Contacts of the helix formed by residues 225 - 235 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53C GLN* 4.0 3.6 + - - -
189C LYS* 3.6 4.3 - - - +
192C PRO* 4.2 16.4 - - - -
224C GLY* 1.3 75.3 - - - +
226C ALA* 1.3 66.1 + - - -
227C ASP* 3.2 12.2 + - - +
228C ILE 3.3 2.3 + - - -
229C GLY 3.1 16.8 + - - -
1510C NAD 4.1 6.5 - - - -
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Residues in contact with ALA 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225C GLY* 1.3 67.4 - - - -
227C ASP* 1.3 60.7 + - - +
230C THR* 2.7 39.8 + - - +
1510C NAD 3.5 48.0 + - + +
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Residues in contact with ASP 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C ALA 4.1 7.6 - - - +
55C THR* 5.7 0.2 - - - -
56C LEU* 3.5 24.9 + - - +
224C GLY* 4.9 1.0 - - - -
225C GLY* 3.9 15.2 + - - +
226C ALA* 1.3 76.1 - - - +
228C ILE* 1.3 83.9 + - - +
230C THR* 3.6 4.6 + - - -
231C ALA* 3.6 14.9 + - - +
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Residues in contact with ILE 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C ALA* 3.9 18.6 - - + +
55C THR 4.1 17.7 - - - +
56C LEU* 4.3 9.0 - - + +
59C TYR* 3.8 26.7 - - + -
189C LYS* 3.9 17.5 - - + -
222C THR* 3.7 22.7 - - - +
223C CYS 4.3 3.8 - - - +
224C GLY* 4.2 15.0 - - - -
225C GLY 3.3 1.8 + - - +
227C ASP* 1.3 100.3 - - - +
229C GLY* 1.3 66.8 + - - +
231C ALA* 3.0 16.2 + - + +
232C MET* 3.0 17.3 + - - +
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Residues in contact with GLY 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C ILE* 3.7 13.5 - - - +
189C LYS* 3.5 14.4 - - - +
225C GLY 3.1 7.6 + - - -
226C ALA 3.1 3.5 + - - -
228C ILE* 1.3 77.6 - - - +
230C THR* 1.3 59.9 + - - +
232C MET* 3.5 5.2 + - - +
233C ALA* 3.1 19.6 + - - +
1510C NAD 3.2 28.3 - - - -
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Residues in contact with THR 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226C ALA* 2.7 23.1 + - - +
227C ASP* 3.9 4.7 - - - -
229C GLY* 1.3 68.4 - - - -
231C ALA* 1.3 67.0 + - - +
233C ALA* 3.1 7.3 + - - +
234C LYS* 2.9 39.2 + - + +
256C MET* 3.7 23.6 - - + +
1510C NAD 3.1 24.2 + - - -
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Residues in contact with ALA 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C LEU* 4.9 17.3 - - + -
59C TYR* 3.9 25.5 - - + -
227C ASP 3.6 9.8 + - - +
228C ILE* 3.0 13.6 + - - +
230C THR* 1.3 78.7 - - - +
232C MET* 1.3 57.0 + - - +
234C LYS* 3.4 6.3 + - - +
235C ASP* 2.9 30.3 + - - +
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Residues in contact with MET 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C TYR* 3.4 29.4 - - + +
160C GLY* 3.7 13.0 - - - -
161C ILE 3.6 31.0 - - - +
162C ILE* 3.7 24.9 - - + -
187C LEU* 3.8 20.4 - - + +
189C LYS* 3.9 22.4 - - + -
228C ILE* 3.0 18.2 + - - +
229C GLY* 3.5 7.6 - - - +
231C ALA* 1.3 77.0 - - - +
233C ALA* 1.3 62.9 + - - +
235C ASP* 3.1 13.2 + - - +
238C VAL* 3.8 13.4 - - + +
241C LEU* 4.0 7.2 - - + -
260C ARG* 3.5 11.8 + - - -
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Residues in contact with ALA 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229C GLY 3.1 10.9 + - - +
230C THR* 3.1 10.8 + - - +
232C MET* 1.3 77.6 - - - +
234C LYS* 1.3 57.9 + - - +
241C LEU* 3.6 21.9 - - + +
253C VAL* 4.1 17.5 - - + +
256C MET* 3.8 24.9 - - + -
257C VAL* 3.4 15.6 + - - +
260C ARG* 2.9 20.4 + - - -
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Residues in contact with LYS 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230C THR* 2.9 30.7 + - + +
231C ALA* 3.9 4.9 - - - +
233C ALA* 1.3 75.2 - - - +
235C ASP* 1.3 61.7 + - - +
236C GLU* 3.3 5.0 + - - +
256C MET* 3.8 35.9 - - + +
260C ARG* 3.3 15.4 - - - +
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Residues in contact with ASP 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C TYR* 2.8 27.8 + - - +
63C VAL* 3.9 3.3 - - - +
231C ALA 2.9 16.0 + - - +
232C MET 3.1 8.0 + - - +
234C LYS* 1.3 74.8 - - - +
236C GLU* 1.3 64.3 + - - +
237C ARG* 3.0 60.5 + - - +
238C VAL* 3.1 13.7 + - + +
260C ARG* 2.9 22.4 + - - -
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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