Contacts of the helix formed by residues 225 - 235 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53E GLN* 4.2 3.0 + - - -
189E LYS* 3.6 4.2 - - - +
192E PRO* 4.1 16.6 - - - -
224E GLY* 1.3 75.1 - - - +
226E ALA* 1.3 66.0 + - - -
227E ASP* 3.2 11.6 - - - +
228E ILE 3.3 3.0 + - - +
229E GLY 3.2 16.3 + - - -
1510E NAD 4.1 5.8 - - - -
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Residues in contact with ALA 226 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225E GLY* 1.3 69.0 - - - -
227E ASP* 1.3 57.6 + - - +
229E GLY 3.1 0.2 + - - -
230E THR* 2.7 39.6 + - - +
1510E NAD 3.5 48.6 + - + +
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Residues in contact with ASP 227 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E ALA 4.9 4.3 - - - +
55E THR* 5.9 0.2 - - - -
56E LEU* 3.6 28.8 + - - +
225E GLY* 4.2 11.7 - - - +
226E ALA* 1.3 76.1 - - - +
228E ILE* 1.3 71.7 + - + +
230E THR* 3.9 4.3 - - - -
231E ALA* 3.5 15.4 + - - +
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Residues in contact with ILE 228 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E ALA* 4.0 21.1 - - + +
55E THR 4.1 17.9 - - - +
56E LEU* 4.2 9.4 - - + +
59E TYR* 3.8 26.2 - - + -
189E LYS* 4.0 17.5 - - + -
222E THR* 3.7 22.7 - - - +
223E CYS 4.3 6.3 - - - +
224E GLY* 4.2 18.8 - - - -
225E GLY 3.3 2.4 + - - +
227E ASP* 1.3 89.4 - - + +
229E GLY* 1.3 65.9 + - - +
231E ALA* 2.9 18.2 + - + +
232E MET* 3.0 17.1 + - - +
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Residues in contact with GLY 229 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162E ILE* 3.7 13.2 - - - +
189E LYS* 3.5 14.8 - - - +
225E GLY 3.2 7.8 + - - -
226E ALA 3.1 3.0 + - - -
228E ILE* 1.3 76.6 - - - +
230E THR* 1.3 60.1 + - - +
232E MET* 3.5 5.6 + - - +
233E ALA* 3.1 19.2 + - - +
1510E NAD 3.2 28.4 - - - -
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Residues in contact with THR 230 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226E ALA* 2.7 21.2 + - - +
227E ASP* 3.9 4.7 - - - -
229E GLY* 1.3 70.0 - - - +
231E ALA* 1.3 65.9 + - - +
233E ALA* 3.1 8.1 + - - +
234E LYS* 3.0 37.9 + - + +
252E MET* 5.7 0.2 - - - +
256E MET* 3.7 24.2 - - + +
1510E NAD 3.1 26.1 + - - -
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Residues in contact with ALA 231 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56E LEU* 4.9 17.3 - - + -
59E TYR* 3.9 25.2 - - + -
227E ASP 3.5 9.5 + - - +
228E ILE* 2.9 13.8 + - - +
230E THR* 1.3 77.6 - - - +
232E MET* 1.3 57.8 + - - +
234E LYS* 3.3 6.9 + - - +
235E ASP* 2.9 29.8 + - - +
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Residues in contact with MET 232 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E TYR* 3.4 31.4 + - + +
160E GLY* 3.7 13.0 - - - -
161E ILE 3.6 30.7 - - - +
162E ILE* 3.7 31.4 - - + -
187E LEU* 3.8 20.9 - - + +
189E LYS* 3.8 17.0 - - - -
228E ILE* 3.0 17.5 + - - +
229E GLY* 3.5 7.4 - - - +
231E ALA* 1.3 76.7 - - - +
233E ALA* 1.3 62.7 + - - +
235E ASP* 3.0 16.0 + - - +
238E VAL* 3.8 11.0 - - + +
241E LEU* 4.0 7.6 - - + -
260E ARG* 3.6 10.4 + - - -
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Residues in contact with ALA 233 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229E GLY 3.1 9.9 + - - +
230E THR* 3.1 11.3 + - - +
232E MET* 1.3 77.9 - - - +
234E LYS* 1.3 57.2 + - - +
241E LEU* 3.6 21.3 - - + +
253E VAL* 4.1 17.9 - - + +
256E MET* 3.8 24.3 - - + -
257E VAL* 3.4 18.3 + - - +
260E ARG* 2.9 17.7 + - - -
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Residues in contact with LYS 234 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230E THR* 3.0 29.1 + - + +
231E ALA* 3.9 5.6 - - - +
233E ALA* 1.3 74.5 - - - +
235E ASP* 1.3 64.0 + - - +
236E GLU* 3.3 6.4 + - - +
256E MET* 3.8 35.9 - - + +
260E ARG* 3.3 14.4 - - - +
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Residues in contact with ASP 235 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E TYR* 2.7 29.1 + - - +
63E VAL* 3.9 2.9 - - - +
231E ALA 2.9 16.5 + - - +
232E MET 3.0 6.7 + - - +
234E LYS* 1.3 75.1 - - - +
236E GLU* 1.3 64.8 + - - +
237E ARG* 3.0 59.3 + - - +
238E VAL* 3.1 14.0 + - + +
260E ARG* 2.9 21.9 + - - -
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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