Contacts of the helix formed by residues 226 - 240 (chain B) in PDB entry 2IGT
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 LEU 226 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212B PRO* 3.8 35.7 - - + +
213B PRO 3.6 13.5 - - - +
214B LYS* 2.9 18.5 + - - +
224B TRP* 3.7 16.5 - - + +
225B GLN* 1.3 69.3 - - - +
227B PHE* 1.3 79.1 + - + +
230B LEU* 2.9 59.9 + - + +
231B PRO* 4.4 0.7 - - - +
252B ALA* 4.5 17.7 - - + -
253B TYR 5.9 1.6 - - - +
262B MSE 4.3 16.6 - - + -
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Residues in contact with PHE 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-5B ASN* 5.6 4.3 + - - +
214B LYS* 3.2 38.1 - - + -
225B GLN* 3.1 1.6 + - + +
226B LEU* 1.3 92.6 - - + +
228B ASP* 1.3 65.4 + - - +
230B LEU 4.9 0.2 - - - -
231B PRO* 4.9 7.0 - - - +
256B ARG* 5.8 5.6 - - + -
257B ALA* 3.8 32.8 - - + -
261B SER* 6.2 1.1 - - - -
262B MSE 4.8 9.2 - - + -
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Residues in contact with ASP 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-5B ASN* 4.4 8.8 + - - -
-2B PHE* 3.3 27.1 - - + +
225B GLN* 2.7 42.0 + - - +
227B PHE* 1.3 84.7 - - - +
229B HIS* 1.3 78.4 + - + +
230B LEU 3.8 0.4 - - - -
231B PRO* 4.3 4.6 - - - +
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Residues in contact with HIS 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A THR* 4.7 1.6 + - - -
79A ARG* 3.6 11.5 + - + +
-2B PHE* 3.6 40.7 - + - -
192B MSE 3.7 15.4 - - + +
223B VAL* 3.1 28.2 + - + -
224B TRP* 3.4 24.7 - - + -
225B GLN* 2.9 34.5 + - + +
228B ASP* 1.3 99.3 + - + +
230B LEU* 1.3 67.3 + - - +
231B PRO* 3.4 3.8 - - - -
232B LEU* 3.3 4.9 + - - -
233B MSE 3.1 17.2 + - - +
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Residues in contact with LEU 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B PRO* 4.2 13.7 - - + -
224B TRP* 4.1 6.6 - - + -
226B LEU* 2.9 34.8 + - + +
229B HIS* 1.3 77.8 - - - +
231B PRO* 1.4 69.6 - - + +
233B MSE 3.1 12.5 + - - -
234B LEU* 2.9 42.5 + - + +
250B LEU* 4.0 24.0 - - + -
262B MSE 3.8 28.7 - - + -
265B LEU* 3.6 22.0 - - + -
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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
----------------------------------------------------------
-5B ASN* 3.9 15.3 - - - +
-2B PHE 3.4 12.6 - - - +
-1B GLN* 4.9 0.4 - - - -
0B GLY* 4.5 11.6 - - - +
226B LEU 4.4 1.8 - - - +
227B PHE 4.9 4.5 - - - +
228B ASP 4.3 4.9 - - - +
229B HIS* 3.4 9.4 - - - +
230B LEU* 1.4 93.6 - - + +
232B LEU* 1.3 62.1 + - - +
234B LEU* 3.5 2.5 + - + +
235B ASP* 3.1 23.2 + - - +
265B LEU* 4.0 32.5 - - + -
269B THR* 4.9 2.1 + - - -
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Residues in contact with LEU 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ARG* 3.7 44.2 - - - +
-2B PHE* 3.4 43.4 + - + +
-1B GLN 4.5 9.6 - - - +
192B MSE 3.9 16.2 - - + -
196B GLN* 5.7 1.8 - - - +
229B HIS 3.3 7.4 + - - +
230B LEU 3.2 0.6 - - - -
231B PRO* 1.3 77.8 - - - +
233B MSE 1.3 66.7 + - - +
235B ASP* 3.2 11.5 + - + +
236B ILE* 2.9 45.9 + - + +
1012B FMT 5.3 2.2 - - - +
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Residues in contact with MSE 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B LEU* 4.4 3.8 - - + -
140B PHE* 3.4 30.7 - - + -
191B ALA* 4.0 4.9 - - + -
192B MSE 3.6 36.0 - - + +
195B ILE* 3.5 17.3 - - + +
210B THR* 3.4 25.8 - - - -
212B PRO* 4.9 0.9 - - - -
