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Residues in contact with LEU 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C ALA* 3.0 19.8 + - + +
185C LEU* 3.8 21.5 - - + +
187C ALA* 1.3 78.7 - - + +
189C ALA* 1.3 53.8 + - - +
190C ASP 2.5 15.1 + - - -
191C GLY* 2.6 14.1 + - - +
192C GLY* 2.9 12.0 + - - -
206C GLY* 4.7 14.1 - - - -
209C ALA* 6.4 0.7 - - + -
210C LEU* 4.8 14.8 - - + -
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Residues in contact with ALA 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C LEU* 2.9 12.9 + - + +
186C ASP* 3.1 5.2 - - - +
188C LEU* 1.3 74.6 - - - +
190C ASP* 1.3 56.9 + - - +
192C GLY* 4.7 1.3 - - - +
193C VAL* 3.5 6.7 - - - -
199C ARG* 3.0 28.3 + - - +
202C ALA* 3.6 14.1 - - + +
203C VAL* 3.2 48.9 - - + +
206C GLY* 5.9 0.2 - - - -
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Residues in contact with ASP 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A LYS* 3.1 23.8 + - - +
239A ILE* 2.9 36.8 - - + +
242A LEU* 5.7 2.4 - - - +
246A GLU* 5.4 6.8 - - - +
251A ARG* 5.8 1.0 + - - -
186C ASP* 3.2 16.0 - - - +
187C ALA* 2.7 21.0 - - - +
188C LEU 2.5 1.2 + - - -
189C ALA* 1.3 67.2 - - - +
191C GLY* 1.3 62.4 + - - +
192C GLY 3.5 0.2 - - - -
193C VAL* 3.3 10.7 - - - +
194C LYS* 2.9 12.3 + - - +
199C ARG* 2.6 30.0 + - - -
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Residues in contact with GLY 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C ALA 3.2 3.5 + - - -
188C LEU* 2.6 7.9 + - - -
190C ASP* 1.3 77.1 - - - +
192C GLY* 1.3 55.2 + - - -
193C VAL 2.9 1.1 - - - -
194C LYS* 2.4 40.4 + - - +
195C MET* 2.9 10.7 + - - +
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Residues in contact with GLY 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188C LEU 2.9 11.4 + - - -
190C ASP 4.7 0.2 - - - -
191C GLY* 1.3 73.9 - - - +
193C VAL* 1.3 63.1 + - - +
195C MET* 3.0 21.9 + - - -
197C LEU* 3.3 37.1 - - - +
202C ALA* 4.9 3.4 - - - -
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Residues in contact with VAL 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A SER* 4.5 11.2 - - - +
233A SER 5.0 0.2 - - - -
234A PRO* 3.0 25.6 - - + +
239A ILE* 4.4 11.0 - - + -
189C ALA 3.5 9.4 - - - +
190C ASP* 3.3 30.5 - - - +
192C GLY* 1.3 75.1 - - - +
194C LYS* 1.3 55.9 + - - +
196C GLY 2.6 35.6 + - - +
197C LEU* 3.8 15.7 - - - +
199C ARG* 3.8 29.2 - - + +
202C ALA* 4.2 10.2 - - + +
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Residues in contact with LYS 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A PRO 4.4 0.2 - - - -
235A GLY 4.1 7.3 - - - +
239A ILE* 3.6 19.5 - - + +
240A HIS* 3.1 54.2 + - + +
243A HIS* 2.9 44.6 + - + -
190C ASP 2.9 15.4 + - - +
191C GLY* 2.4 28.6 + - - +
193C VAL* 1.3 69.1 - - - +
195C MET* 1.3 70.4 + - - +
196C GLY 3.3 2.4 + - - -
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Residues in contact with MET 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C GLY 2.9 14.1 + - - +
192C GLY* 3.0 10.2 + - - +
193C VAL 2.8 1.4 + - - -
194C LYS* 1.3 97.5 - - - +
196C GLY* 1.3 58.0 + - - +
197C LEU* 3.7 6.4 + - + +
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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