Contacts of the helix formed by residues 198 - 219 (chain A) 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 PRO 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A GLY 3.4 2.2 - - - +
197A LEU* 1.3 85.7 - - + +
199A ARG* 1.3 55.8 + - - +
200A ARG* 5.0 0.9 - - + +
201A LEU* 3.1 45.6 + - + +
202A ALA* 2.7 36.2 + - - +
234E PRO* 4.2 13.2 - - + -
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Residues in contact with ARG 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A ASP* 3.0 29.1 + - - +
189A ALA* 2.8 32.9 + - - +
190A ASP* 2.8 31.8 + - - +
193A VAL* 4.1 17.8 - - + +
197A LEU 3.9 0.4 + - - -
198A PRO* 1.3 72.6 - - - +
200A ARG* 1.3 59.2 + - + +
201A LEU 2.5 17.0 + - - -
202A ALA* 2.8 9.1 + - - -
203A VAL* 3.1 31.1 + - + +
229E ASP* 2.9 47.2 + - + +
234E PRO* 5.2 1.4 - - - +
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Residues in contact with ARG 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A PRO* 3.7 1.7 - - + +
199A ARG* 1.3 78.6 - - + +
201A LEU* 1.3 55.0 + - - +
203A VAL* 5.0 0.4 - - - -
204A ARG* 2.5 53.0 - - - +
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Residues in contact with LEU 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A LEU* 4.5 10.3 - - + -
198A PRO* 3.1 40.1 + - + +
199A ARG 2.5 6.5 + - - -
200A ARG* 1.3 74.2 - - - +
202A ALA* 1.3 62.7 + - - +
204A ARG* 3.4 7.1 - - + +
205A LEU* 3.0 54.4 + - + +
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Residues in contact with ALA 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A ALA* 4.0 22.5 - - - +
192A GLY* 4.1 5.2 - - - -
193A VAL 4.4 0.4 - - - +
197A LEU* 3.7 26.5 - - + -
198A PRO 2.7 21.4 + - - +
199A ARG* 2.8 4.2 + - - +
201A LEU* 1.3 70.0 - - - +
203A VAL* 1.3 69.2 + - - +
205A LEU* 2.8 24.9 + - - +
206A GLY* 3.0 8.7 + - - -
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Residues in contact with VAL 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A LEU* 5.3 12.3 - - + +
186A ASP* 5.9 0.9 - - - -
189A ALA* 3.1 33.1 - - + +
199A ARG* 3.1 40.7 + - + +
200A ARG* 5.3 0.2 - - - -
202A ALA* 1.3 79.0 - - - +
204A ARG* 1.3 91.5 + - - +
206A GLY* 3.0 3.6 + - - -
207A ALA* 3.0 25.5 + - + +
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Residues in contact with ARG 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A ARG* 2.5 47.7 + - - +
201A LEU* 3.4 7.2 - - + +
202A ALA 3.1 0.2 - - - -
203A VAL* 1.3 91.7 - - - +
205A LEU* 1.3 62.8 + - + +
207A ALA* 3.5 8.9 + - - +
208A GLN* 3.0 26.9 + - - +
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Residues in contact with LEU 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A LEU* 4.3 15.9 - - + -
201A LEU* 3.0 53.3 + - + +
202A ALA* 2.8 15.3 + - - +
204A ARG* 1.3 74.0 - - + +
206A GLY* 1.3 59.1 + - - +
208A GLN* 3.4 8.4 + - + +
209A ALA* 3.0 27.5 + - - +
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Residues in contact with GLY 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A LEU* 4.2 7.0 - - - -
188A LEU* 4.9 19.3 - - - -
202A ALA 3.0 11.1 + - - -
203A VAL 3.0 4.9 + - - -
205A LEU* 1.3 75.4 - - - +
207A ALA* 1.3 68.0 + - - +
209A ALA* 3.0 9.4 + - - +
210A LEU* 3.0 23.7 + - - +
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Residues in contact with ALA 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A LEU* 4.1 25.1 - - + +
203A VAL* 3.0 14.7 + - + +
204A ARG* 3.6 13.2 - - - +
206A GLY* 1.3 75.0 - - - +
208A GLN* 1.3 59.2 + - - +
210A LEU* 2.8 21.9 + - - +
211A LEU* 2.9 15.6 + - - +
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Residues in contact with GLN 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A ARG 3.0 14.7 + - - +
205A LEU* 3.6 9.9 - - + +
206A GLY 3.3 0.2 - - - -
207A ALA* 1.3 78.6 - - - +
209A ALA* 1.3 60.2 + - - +
211A LEU* 4.1 19.2 - - - +
212A GLY* 3.2 20.1 + - - -
