Contacts of the helix formed by residues 219 - 238 (chain V) in PDB entry 1J0B
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 PHE 219 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215V ALA* 4.0 10.5 - - + -
218V ARG* 1.3 83.5 - - - +
220V GLY* 1.3 72.5 + - - +
222V VAL* 2.6 36.1 - - - +
223V MET* 3.2 24.6 - - - +
224V THR* 3.9 13.7 - - - -
248V LEU* 3.3 42.8 - - + -
249V TYR* 3.8 3.6 - - - -
250V ASP* 3.5 48.2 - - + +
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Residues in contact with GLY 220 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219V PHE* 1.3 86.9 - - - +
221V GLU* 1.3 64.0 + - - -
222V VAL* 3.4 2.2 - - - -
224V THR* 2.9 28.3 + - - -
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Residues in contact with GLU 221 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220V GLY* 1.3 68.2 - - - -
222V VAL* 1.3 61.6 + - - +
224V THR* 3.0 12.2 - - - +
225V SER* 2.3 72.9 + - - +
228V ASP* 5.4 0.2 - - - +
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Residues in contact with VAL 222 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218V ARG* 3.4 30.5 - - + +
219V PHE 2.6 30.1 - - - +
220V GLY* 4.0 3.1 - - - -
221V GLU* 1.3 85.7 - - - +
223V MET* 1.3 62.6 + - - +
225V SER* 3.5 1.9 - - - -
226V LYS* 2.7 37.4 + - + +
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Residues in contact with MET 223 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189V ALA* 3.8 19.7 - - + +
190V GLY 4.4 14.1 - - - +
191V SER 6.6 0.2 - - - -
192V GLY* 5.8 2.7 - - - +
215V ALA* 3.5 26.2 - - + -
216V VAL 5.2 0.2 - - - +
217V GLY 5.7 1.3 - - - +
218V ARG* 4.3 10.8 - - + +
219V PHE* 3.2 44.4 - - - +
222V VAL* 1.3 86.8 - - + +
224V THR* 1.3 62.1 + - - +
226V LYS* 4.0 6.4 - - - +
227V LEU* 3.2 24.2 + - + +
248V LEU* 3.7 29.8 - - + -
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Residues in contact with THR 224 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219V PHE* 3.9 20.5 - - - -
220V GLY 2.9 22.6 + - - +
221V GLU* 3.0 21.2 + - - +
223V MET* 1.3 83.9 - - - +
225V SER* 1.3 64.2 + - - +
227V LEU* 3.7 8.7 + - - +
228V ASP* 2.9 26.0 + - - +
245V ARG* 2.8 31.7 + - - +
248V LEU* 4.6 6.1 - - - +
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Residues in contact with SER 225 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221V GLU* 2.3 62.4 + - - +
222V VAL* 3.6 2.2 - - - -
224V THR* 1.3 65.6 - - - +
226V LYS* 1.3 61.3 + - - +
227V LEU 3.0 4.5 - - - -
228V ASP* 3.0 23.7 + - - +
229V ASN* 3.4 9.9 + - - +
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Residues in contact with LYS 226 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156V PRO* 5.7 10.1 - - - +
159V ALA* 5.6 6.5 - - - +
191V SER* 5.2 15.8 + - - +
222V VAL* 2.7 26.0 + - + +
223V MET* 4.0 6.5 - - - +
225V SER* 1.3 73.8 - - - +
227V LEU* 1.3 56.5 + - - +
229V ASN* 3.7 7.6 + - + +
230V LEU* 3.2 33.0 + - - +
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Residues in contact with LEU 227 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192V GLY* 3.9 33.4 - - - +
195V LEU* 3.6 26.2 - - + -
196V ALA* 4.2 18.4 - - + +
223V MET* 3.2 18.6 + - + +
224V THR* 3.7 9.4 - - - +
225V SER 3.0 0.4 - - - -
226V LYS* 1.3 77.1 - - - +
228V ASP* 1.3 66.5 + - - +
229V ASN 3.3 0.2 - - - -
230V LEU* 3.8 9.6 - - + -
231V ILE* 3.4 24.4 + - + +
245V ARG* 6.0 4.0 - - - +
246V PRO* 4.7 11.4 - - + -
248V LEU* 5.1 12.6 - - + -
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Residues in contact with ASP 228 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221V GLU* 5.4 0.2 - - - +
224V THR* 2.9 18.6 - - - +
225V SER* 3.0 14.2 + - - +
227V LEU* 1.3 78.0 - - - +
229V ASN* 1.3 67.1 + - - +
231V ILE* 3.5 11.4 - - - +
232V LYS* 3.1 23.0 + - - +
245V ARG* 3.0 46.9 + - - +
246V PRO* 5.6 0.3 - - - +
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Residues in contact with ASN 229 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225V SER 3.4 7.8 + - - +
226V LYS* 3.9 9.2 - - + +
227V LEU 3.3 0.2 - - - -
