Contacts of the helix formed by residues 226 - 240 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212A PRO* 3.7 38.6 - - + +
213A PRO 3.6 12.8 - - - +
214A LYS* 2.9 17.0 + - - +
224A TRP* 3.7 15.3 - - - +
225A GLN* 1.3 68.4 - - - +
227A PHE* 1.3 90.7 + - + +
230A LEU* 2.9 58.2 + - + +
231A PRO* 4.3 0.3 - - - +
252A ALA* 4.4 14.4 - - + -
254A SER* 4.1 13.9 - - - +
262A MSE 4.4 9.0 - - + -
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Residues in contact with PHE 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-5A ASN* 5.4 4.2 - - - +
214A LYS* 4.0 32.8 - - + -
225A GLN* 3.2 2.0 - - + +
226A LEU* 1.3 100.2 - - + +
228A ASP* 1.3 64.9 + - - +
230A LEU 5.0 0.2 - - - -
231A PRO* 4.8 7.4 - - - +
254A SER* 4.4 16.4 - - - -
256A ARG* 6.3 1.8 - - + -
257A ALA* 4.0 30.1 - - + -
261A SER* 6.2 1.3 - - - -
262A MSE 4.5 7.4 - - + -
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Residues in contact with ASP 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-5A ASN* 4.0 12.7 + - - +
-2A PHE* 3.3 25.1 - - + +
225A GLN* 2.9 41.2 + - + +
227A PHE* 1.3 85.9 - - - +
229A HIS* 1.3 75.5 + - + +
230A LEU 3.9 0.2 - - - -
231A PRO* 4.3 3.0 - - - +
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Residues in contact with HIS 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-2A PHE* 3.6 44.2 - + - -
192A MSE 3.7 15.1 - - + +
223A VAL* 3.2 28.6 + - + -
224A TRP* 3.5 24.8 - - + -
225A GLN* 2.9 33.8 + - + +
228A ASP* 1.3 94.0 + - + +
230A LEU* 1.3 66.3 + - - +
231A PRO* 3.4 3.8 - - - -
232A LEU* 3.2 5.1 + - - +
233A MSE 3.1 17.0 + - - +
69C THR* 4.7 1.6 + - - -
79C ARG* 3.7 12.6 + - + +
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Residues in contact with LEU 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A PRO* 4.2 14.8 - - + -
224A TRP* 3.9 7.4 - - + -
226A LEU* 2.9 43.8 + - + +
229A HIS* 1.3 77.3 - - - +
231A PRO* 1.4 65.6 - - + +
233A MSE 3.1 22.6 + - - -
234A LEU* 2.9 40.4 + - + +
250A LEU* 4.1 15.9 - - + -
262A MSE 4.0 17.7 - - + -
265A LEU* 3.7 23.1 - - + -
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Residues in contact with PRO 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-5A ASN* 3.9 13.0 - - - +
-2A PHE 3.5 10.8 - - - +
-1A GLN* 4.8 0.7 - - - -
0A GLY* 4.4 12.4 - - - +
226A LEU 4.3 2.2 - - - +
227A PHE* 4.8 5.8 - - - +
228A ASP 4.3 5.8 - - - +
229A HIS 3.4 9.6 - - - +
230A LEU* 1.4 93.6 - - + +
232A LEU* 1.3 62.0 + - - +
234A LEU* 3.4 2.5 + - + +
235A ASP* 3.1 23.2 + - - +
265A LEU* 4.1 30.5 - - + -
269A THR* 4.9 2.1 + - - -
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Residues in contact with LEU 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-2A PHE* 3.4 44.9 + - + +
-1A GLN 4.3 8.7 - - - +
0A GLY 4.8 1.8 - - - +
192A MSE 3.9 13.0 - - + -
196A GLN* 5.5 2.7 - - - +
229A HIS 3.2 8.5 + - - +
231A PRO* 1.3 74.2 - - - +
233A MSE 1.3 68.6 + - - +
235A ASP* 3.2 12.2 + - - +
236A ILE* 2.9 44.7 + - + +
81C ARG* 3.6 44.0 - - - +
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Residues in contact with MSE 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A LEU* 4.3 5.2 - - + -
140A PHE* 3.6 30.5 - - + -
191A ALA* 3.8 5.4 - - + -
192A MSE 3.6 40.9 - - - +
195A ILE* 3.5 18.1 - - + +
210A THR* 3.5 24.2 - - - -
212A PRO* 4.9 0.7 - - - -
224A TRP* 3.7 20.2 - - + -
