Contacts of the helix formed by residues 198 - 220 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193B VAL* 3.9 0.4 - - - -
196B GLY 3.5 0.9 - - - +
197B LEU* 1.3 89.8 - - + +
199B ARG* 1.3 70.7 + - - +
200B ARG 5.0 0.7 - - - +
201B LEU* 3.2 44.4 - - + +
202B ALA* 3.2 12.8 + - - +
234D PRO* 3.9 12.6 - - + -
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Residues in contact with ARG 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B ASP* 2.8 29.1 + - - +
189B ALA* 2.9 20.5 + - - +
190B ASP* 2.9 45.1 + - - +
193B VAL* 3.7 16.5 - - + +
197B LEU 3.9 0.6 + - - -
198B PRO* 1.3 76.1 - - - +
200B ARG* 1.3 70.6 + - - +
202B ALA* 3.1 12.8 - - - +
203B VAL* 3.4 18.4 + - + +
226D GLN* 6.0 1.1 - - - +
229D ASP* 2.7 48.6 + - + +
232D SER 6.0 1.6 - - - +
234D PRO* 4.8 2.2 - - - +
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Residues in contact with ARG 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B PRO* 3.6 1.0 - - - +
199B ARG* 1.3 81.7 - - + +
201B LEU* 1.3 61.4 + - - +
202B ALA 2.6 2.4 + - - -
203B VAL* 3.0 7.8 + - - -
204B ARG* 2.4 66.7 + - + +
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Residues in contact with LEU 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B LEU* 4.7 9.2 - - + -
198B PRO* 3.2 39.0 + - + +
199B ARG 3.6 0.2 - - - -
200B ARG* 1.3 76.7 - - - +
202B ALA* 1.3 56.9 + - - +
204B ARG* 3.0 24.9 - - + +
205B LEU* 3.0 51.0 + - + +
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Residues in contact with ALA 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B LEU 5.3 0.7 - - - +
189B ALA* 3.8 12.1 - - - +
192B GLY* 5.1 1.1 - - - -
193B VAL* 3.7 17.9 - - + +
197B LEU* 4.0 24.5 - - + -
198B PRO 3.2 12.4 + - - +
199B ARG 3.1 12.5 + - - +
200B ARG 2.6 4.4 + - - -
201B LEU* 1.3 70.7 - - - +
203B VAL* 1.3 67.7 + - - +
204B ARG 2.8 2.0 + - - -
205B LEU* 2.9 14.3 + - - +
206B GLY* 3.1 10.9 + - - -
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Residues in contact with VAL 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B LEU* 4.2 19.3 - - + +
186B ASP* 5.7 1.1 - - - +
189B ALA* 3.5 31.1 - - + +
199B ARG* 3.5 29.6 - - + +
200B ARG* 3.0 7.2 + - - +
202B ALA* 1.3 73.4 - - - +
204B ARG* 1.3 80.0 + - - +
206B GLY* 3.3 1.6 + - - -
207B ALA* 2.6 40.5 + - + +
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Residues in contact with ARG 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B ARG* 2.4 63.0 + - + +
201B LEU* 3.0 16.8 - - + +
202B ALA 2.8 0.2 + - - -
203B VAL* 1.3 94.9 - - - +
205B LEU* 1.3 62.1 + - + +
207B ALA* 3.2 7.6 - - - +
208B GLN* 3.0 22.2 + - - +
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Residues in contact with LEU 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B LEU* 4.0 19.7 - - + -
201B LEU* 3.0 55.2 + - + +
202B ALA* 2.9 6.8 + - - +
204B ARG* 1.3 70.0 - - + +
206B GLY* 1.3 55.4 + - - +
208B GLN* 2.9 11.3 + - - +
209B ALA* 2.7 35.4 + - - +
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Residues in contact with GLY 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B LEU* 3.5 11.0 - - - -
188B LEU* 4.7 15.5 - - - -
202B ALA 3.1 9.3 + - - -
203B VAL* 3.7 3.1 - - - -
205B LEU* 1.3 78.2 - - - +
207B ALA* 1.3 65.8 + - - +
209B ALA* 2.9 25.2 + - - +
210B LEU* 3.0 11.1 + - - +
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Residues in contact with ALA 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B LEU* 3.4 25.1 - - + +
203B VAL* 2.6 25.5 + - + +
204B ARG* 3.2 12.1 - - - +
206B GLY* 1.3 73.8 - - - +
208B GLN* 1.3 64.7 + - - +
210B LEU* 3.0 4.3 + - - +
211B LEU* 2.9 21.9 + - - +
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Residues in contact with GLN 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B ARG 3.0 9.7 + - - +
205B LEU* 2.9 13.8 + - - +
207B ALA* 1.3 79.5 - - - +
209B ALA* 1.3 52.8 + - - +
211B LEU* 3.0 27.4 + - - +
212B GLY* 2.6 39.5 + - - +
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Residues in contact with ALA 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B LEU* 6.0 1.8 - - + -
