Contacts of the helix formed by residues 225 - 235 (chain H) in PDB entry 2JG7
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 GLY 225 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53H GLN* 4.1 3.2 + - - -
189H LYS* 3.6 4.0 - - - +
192H PRO* 4.1 16.4 - - - -
224H GLY* 1.3 74.9 - - - +
226H ALA* 1.3 67.1 + - - -
227H ASP* 3.1 12.8 + - - +
228H ILE 3.2 2.1 + - - -
229H GLY 3.1 16.3 + - - -
1510H NAD 4.1 5.8 - - - -
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Residues in contact with ALA 226 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225H GLY* 1.3 69.2 - - - -
227H ASP* 1.3 57.5 + - - +
229H GLY 3.1 0.3 + - - -
230H THR* 2.7 39.5 + - - +
1510H NAD 3.5 48.7 + - + +
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Residues in contact with ASP 227 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54H ALA 4.5 6.1 - - - +
55H THR* 5.6 0.2 - - - -
56H LEU* 3.0 32.0 + - - +
225H GLY* 4.2 11.6 + - - +
226H ALA* 1.3 78.4 - - - +
228H ILE* 1.3 77.6 + - - +
230H THR* 3.6 5.0 + - - -
231H ALA* 3.5 15.4 + - - +
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Residues in contact with ILE 228 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54H ALA* 4.0 18.8 - - + +
55H THR 4.1 18.2 - - - +
56H LEU* 4.2 7.9 - - + +
59H TYR* 3.8 26.2 - - + -
189H LYS* 4.0 18.8 - - + -
222H THR* 3.7 22.9 - - - +
223H CYS 4.4 3.8 - - - +
224H GLY* 4.2 17.9 - - - -
225H GLY 3.2 2.0 + - - +
227H ASP* 1.3 95.6 - - - +
229H GLY* 1.3 67.1 + - - +
231H ALA* 2.9 17.4 + - + +
232H MET* 3.0 16.5 + - - +
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Residues in contact with GLY 229 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162H ILE* 3.7 13.5 - - - +
189H LYS* 3.6 14.1 - - - +
225H GLY 3.1 7.8 + - - -
226H ALA 3.1 3.5 + - - -
228H ILE* 1.3 78.2 - - - +
230H THR* 1.3 58.6 + - - +
232H MET* 3.5 5.7 + - - +
233H ALA* 3.2 19.4 + - - +
1510H NAD 3.2 27.5 - - - -
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Residues in contact with THR 230 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226H ALA* 2.7 23.4 + - - +
227H ASP* 3.8 5.2 - - - -
229H GLY* 1.3 69.4 - - - +
231H ALA* 1.3 66.1 + - - +
233H ALA* 3.1 7.6 + - - +
234H LYS* 2.9 37.8 + - + +
256H MET* 3.7 23.2 - - + +
1510H NAD 3.2 24.3 + - - -
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Residues in contact with ALA 231 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56H LEU* 4.9 17.3 - - + -
59H TYR* 4.0 25.1 - - + -
227H ASP 3.5 9.8 + - - +
228H ILE* 2.9 13.1 + - - +
230H THR* 1.3 76.8 - - - +
232H MET* 1.3 58.5 + - - +
234H LYS* 3.3 7.0 + - - +
235H ASP* 2.9 30.8 + - - +
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Residues in contact with MET 232 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59H TYR* 3.4 31.6 - - + +
160H GLY* 3.7 13.0 - - - -
161H ILE 3.6 30.3 - - - +
162H ILE* 3.7 30.3 - - + -
187H LEU* 3.8 20.4 - - + +
189H LYS* 3.9 17.0 - - + -
228H ILE* 3.0 18.1 + - - +
229H GLY* 3.6 7.4 - - - +
231H ALA* 1.3 77.0 - - - +
233H ALA* 1.3 62.1 + - - +
235H ASP* 3.1 14.2 + - - +
238H VAL* 3.8 11.6 - - + +
241H LEU* 4.0 7.9 - - + -
260H ARG* 3.5 11.8 + - - -
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Residues in contact with ALA 233 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229H GLY 3.2 11.0 + - - +
230H THR* 3.1 11.1 + - - +
232H MET* 1.3 78.5 - - - +
234H LYS* 1.3 57.5 + - - +
241H LEU* 3.6 21.3 - - + +
253H VAL* 4.1 17.3 - - + +
256H MET* 3.8 24.8 - - + -
257H VAL* 3.4 17.8 + - - +
260H ARG* 2.9 18.0 + - - -
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Residues in contact with LYS 234 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230H THR* 2.9 30.1 + - + +
231H ALA* 3.9 5.8 - - - +
233H ALA* 1.3 75.9 - - - +
235H ASP* 1.3 63.3 + - - +
236H GLU* 3.4 5.0 + - - +
256H MET* 3.8 35.2 - - + +
260H ARG* 3.3 15.9 - - - +
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Residues in contact with ASP 235 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59H TYR* 2.8 27.5 + - - +
63H VAL* 3.9 3.1 - - - +
231H ALA 2.9 17.5 + - - +
232H MET 3.1 5.9 + - - +
234H LYS* 1.3 75.1 - - - +
236H GLU* 1.3 58.6 + - - +
237H ARG* 3.0 61.3 + - - +
238H VAL* 3.1 17.5 + - + +
260H ARG* 2.9 23.1 + - - -
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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