Contacts of the helix formed by residues 230 - 248 (chain B) in PDB entry 4I93
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 230 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B LEU* 3.5 6.5 - - - -
222B GLU* 4.1 10.1 + - + +
226B THR* 5.6 1.3 - - - +
228B ARG* 3.6 17.2 + - + +
229B VAL* 1.3 77.5 - - - +
231B PRO* 1.3 77.2 - - + +
232B GLU* 3.2 17.3 + - - +
233B SER* 2.8 35.2 + - - -
234B VAL* 3.4 9.2 + - - +
297B PRO* 5.5 1.0 - - - +
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Residues in contact with PRO 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B THR* 6.4 0.9 - - + -
177B ALA* 3.7 38.1 - - + +
178B LEU* 3.7 9.0 - - + -
230B THR* 1.3 87.0 - - - +
232B GLU* 1.3 71.9 + - - +
234B VAL* 3.3 18.6 + - + +
235B ILE* 3.5 11.9 + - - +
303B PRO* 6.0 2.8 - - + +
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Residues in contact with GLU 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B THR* 3.2 20.6 + - - +
231B PRO* 1.3 88.5 - - - +
233B SER* 1.3 61.0 + - - +
235B ILE* 3.2 20.3 + - + +
236B TYR 3.2 4.9 + - - -
297B PRO* 3.6 45.9 - - + +
298B ARG* 4.8 3.2 - - - +
300B ARG* 3.0 18.3 + - + +
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Residues in contact with SER 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B PRO* 3.7 18.7 - - - +
222B GLU* 3.2 23.8 + - - -
223B TYR* 5.8 2.2 - - - -
228B ARG 5.1 0.9 - - - -
229B VAL* 3.2 18.7 - - - +
230B THR* 2.8 38.6 + - - -
232B GLU* 1.3 73.6 - - - +
234B VAL* 1.3 64.7 + - - +
236B TYR* 3.2 4.5 + - - +
237B SER* 3.0 24.4 + - - -
300B ARG* 3.8 2.2 - - - +
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Residues in contact with VAL 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B LEU* 3.8 35.7 - - + -
177B ALA 3.8 14.4 - - - +
178B LEU* 4.1 1.3 - - - -
179B TYR* 3.4 43.7 - - + +
182B LEU* 4.4 4.8 - - + +
229B VAL* 4.4 2.9 - - + -
230B THR 3.5 14.1 - - - +
231B PRO 3.3 7.4 - - - +
233B SER* 1.3 75.9 + - - +
235B ILE* 1.3 61.6 + - + +
237B SER* 3.1 10.0 + - - -
238B PHE* 2.9 26.2 + - - +
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Residues in contact with ILE 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B LEU* 5.3 3.4 - - + -
231B PRO 3.6 14.4 - - - +
232B GLU* 3.2 11.8 + - - +
233B SER 3.1 0.6 - - - -
234B VAL* 1.3 81.2 - - + +
236B TYR* 1.3 65.6 + - - +
238B PHE* 3.1 6.3 + - - +
239B GLY 2.9 17.2 + - - -
292B CYS* 3.5 24.9 - - + +
300B ARG* 3.9 15.7 - - + -
301B PRO* 3.3 30.5 - - + +
302B ASN* 4.9 0.4 - - - -
303B PRO* 3.9 26.5 - - + -
306B LEU* 3.8 24.9 - - + -
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Residues in contact with TYR 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B PHE* 4.3 4.9 - - - -
219B THR 4.0 9.1 + - - -
220B PRO* 3.7 28.5 - - + -
221B PRO* 3.6 20.8 - - + +
232B GLU 3.2 3.2 + - - -
233B SER 3.2 9.1 + - - +
235B ILE* 1.3 78.2 - - - +
237B SER* 1.3 60.6 + - - +
239B GLY* 2.9 17.0 + - - -
240B THR* 3.1 28.6 + - + +
253B PRO* 3.6 22.3 - - + +
257B LEU* 5.5 2.6 - - + +
292B CYS 3.3 12.8 + - - +
293B LEU* 3.6 43.9 - - + +
300B ARG* 3.7 29.4 - - - +
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Residues in contact with SER 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B TYR 5.7 0.8 + - - -
181B ASP* 5.5 2.8 + - - -
182B LEU* 3.9 37.3 + - - +
218B PHE 4.7 6.7 + - - -
220B PRO* 4.4 10.0 - - - +
233B SER 3.0 13.5 + - - -
234B VAL* 3.1 11.2 + - - -
236B TYR* 1.3 76.8 - - - +
238B PHE* 1.3 61.0 + - - +
240B THR* 2.7 28.0 + - - -
241B LEU* 3.0 9.2 + - - +
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Residues in contact with PHE 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B ALA* 3.4 28.5 - - + -
164B ILE* 4.1 13.9 - - + -
165B ALA* 3.8 22.7 - - + -
168B LEU* 4.0 18.4 - - + -
182B LEU* 4.0 10.0 - - + +
234B VAL 2.9 12.8 + - - +
235B ILE* 3.1 13.0 + - - +
237B SER* 1.3 73.0 - - - +
239B GLY* 1.3 62.0 + - - +
241B LEU* 3.1 14.6 + - + +
242B LEU* 2.9 60.7 + - + +
288B LEU* 4.8 4.3 - - + -
292B CYS* 4.1 1.6 - - - -
306B LEU* 3.7 34.3 - - + -
310B MSE 4.9 2.9 - - + -
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Residues in contact with GLY 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B ILE 2.9 7.5 + - - -
236B TYR 2.9 9.5 + - - -
238B PHE* 1.3 76.4 - - - +
240B THR* 1.3 55.4 + - - +
242B LEU* 3.2 9.8 + - - +
243B LEU* 3.0 29.5 + - - +