229A HIS 3.1 13.3 + - - +
230A LEU* 3.1 20.2 + - + +
232A LEU* 1.3 77.1 - - - +
234A LEU* 1.3 60.5 + - + +
236A ILE 3.2 0.5 + - - -
237A CYS* 2.8 33.3 + - - -
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Residues in contact with LEU 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A THR* 4.3 20.2 - - + -
230A LEU* 2.9 34.9 + - + +
231A PRO* 4.1 2.0 - - + +
233A MSE 1.3 76.2 - - + +
235A ASP* 1.3 58.7 + - - +
237A CYS* 3.3 5.7 + - - +
238A ARG 2.9 24.3 + - - -
248A LEU* 4.6 13.7 - - + +
250A LEU* 4.2 15.3 - - + -
265A LEU* 3.7 33.9 - - + -
266A MSE 4.3 28.0 - - + -
269A THR* 3.4 28.0 - - + +
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Residues in contact with ASP 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0A GLY* 3.8 11.5 - - - -
1A MSE 3.3 41.5 + - - +
3A ARG* 2.7 36.8 + - - -
231A PRO 3.1 17.7 + - - +
232A LEU* 3.6 12.2 - - + +
234A LEU* 1.3 76.9 - - - +
236A ILE* 1.3 60.9 + - - +
238A ARG* 3.3 4.4 + - - +
239A GLU* 3.1 21.6 + - - +
269A THR* 3.9 12.8 - - + +
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Residues in contact with ILE 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A MSE 4.1 17.5 - - + -
195A ILE* 3.3 40.4 - - + +
196A GLN* 3.9 25.6 - - + +
199A GLU* 3.8 24.5 - - + +
232A LEU* 2.9 45.8 + - + +
233A MSE 3.6 5.2 - - - +
235A ASP* 1.3 73.0 - - + +
237A CYS* 1.3 68.0 + - - +
239A GLU* 2.9 17.0 + - - +
240A ILE* 3.0 12.9 + - + +
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Residues in contact with CYS 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A LEU* 4.1 11.7 - - - -
195A ILE* 4.0 13.9 - - - -
208A ILE* 3.4 34.3 - - + +
210A THR* 5.0 2.2 - - - -
233A MSE 2.8 25.4 + - - -
234A LEU* 3.3 15.2 + - - +
236A ILE* 1.3 75.4 - - - +
238A ARG* 1.3 62.5 + - - +
240A ILE* 3.1 18.2 + - - -
241A LEU* 3.2 12.9 + - - +
248A LEU* 4.0 21.8 - - + -
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Residues in contact with ARG 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ARG* 3.5 40.0 - - - +
234A LEU 2.9 13.4 + - - +
235A ASP 3.5 9.0 - - - +
236A ILE 3.2 0.2 - - - -
237A CYS* 1.3 76.9 - - - +
239A GLU* 1.3 65.1 + - - +
241A LEU* 3.1 30.1 + - + +
248A LEU* 4.7 1.0 - - - +
269A THR* 2.8 37.5 + - + -
270A MSE 3.4 26.5 - - + +
271A ARG 2.8 30.5 + - - +
272A GLY* 4.1 2.8 + - - -
273A ALA* 3.7 26.1 - - - +
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Residues in contact with GLU 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MSE 3.8 19.5 - - + +
3A ARG* 2.6 33.8 + - - -
199A GLU* 3.5 36.2 - - + +
203A SER 4.6 1.9 - - - +
204A THR* 4.8 4.0 - - - +
235A ASP 3.1 12.1 + - - +
236A ILE* 2.9 10.1 + - - +
238A ARG* 1.3 80.0 + - - +
240A ILE* 1.3 61.0 + - - +
241A LEU 3.5 3.8 + - - +
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Residues in contact with ILE 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A LEU* 3.7 30.7 - - + -
195A ILE* 3.7 24.7 - - + +
198A GLU* 4.0 6.5 - - + -
199A GLU* 3.6 38.6 - - + +
203A SER 3.4 21.1 - - - +
204A THR* 3.2 3.0 - - - -
205A TYR* 2.8 40.4 + - + +
208A ILE* 3.9 4.0 - - + -
236A ILE 3.0 16.8 + - - +
237A CYS* 3.1 13.1 + - - +
239A GLU* 1.3 78.3 - - - +
241A LEU* 1.3 59.7 + - - +
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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