228V ASP* 1.3 78.8 - - - +
230V LEU* 1.3 65.3 - - - +
232V LYS* 2.9 38.6 + - - +
233V GLU* 2.8 48.3 + - - +
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Residues in contact with LEU 230 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159V ALA* 3.6 28.5 - - + +
160V SER 4.3 11.7 - - - +
161V PRO* 4.3 5.5 - - + +
164V THR* 3.7 24.2 - - - +
191V SER 4.2 11.4 - - - +
192V GLY 3.9 21.3 - - - +
196V ALA* 3.9 5.8 - - + -
226V LYS* 3.2 22.7 + - - +
227V LEU* 3.7 15.3 - - + +
228V ASP 3.3 0.2 - - - -
229V ASN* 1.3 79.1 - - - +
231V ILE* 1.3 57.0 + - - +
233V GLU* 3.4 10.9 + - - +
234V ALA* 2.9 22.2 + - - +
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Residues in contact with ILE 231 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196V ALA* 3.0 50.7 - - + +
199V SER* 4.6 9.6 - - - +
200V LEU* 4.8 5.5 - - + +
227V LEU* 3.4 23.1 + - + +
228V ASP* 3.5 14.6 - - - +
230V LEU* 1.3 73.0 - - - +
232V LYS* 1.3 61.0 + - - +
233V GLU 3.2 1.6 - - - -
234V ALA* 3.9 7.3 - - + +
235V ALA* 2.9 28.3 + - - +
242V VAL* 4.7 18.1 - - + +
245V ARG* 4.8 8.7 - - + -
246V PRO* 4.2 25.6 - - + -
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Residues in contact with LYS 232 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228V ASP 3.1 17.0 + - - +
229V ASN* 2.9 29.1 + - - +
231V ILE* 1.3 77.0 - - - +
233V GLU* 1.3 66.7 + - - +
235V ALA* 3.6 5.4 - - - +
236V GLU* 2.9 58.9 + - + +
242V VAL* 4.8 13.5 - - + -
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Residues in contact with GLU 233 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161V PRO* 3.5 26.4 - - + +
229V ASN* 2.8 48.4 + - - +
230V LEU* 3.4 7.7 + - - +
232V LYS* 1.3 81.5 - - - +
234V ALA* 1.3 57.3 + - - +
236V GLU* 2.7 9.4 + - - +
237V LEU* 2.6 36.8 + - - +
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Residues in contact with ALA 234 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161V PRO* 4.1 9.8 - - + +
164V THR* 3.3 35.9 - - + +
165V LEU* 5.0 1.0 - - + +
200V LEU* 3.4 11.7 - - + -
230V LEU 2.9 18.4 + - - +
231V ILE* 3.9 8.5 - - + -
233V GLU* 1.3 73.9 - - - +
235V ALA* 1.3 62.3 + - - +
237V LEU* 3.3 10.8 + - - +
238V LEU* 3.2 26.9 + - - +
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Residues in contact with ALA 235 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200V LEU* 4.1 10.3 - - + +
231V ILE 2.9 21.4 + - - +
232V LYS* 3.6 8.5 - - + +
234V ALA* 1.3 73.6 - - - +
236V GLU* 1.3 59.4 + - + +
238V LEU 3.2 1.7 + - - -
239V GLY 2.9 20.3 + - - -
240V VAL* 2.9 44.1 + - + +
242V VAL* 4.2 17.3 - - + -
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Residues in contact with GLU 236 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232V LYS* 2.9 52.7 + - + +
233V GLU* 2.7 12.8 + - - +
235V ALA* 1.3 69.9 - - + +
237V LEU* 1.3 59.8 + - - +
238V LEU 3.0 2.0 - - - -
239V GLY* 2.7 24.3 + - - +
240V VAL 4.5 3.4 - - - +
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Residues in contact with LEU 237 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11V LYS* 4.9 5.4 + - - -
12V PHE* 3.3 40.1 - - + -
161V PRO* 3.6 29.2 - - + -
162V ILE* 3.9 18.6 - - + +
165V LEU* 4.8 6.5 - - + -
233V GLU 2.6 16.6 + - - +
234V ALA* 3.3 11.7 - - - +
236V GLU* 1.3 73.0 - - - +
238V LEU* 1.3 61.0 + - + +
239V GLY 3.6 0.2 + - - -
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Residues in contact with LEU 238 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8V LEU* 4.3 30.1 - - + +
9V LEU* 4.1 11.7 - - + -
11V LYS* 6.4 0.2 - - - +
12V PHE* 4.0 24.0 - - + -
165V LEU* 3.5 36.8 - - + -
168V VAL* 4.1 20.0 - - + -
200V LEU* 4.1 13.2 - - + -
204V ILE* 4.1 8.7 - - + -
234V ALA 3.2 13.0 + - - +
235V ALA* 3.7 6.1 - - - +
236V GLU 3.0 0.6 - - - -
237V LEU* 1.3 81.1 - - + +
239V GLY* 1.3 66.2 + - - +
240V VAL* 4.3 9.8 - - + +
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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
------------------------------------------------------------
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