289B ALA* 4.2 3.8 - - - +
292B CYS* 3.5 24.3 - - - +
293B LEU* 4.0 12.3 - - - -
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Residues in contact with THR 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B LEU 4.4 7.1 + - - -
183B ASN* 5.6 1.9 - - - +
218B PHE* 3.8 30.7 - - + +
236B TYR* 3.1 24.7 + - + +
237B SER* 2.7 21.3 + - - -
239B GLY* 1.3 75.7 - - - +
241B LEU* 1.3 61.2 + - - +
243B LEU* 3.2 11.2 + - - +
244B ASP* 3.0 28.3 + - - +
250B HIS* 5.5 1.9 - - - -
253B PRO* 3.8 26.7 - - + -
293B LEU* 3.9 7.2 - - + -
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Residues in contact with LEU 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B LEU* 3.6 30.3 - - + -
160B VAL* 5.2 2.0 - - + -
161B ALA* 5.7 0.7 - - - -
164B ILE* 4.0 29.8 - - + -
182B LEU* 4.6 10.3 - - + -
183B ASN* 4.1 8.3 - - - +
184B ALA* 4.0 21.8 - - + +
187B VAL* 4.3 10.3 - - + -
237B SER 3.0 12.9 + - - +
238B PHE* 3.1 22.2 + - + +
240B THR* 1.3 77.3 + - - +
242B LEU* 1.3 62.2 + - + +
244B ASP* 3.1 9.2 + - + +
245B LEU* 3.0 34.3 + - + +
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Residues in contact with LEU 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B ALA* 3.8 24.5 - - + -
238B PHE* 2.9 48.7 + - + +
239B GLY 3.5 7.2 - - - +
241B LEU* 1.3 76.6 - - + +
243B LEU* 1.3 55.7 + - - +
245B LEU* 3.2 10.3 + - + +
246B LEU* 2.9 37.1 + - + +
285B LEU* 3.9 21.3 - - + +
288B LEU* 4.0 18.4 - - + +
289B ALA* 3.8 35.9 - - + +
292B CYS* 4.6 1.8 - - - -
310B MSE 4.6 0.7 - - - -
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Residues in contact with LEU 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B GLY 3.0 16.8 + - - +
240B THR* 3.5 12.1 - - - +
242B LEU* 1.3 76.1 - - - +
244B ASP* 1.3 59.7 + - - +
246B LEU* 3.3 11.3 + - + +
247B SER* 2.8 35.3 + - - -
251B ILE* 3.8 15.9 - - + +
253B PRO* 4.1 17.3 - - + -
256B ALA* 3.6 31.4 - - + -
260B ILE* 4.3 13.9 - - + -
268B LEU* 4.6 6.9 - - + +
289B ALA* 4.2 16.8 - - + -
293B LEU* 3.6 24.7 - - + -
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Residues in contact with ASP 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B LEU* 3.5 11.1 - - + +
145B PHE* 3.6 16.5 - - + -
183B ASN* 5.6 0.3 - - - +
184B ALA* 4.7 8.4 + - + +
218B PHE* 4.4 3.5 - - - -
240B THR 3.0 19.4 + - - +
241B LEU* 3.1 15.5 + - + +
243B LEU* 1.3 76.9 - - - +
245B LEU* 1.3 57.7 + - - +
248B GLY* 2.8 31.2 + - - -
249B LYS 3.0 23.0 - - - +
250B HIS* 2.6 36.2 + - - -
251B ILE* 3.5 8.8 + - - +
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Residues in contact with LEU 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B LEU* 4.0 35.2 - - + -
144B LEU* 4.2 7.2 - - + -
154B TRP* 5.1 2.3 - - - -
157B ARG* 2.8 81.4 + - + +
160B VAL* 4.4 7.2 - - + -
161B ALA* 4.0 22.7 - - + +
241B LEU* 3.0 25.1 + - + +
242B LEU* 3.2 14.3 + - + +
244B ASP* 1.3 77.9 - - - +
246B LEU* 1.3 55.8 + - - +
273B LEU* 4.2 1.2 - - - +
285B LEU* 5.3 7.6 - - + -
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Residues in contact with LEU 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B TRP* 4.2 2.7 - - + -
242B LEU 2.9 25.9 + - - +
243B LEU* 3.7 19.3 - - + +
245B LEU* 1.3 75.5 - - - +
247B SER* 1.3 53.0 + - - +
248B GLY 3.6 0.2 - - - -
268B LEU* 4.3 9.4 - - + -
269B MSE 3.3 40.0 - - + +
270B ASP* 2.8 30.8 + - - +
273B LEU* 3.7 9.1 - - - +
285B LEU* 3.8 32.1 - - + +
286B ILE* 3.8 35.7 - - + +
289B ALA* 4.5 5.2 - - + -
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Residues in contact with SER 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B LEU 2.8 22.7 + - - -
246B LEU* 1.3 77.4 - - - +
248B GLY* 1.3 59.7 + - - +
249B LYS* 3.0 43.2 + - - +
251B ILE* 3.8 20.4 - - - +
268B LEU* 3.3 24.1 - - - +
270B ASP* 3.4 22.1 - - - +
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Residues in contact with GLY 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A GLU* 5.0 1.9 - - - +
144B LEU* 4.2 15.2 - - - +
145B PHE* 3.4 19.6 - - - -
157B ARG* 4.0 6.5 - - - +
244B ASP 2.8 17.4 + - - -
246B LEU 3.6 1.6 - - - -
247B SER* 1.3 72.9 - - - +
249B LYS* 1.3 60.1 + - - +
270B ASP* 3.4 20.2 + - - -
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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
------------------------------------------------------------
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