205B LEU 2.7 16.9 + - - +
206B GLY* 3.0 19.1 - - - +
208B GLN* 1.3 73.8 - - - +
210B LEU* 1.3 59.7 + - + +
212B GLY* 3.7 1.2 - - - -
213B ALA* 3.0 30.2 + - - +
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Residues in contact with LEU 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181B ALA* 4.8 11.7 - - + +
184B ALA* 5.1 6.3 - - + -
185B LEU* 3.2 43.3 - - + +
188B LEU* 4.7 14.8 - - + -
206B GLY 3.4 9.2 - - - +
207B ALA 3.0 4.4 + - - +
209B ALA* 1.3 76.0 - - + +
211B LEU* 1.3 69.8 + - - +
213B ALA* 4.6 6.5 - - + -
214B ALA* 3.0 29.1 + - - +
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Residues in contact with LEU 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B GLU* 6.4 1.8 - - + -
207B ALA 2.9 12.9 + - - +
208B GLN* 3.1 30.3 - - - +
210B LEU* 1.3 78.1 - - - +
212B GLY* 1.3 68.4 + - - +
214B ALA* 3.8 3.5 - - - +
215B LYS* 3.4 27.2 + - + +
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Residues in contact with GLY 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B GLN* 2.6 24.1 + - - +
209B ALA* 3.7 1.3 - - - -
210B LEU 3.1 0.8 - - - -
211B LEU* 1.3 77.7 - - - +
213B ALA* 1.3 67.2 + - - -
214B ALA 2.9 1.2 + - - -
215B LYS* 3.0 4.4 + - - +
216B MET* 2.9 22.7 + - - +
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Residues in contact with ALA 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B ALA 3.0 19.1 + - - +
210B LEU* 3.9 7.6 - - + +
212B GLY* 1.3 66.8 - - - -
214B ALA* 1.3 52.2 + - - +
216B MET* 2.9 13.8 + - - +
217B LEU* 2.6 37.4 + - - +
227B LEU* 5.0 1.7 - - - +
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Residues in contact with ALA 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B LEU 3.0 15.8 + - - +
211B LEU* 3.8 4.9 - - - +
212B GLY 2.9 2.6 + - - -
213B ALA* 1.3 74.3 - - - +
215B LYS* 1.3 67.9 + - - +
217B LEU* 2.6 21.8 + - - +
218B LEU* 2.7 27.0 + - + +
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Residues in contact with LYS 215 (chain B).
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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211B LEU* 3.4 19.9 + - + +
212B GLY* 3.0 11.5 + - - +
214B ALA* 1.3 75.1 - - - +
216B MET* 1.3 66.2 - - - +
218B LEU* 3.0 15.5 + - - +
219B HIS* 2.9 59.4 + - + +
2300B NAP 4.6 15.1 + - - +
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Residues in contact with MET 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B GLY 2.9 11.3 + - - +
213B ALA* 2.9 18.4 - - - +
215B LYS* 1.3 77.5 - - - +
217B LEU* 1.3 60.5 + - - +
219B HIS* 5.1 2.7 - - - -
220B SER* 2.4 40.5 + - - +
227B LEU* 3.8 34.1 - - + -
230B ASN* 6.0 3.1 - - + +
231B VAL* 5.2 13.0 - - + -
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Residues in contact with LEU 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B ALA 2.6 15.9 + - - +
214B ALA* 2.6 12.2 + - - +
216B MET* 1.3 72.4 - - - +
218B LEU* 1.3 67.2 + - + +
220B SER* 4.4 0.2 - - - -
221B GLU* 3.1 33.9 + - - +
224B PRO* 3.6 48.7 - - + -
227B LEU* 3.8 21.2 - - + +
2300B NAP 3.7 3.9 + - - +
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Residues in contact with LEU 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B ALA* 2.7 37.3 + - + +
215B LYS* 3.0 14.1 + - - +
217B LEU* 1.3 78.9 - - + +
219B HIS* 1.3 68.6 + - - +
2300B NAP 2.8 94.7 + - - +
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Residues in contact with HIS 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B LYS* 2.9 55.5 + - + +
216B MET* 4.3 2.5 - - - +
218B LEU* 1.3 74.3 - - - +
220B SER* 1.3 75.7 + - - +
2300B NAP 3.6 39.3 + - - -
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Residues in contact with SER 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B MET* 2.4 38.3 + - - +
217B LEU* 3.9 2.0 - - - -
219B HIS* 1.3 87.8 - - - +
221B GLU* 1.3 84.1 + - - +
222B GLN* 3.7 7.6 - - - -
227B LEU* 4.8 13.1 - - - +
2300B NAP 4.4 0.3 + - - -
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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