Contacts of the helix formed by residues 238 - 248 (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 THR 238 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A LYS 5.7 0.2 - - - +
231A VAL* 4.1 18.5 + - + +
232A SER* 3.5 25.6 - - - +
233A SER 5.4 0.2 - - - -
236A GLY 2.6 13.1 + - - -
237A ALA* 1.3 75.5 - - - +
239A ILE* 1.3 57.0 + - - +
240A HIS 2.5 5.6 + - - -
241A ALA* 2.5 27.3 + - - +
242A LEU* 2.7 28.1 + - + +
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Residues in contact with ILE 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A SER* 3.9 13.4 - - - +
233A SER 4.0 9.6 - - - +
234A PRO 5.0 0.9 - - - +
235A GLY 4.2 2.9 - - - +
236A GLY* 3.1 33.7 - - - +
238A THR* 1.3 78.5 - - - +
240A HIS* 1.3 60.3 + - + +
242A LEU* 3.8 17.9 - - + -
243A HIS* 3.0 26.3 + - + +
190C ASP* 2.9 49.6 - - + +
193C VAL* 4.4 8.1 - - + +
194C LYS* 3.6 23.2 - - + +
199C ARG* 5.4 0.2 - - - +
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Residues in contact with HIS 240 (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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235A GLY 4.3 8.6 + - - -
236A GLY* 4.2 2.2 - - - -
237A ALA* 3.7 20.5 + - - +
238A THR 2.5 4.6 + - - -
239A ILE* 1.3 83.5 - - + +
241A ALA* 1.3 65.0 + - - +
242A LEU 3.1 1.3 - - - -
243A HIS* 3.2 13.4 + - - +
244A VAL* 3.1 19.5 + - - +
194C LYS* 3.1 53.7 + - + +
195C MET* 6.0 0.2 - - - -
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Residues in contact with ALA 241 (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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237A ALA 3.5 15.7 + - - +
238A THR* 2.5 13.7 + - - +
240A HIS* 1.3 72.2 - - - +
242A LEU* 1.3 71.4 + - + +
244A VAL* 2.9 28.6 - - + +
245A LEU* 3.2 9.4 + - + +
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Residues in contact with LEU 242 (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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228A LYS* 4.0 34.3 - - + +
232A SER* 4.6 6.1 - - - +
238A THR* 2.7 35.9 + - + +
239A ILE* 3.5 24.2 - - + +
241A ALA* 1.3 72.7 - - + +
243A HIS* 1.3 70.0 - - - +
245A LEU* 2.6 33.4 + - + -
246A GLU* 2.7 17.3 + - + +
190C ASP* 5.5 2.0 - - - +
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Residues in contact with HIS 243 (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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239A ILE* 3.0 12.8 + - + +
240A HIS 3.3 10.1 - - - +
242A LEU* 1.3 77.3 - - - +
244A VAL* 1.3 50.5 + - + +
246A GLU* 3.2 10.3 - - - +
247A SER* 2.6 53.2 + - - -
194C LYS* 2.9 42.6 + - + -
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Residues in contact with VAL 244 (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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240A HIS 3.1 17.0 - - - +
241A ALA* 2.9 17.9 - - + +
242A LEU 2.7 4.2 + - - -
243A HIS* 1.3 69.7 - - + +
245A LEU* 1.3 90.4 + - + +
247A SER* 2.8 23.8 + - - -
248A GLY* 3.1 4.9 + - - -
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Residues in contact with LEU 245 (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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241A ALA* 3.5 14.8 - - + +
242A LEU* 2.6 26.4 + - + +
244A VAL* 1.3 85.0 - - + +
246A GLU* 1.3 65.7 + - - +
248A GLY* 2.9 14.3 + - - -
250A PHE* 3.4 65.1 + - + +
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Residues in contact with GLU 246 (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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242A LEU* 2.7 14.7 + - + +
243A HIS* 3.2 18.2 - - - +
245A LEU* 1.3 80.9 - - - +
247A SER* 1.3 62.7 + - - +
249A GLY* 3.5 10.2 + - - +
250A PHE* 5.2 3.0 - - - +
251A ARG* 2.7 49.9 + - - +
190C ASP* 5.4 6.0 - - - +
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Residues in contact with SER 247 (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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243A HIS* 2.6 42.7 + - - -
244A VAL* 2.8 16.3 + - - -
246A GLU* 1.3 75.7 - - - +
248A GLY* 1.3 55.2 + - - +
249A GLY 3.4 3.3 + - - -
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Residues in contact with GLY 248 (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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244A VAL 3.1 6.8 + - - -
245A LEU 2.9 7.6 + - - -
247A SER* 1.3 76.3 - - - +
249A GLY* 1.3 62.9 + - - -
250A PHE* 3.0 5.6 + - - -
253A LEU* 4.5 11.6 - - - +
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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