Contacts of the helix formed by residues 205 - 219 (chain D) 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 LEU 205 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197D LEU* 4.9 13.0 - - + -
201D LEU* 3.3 47.8 - - + +
202D ALA* 3.0 9.6 + - - +
204D ARG* 1.3 79.9 - - + +
206D GLY* 1.3 57.5 + - - +
207D ALA 3.0 1.6 - - - -
208D GLN* 3.1 8.0 + - + +
209D ALA* 2.5 36.9 + - - +
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Residues in contact with GLY 206 (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* 3.9 6.5 - - - -
188D LEU* 4.7 21.4 - - - +
202D ALA 3.5 8.6 + - - -
203D VAL 5.7 0.4 - - - -
205D LEU* 1.3 77.6 - - - +
207D ALA* 1.3 63.8 + - - +
209D ALA* 3.3 8.6 - - - +
210D LEU* 3.0 29.8 + - - +
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Residues in contact with ALA 207 (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* 3.7 26.9 - - + +
203D VAL 4.7 5.5 - - - +
204D ARG* 4.4 19.1 - - - +
205D LEU 3.0 1.2 - - - +
206D GLY* 1.3 75.4 - - - +
208D GLN* 1.3 66.1 + - - +
210D LEU* 2.8 16.0 + - - +
211D LEU* 3.0 15.4 + - - +
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Residues in contact with GLN 208 (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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204D ARG 3.9 13.1 + - - +
205D LEU* 3.1 12.8 + - + +
207D ALA* 1.3 78.5 - - - +
209D ALA* 1.3 61.9 + - - +
211D LEU* 3.5 27.2 - - - +
212D GLY* 3.0 16.5 + - - -
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Residues in contact with ALA 209 (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* 6.4 0.2 - - + -
205D LEU 2.5 21.4 + - - +
206D GLY* 3.3 12.6 - - - +
207D ALA 2.9 0.2 + - - -
208D GLN* 1.3 72.4 - - - +
210D LEU* 1.3 55.0 + - + +
212D GLY* 3.1 3.1 + - - -
213D ALA* 2.7 35.7 + - - +
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Residues in contact with LEU 210 (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* 4.9 14.6 - - + +
184D ALA* 5.2 7.6 - - + -
185D LEU* 3.2 31.2 - - + -
188D LEU* 5.0 11.9 - - + -
206D GLY 3.0 18.0 + - - +
207D ALA* 2.8 10.8 + - - +
209D ALA* 1.3 71.1 - - + +
211D LEU* 1.3 58.3 + - - +
213D ALA* 2.8 10.6 + - + +
214D ALA* 2.6 37.1 + - - +
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Residues in contact with LEU 211 (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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207D ALA 3.0 15.6 + - - +
208D GLN* 3.5 24.0 - - - +
210D LEU* 1.3 75.2 - - - +
212D GLY* 1.3 61.0 + - - +
214D ALA* 3.6 6.0 - - - +
215D LYS* 2.9 45.7 + - + +
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Residues in contact with GLY 212 (chain D).
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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208D GLN* 3.0 17.2 + - - -
209D ALA 3.5 3.1 - - - -
210D LEU 3.0 1.2 - - - -
211D LEU* 1.3 79.8 - - - +
213D ALA* 1.3 65.3 + - - +
215D LYS* 3.7 3.7 - - - +
216D MET* 2.8 28.1 + - - +
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Residues in contact with ALA 213 (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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209D ALA 2.7 17.6 + - - +
210D LEU* 2.8 18.2 + - + +
212D GLY* 1.3 71.1 - - - +
214D ALA* 1.3 63.3 + - - +
216D MET* 3.1 20.5 - - - +
217D LEU* 3.2 8.5 + - - +
227D LEU* 5.6 0.5 - - - +
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Residues in contact with ALA 214 (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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210D LEU 2.6 19.1 + - - +
211D LEU* 3.6 7.2 - - - +
213D ALA* 1.3 67.5 - - - +
215D LYS* 1.3 65.5 + - - +
216D MET 2.7 5.6 + - - -
217D LEU* 2.8 17.5 + - - +
218D LEU* 3.1 25.5 + - + +
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Residues in contact with LYS 215 (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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211D LEU* 2.9 33.3 + - + +
212D GLY* 3.8 4.7 - - - +
214D ALA* 1.3 76.4 - - - +
216D MET* 1.3 61.9 + - - +
218D LEU* 3.8 10.9 - - - +
219D HIS* 2.8 62.2 + - + +
4300D NAP 4.1 17.8 + - - +
4301D GLU* 5.4 0.4 + - - -
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Residues in contact with MET 216 (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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212D GLY 2.8 14.3 + - - +
213D ALA* 3.1 16.2 - - - +
214D ALA 2.7 4.6 + - - -
215D LYS* 1.3 76.7 - - - +
217D LEU* 1.3 52.9 + - - +
218D LEU 3.4 0.5 + - - -
219D HIS* 3.5 5.9 + - - +
220D SER* 2.6 29.0 + - - +
227D LEU* 4.2 36.3 - - + +
230D ASN* 6.2 1.6 - - + -
231D VAL* 5.0 15.0 - - + -
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Residues in contact with LEU 217 (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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213D ALA 3.2 6.8 + - - +
214D ALA* 2.8 11.2 + - - +
216D MET* 1.3 73.5 - - - +
218D LEU* 1.3 66.5 + - + +
220D SER* 2.8 25.7 - - - +
223D HIS* 3.6 29.4 - - - +
224D PRO* 3.6 35.7 - - + -
227D LEU* 3.6 18.5 - - + +
4300D NAP 3.1 12.5 + - - +
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Residues in contact with LEU 218 (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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214D ALA* 3.1 31.6 + - + +
215D LYS* 3.7 11.9 - - - +
217D LEU* 1.3 81.7 - - + +
219D HIS* 1.3 61.8 + - - +
220D SER 3.0 5.6 + - - -
4300D NAP 2.8 93.9 + - - +
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Residues in contact with HIS 219 (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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215D LYS* 2.8 61.4 + - + +
216D MET* 3.7 3.0 - - - +
218D LEU* 1.3 77.6 - - + +
220D SER* 1.3 63.5 + - - +
4300D NAP 3.7 29.6 + - - -
4301D GLU* 4.8 4.6 + - - -
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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