Contacts of the helix formed by residues 237 - 248 (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 ALA 237 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236D GLY* 1.3 71.1 - - - +
238D THR* 1.3 58.6 + - - +
240D HIS* 2.5 39.8 + - - +
241D ALA* 2.6 19.6 + - - -
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Residues in contact with THR 238 (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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231D VAL* 3.3 37.1 + - + +
232D SER* 4.5 9.4 - - - +
233D SER* 5.5 0.9 - - - -
236D GLY 3.1 4.0 + - - -
237D ALA* 1.3 79.5 - - - +
239D ILE* 1.3 59.1 + - - +
241D ALA* 3.2 8.1 + - + +
242D LEU* 2.8 40.7 + - + +
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Residues in contact with ILE 239 (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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190B ASP* 4.4 20.2 - - + +
193B VAL* 4.4 18.2 - - + +
194B LYS* 3.6 41.5 - - + +
228D LYS* 5.9 0.2 - - - -
232D SER* 3.2 35.9 - - - +
233D SER 3.8 16.8 - - - +
234D PRO* 5.2 0.2 - - + -
236D GLY* 4.0 8.7 + - - -
237D ALA 3.1 0.6 - - - -
238D THR* 1.3 78.4 - - - +
240D HIS* 1.3 59.3 + - + +
242D LEU* 3.1 16.6 - - + +
243D HIS* 2.9 26.9 + - + +
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Residues in contact with HIS 240 (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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194B LYS* 3.1 46.4 + - + +
195B MET* 5.1 3.1 - - + -
235D GLY 3.5 8.9 + - - -
236D GLY* 2.9 35.7 - - - -
237D ALA* 2.5 22.6 + - - +
239D ILE* 1.3 72.6 - - - +
241D ALA* 1.3 64.9 + - - +
243D HIS* 3.3 7.2 + - - +
244D VAL* 3.2 20.3 + - - +
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Residues in contact with ALA 241 (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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237D ALA 2.6 15.0 + - - +
238D THR* 3.5 12.1 - - + +
240D HIS* 1.3 69.9 - - - +
242D LEU* 1.3 56.5 + - + +
244D VAL* 2.6 39.1 + - + +
245D LEU* 3.0 13.0 + - + +
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Residues in contact with LEU 242 (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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190B ASP* 5.2 2.9 - - + +
228D LYS* 4.0 40.4 - - + +
232D SER* 4.3 5.8 - - - +
238D THR* 2.8 25.7 + - + +
239D ILE* 3.1 30.7 - - + +
241D ALA* 1.3 76.6 - - + +
243D HIS* 1.3 66.0 + - - +
244D VAL 2.8 0.7 + - - -
245D LEU* 3.0 18.7 + - + +
246D GLU* 2.7 33.5 + - - +
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Residues in contact with HIS 243 (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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194B LYS* 2.8 41.2 + - + +
239D ILE* 2.9 17.2 + - + +
240D HIS 3.7 8.1 - - - +
241D ALA 3.3 0.4 - - - -
242D LEU* 1.3 71.7 - - - +
244D VAL* 1.3 57.0 + - - +
246D GLU* 3.5 10.3 - - + +
247D SER* 3.0 35.0 + - - -
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Residues in contact with VAL 244 (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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240D HIS 3.2 11.7 + - - +
241D ALA* 2.6 22.7 + - + +
243D HIS* 1.3 69.5 - - - +
245D LEU* 1.3 77.4 + - + +
247D SER* 2.8 23.1 + - - -
248D GLY* 3.3 3.5 + - - -
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Residues in contact with LEU 245 (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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241D ALA* 3.0 12.7 + - + +
242D LEU* 3.7 20.6 - - + +
244D VAL* 1.3 85.8 - - + +
246D GLU* 1.3 68.6 + - - +
248D GLY* 2.8 14.5 + - - +
250D PHE* 3.3 65.4 + - + +
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Residues in contact with GLU 246 (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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190B ASP* 6.1 0.9 - - - -
228D LYS* 6.0 1.5 + - - -
242D LEU* 2.7 25.9 + - - +
243D HIS* 3.5 15.0 - - + +
245D LEU* 1.3 80.6 - - - +
247D SER* 1.3 57.4 + - - +
248D GLY 3.2 4.3 + - - -
249D GLY* 3.2 13.2 + - - +
250D PHE* 5.1 3.1 - - - +
251D ARG* 3.1 40.5 + - - +
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Residues in contact with SER 247 (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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243D HIS* 3.0 33.3 + - - -
244D VAL* 2.8 18.4 + - - -
246D GLU* 1.3 70.4 - - - +
248D GLY* 1.3 56.4 + - - +
249D GLY 3.4 1.1 + - - -
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Residues in contact with GLY 248 (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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244D VAL 3.3 4.1 + - - -
245D LEU* 2.8 8.8 + - - -
247D SER* 1.3 78.8 - - - +
249D GLY* 1.3 66.8 + - - +
250D PHE* 2.8 7.2 + - - -
253D LEU* 4.2 14.7 - - - +
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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