224B TRP* 3.8 21.8 - - + -
229B HIS 3.1 12.9 + - - +
230B LEU* 3.1 16.6 + - - +
232B LEU* 1.3 77.6 - - - +
234B LEU* 1.3 62.0 + - + +
236B ILE* 3.2 1.4 + - - -
237B CYS* 2.8 34.4 + - - -
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Residues in contact with LEU 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B THR* 4.4 18.8 - - + -
230B LEU* 2.9 36.1 + - + +
231B PRO* 4.1 2.0 - - + +
233B MSE 1.3 79.2 - - + +
235B ASP* 1.3 58.0 + - - +
237B CYS* 3.3 5.6 + - - +
238B ARG* 2.9 24.4 + - - +
248B LEU* 4.6 12.3 - - + +
250B LEU* 4.4 8.7 - - + -
265B LEU* 3.8 30.7 - - + -
266B MSE 4.2 37.7 - - + +
269B THR* 3.4 27.6 - - + +
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Residues in contact with ASP 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-1B GLN 5.0 0.2 - - - +
0B GLY* 3.6 9.7 - - - -
1B MSE 2.9 46.6 + - - +
3B ARG* 2.8 32.4 + - - +
231B PRO 3.1 19.3 + - - +
232B LEU* 3.5 12.5 - - + +
234B LEU* 1.3 77.0 - - - +
236B ILE* 1.3 62.3 + - - +
238B ARG* 3.3 5.4 + - - +
239B GLU* 3.1 24.9 + - - +
269B THR* 3.8 14.5 - - + +
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Residues in contact with ILE 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B MSE 4.0 18.8 - - + -
195B ILE* 3.4 43.1 - - + +
196B GLN* 3.9 26.2 - - + +
199B GLU* 3.7 23.8 - - + +
232B LEU* 2.9 48.5 + - + +
235B ASP* 1.3 73.4 - - + +
237B CYS* 1.3 65.9 + - - +
239B GLU* 2.9 17.2 + - - +
240B ILE* 3.0 12.6 + - + +
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Residues in contact with CYS 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B LEU* 4.0 8.3 - - - -
195B ILE* 3.9 15.7 - - - +
208B ILE* 3.4 34.4 - - + +
210B THR* 5.0 2.2 - - - -
233B MSE 2.8 31.7 + - - -
234B LEU* 3.4 13.7 - - - +
236B ILE* 1.3 76.1 - - - +
238B ARG* 1.3 63.1 + - - +
240B ILE* 3.0 18.2 + - - -
241B LEU* 3.1 12.5 + - - +
248B LEU* 3.9 22.9 - - + -
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Residues in contact with ARG 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B ARG* 3.5 37.6 - - - +
234B LEU 2.9 13.2 + - - +
235B ASP 3.6 8.1 - - - +
236B ILE 3.2 0.2 - - - -
237B CYS* 1.3 75.8 - - - +
239B GLU* 1.3 63.9 + - - +
241B LEU* 3.1 28.9 + - + +
248B LEU* 4.8 0.6 - - - +
269B THR* 2.8 30.2 + - + -
270B MSE 3.3 29.6 - - + -
271B ARG 2.8 30.5 + - - +
272B GLY 4.0 3.4 + - - -
273B ALA* 3.7 25.9 - - - +
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Residues in contact with GLU 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MSE 3.5 30.8 - - + +
3B ARG* 2.7 31.6 + - - -
199B GLU* 3.7 30.4 - - + +
203B SER 4.8 1.0 - - - +
204B THR* 5.1 2.8 - - - +
235B ASP 3.1 13.6 + - - +
236B ILE* 2.9 10.1 + - - +
238B ARG* 1.3 77.5 - - - +
240B ILE* 1.3 61.8 + - - +
241B LEU 3.5 3.9 + - - +
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Residues in contact with ILE 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B LEU* 3.8 17.3 - - + -
195B ILE* 3.7 36.6 - - + +
198B GLU* 4.1 6.7 - - + -
199B GLU* 3.6 38.4 - - + +
203B SER 3.5 22.4 - - - +
204B THR* 3.2 4.4 - - - -
205B TYR* 2.7 47.0 + - + +
208B ILE* 3.9 7.2 - - + -
236B ILE 3.0 18.2 + - - +
237B CYS* 3.0 9.1 + - - +
239B GLU* 1.3 81.9 - - - +
241B LEU* 1.3 52.8 + - - +
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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
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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