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Residues in contact with ALA 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A LEU 3.0 13.9 + - - +
206A GLY* 3.4 11.7 - - - +
207A ALA 3.0 0.4 - - - -
208A GLN* 1.3 74.5 - - - +
210A LEU* 1.3 64.5 + - + +
212A GLY* 3.4 1.5 + - - -
213A ALA* 3.0 29.3 + - - +
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Residues in contact with LEU 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A ALA* 5.3 13.2 - - + -
184A ALA* 6.2 2.0 - - + -
185A LEU* 3.9 24.9 - - + -
188A LEU* 4.6 10.5 - - + -
206A GLY 3.0 13.1 + - - +
207A ALA* 2.8 10.5 + - - +
209A ALA* 1.3 76.8 - - + +
211A LEU* 1.3 66.4 + - - +
213A ALA* 3.0 9.1 + - + +
214A ALA* 2.8 25.4 + - + +
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Residues in contact with LEU 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A GLU* 6.2 4.0 - - + -
207A ALA 2.9 11.5 + - - +
208A GLN* 4.1 21.3 - - - +
210A LEU* 1.3 78.2 - - - +
212A GLY* 1.3 63.1 + - - +
214A ALA* 3.2 9.8 - - + +
215A LYS* 3.0 29.0 + - + +
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Residues in contact with GLY 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A GLN* 3.2 16.4 + - - -
209A ALA 3.7 3.4 - - - -
210A LEU 3.0 0.8 - - - -
211A LEU* 1.3 77.5 - - - +
213A ALA* 1.3 65.5 + - - +
215A LYS* 3.2 14.7 + - - +
216A MET* 3.2 20.6 + - - +
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Residues in contact with ALA 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A ALA 3.0 16.4 + - - +
210A LEU* 3.0 9.8 + - + +
212A GLY* 1.3 74.9 - - - +
214A ALA* 1.3 67.7 + - - +
216A MET* 3.5 10.0 + - - +
217A LEU* 3.2 19.6 + - - +
227A LEU* 4.9 2.5 - - - +
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Residues in contact with ALA 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A LEU* 2.8 13.9 + - + +
211A LEU* 3.2 17.5 - - + +
213A ALA* 1.3 79.8 - - - +
215A LYS* 1.4 71.2 + - - +
217A LEU* 2.9 11.4 + - - +
218A LEU* 3.1 26.3 + - + +
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Residues in contact with LYS 215 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211A LEU* 3.0 16.5 + - + +
212A GLY* 3.2 8.3 + - - +
214A ALA* 1.4 76.1 - - - +
216A MET* 1.2 68.3 + - + +
218A LEU* 2.7 21.9 + - - +
219A HIS* 2.9 49.5 + - + +
1300A NAP 3.8 15.5 - - + +
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Residues in contact with MET 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A GLY 3.2 13.1 + - - +
213A ALA* 3.8 11.0 - - - +
215A LYS* 1.2 79.8 - - + +
217A LEU* 1.3 63.7 + - - +
218A LEU 3.2 0.2 + - - -
219A HIS* 3.6 8.6 - - - +
220A SER* 3.1 22.9 + - - -
222A GLN* 6.0 0.4 - - - +
227A LEU* 4.1 31.2 - - + -
230A ASN* 6.5 0.7 - - + -
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Residues in contact with LEU 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A ALA 3.2 8.3 + - - +
214A ALA* 2.9 12.7 + - - +
215A LYS 2.8 1.4 + - - -
216A MET* 1.3 76.0 - - - +
218A LEU* 1.3 62.8 + - + +
220A SER* 2.7 27.2 - - - +
221A GLU 4.2 9.2 - - - +
223A HIS 4.2 5.6 - - - -
224A PRO* 3.9 45.3 - - + -
227A LEU* 3.8 16.2 - - + +
1300A NAP 3.1 7.2 + - - +
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Residues in contact with LEU 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A ALA* 3.4 28.0 - - + +
215A LYS* 2.7 13.2 + - + +
217A LEU* 1.3 79.1 - - + +
219A HIS* 1.4 68.8 + - + +
220A SER 3.0 2.9 + - - -
1300A NAP 2.7 104.6 + - + +
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Residues in contact with HIS 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A LYS* 2.9 44.9 + - + +
216A MET* 3.6 6.2 - - - +
218A LEU* 1.4 87.5 - - + +
220A SER* 1.7 50.7 + - - -
1300A NAP 3.3 41.8 + - + +
1301A GLU* 5.0 4.5 - - + -
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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
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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