Contacts of the helix formed by residues 231 - 245 (chain A) in PDB entry 4IRX
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 ASN 231 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A GLN* 4.7 1.8 + - - +
50A PRO* 6.2 0.4 - - - +
168A ASN* 4.8 0.4 - - + -
203A SER* 3.8 15.4 + - - +
229A CYS* 3.2 4.4 - - - +
230A LEU* 1.3 80.1 - - - +
232A ASP* 1.3 61.1 + - - +
233A ASP* 3.8 15.1 - - - +
234A MSE 2.8 38.4 + - + +
235A ALA* 3.0 21.7 + - - +
257A PHE* 3.2 13.9 - - - -
258A ASP* 3.5 5.4 - - - +
401A INS 3.0 45.9 + - - +
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Residues in contact with ASP 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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231A ASN* 1.3 73.6 - - - +
233A ASP* 1.3 66.4 + - - +
235A ALA* 3.1 5.0 + - - +
236A MSE 2.9 29.2 + - - +
256A GLY* 3.4 6.1 - - - -
257A PHE 2.7 22.4 + - - +
258A ASP* 3.4 4.8 + - + +
259A ALA* 2.7 27.5 + - - -
260A ILE* 2.9 33.4 + - + -
263A ALA* 3.4 17.3 - - + +
272A MSE 4.1 1.7 - - - +
275A THR* 2.7 22.5 + - - -
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Residues in contact with ASP 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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50A PRO* 3.4 36.0 - - + +
203A SER 4.1 9.1 - - - +
204A LYS* 4.7 0.7 - - - +
205A ARG* 2.8 87.6 + - - +
231A ASN* 3.4 15.8 + - - +
232A ASP* 1.3 78.9 - - - +
234A MSE 1.3 62.0 + - + +
236A MSE 3.4 3.6 + - - -
258A ASP* 5.2 1.0 + - - +
260A ILE* 4.3 5.3 - - + +
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Residues in contact with MSE 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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166A ILE* 3.8 8.5 - - + +
167A THR 3.2 30.3 - - - +
168A ASN* 3.5 18.6 - - + +
201A ALA* 3.6 15.5 - - - -
203A SER* 3.5 17.5 - - - -
204A LYS 3.8 24.9 - - - +
205A ARG* 4.5 0.7 - - - +
208A ALA* 3.3 19.6 - - + +
229A CYS* 4.4 6.9 - - + -
230A LEU 3.7 7.9 - - - +
231A ASN* 2.8 49.0 + - - +
233A ASP* 1.3 69.8 - - - +
235A ALA* 1.3 61.4 + - - +
237A GLY 3.0 2.8 + - - -
238A ALA* 2.9 26.0 + - - +
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Residues in contact with ALA 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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229A CYS* 3.8 22.8 - - + +
231A ASN 3.0 15.6 + - - +
232A ASP* 3.4 14.4 - - - +
234A MSE 1.3 75.3 - - - +
236A MSE 1.3 58.5 + - - +
238A ALA* 3.2 1.7 + - - +
239A LEU* 2.8 34.3 + - - +
254A VAL* 3.8 14.6 - - + +
256A GLY* 4.0 11.0 - - - -
272A MSE 4.1 11.0 - - - -
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Residues in contact with MSE 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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205A ARG* 3.4 37.0 - - - +
232A ASP 2.9 20.1 + - - +
233A ASP 3.5 1.8 - - - +
235A ALA* 1.3 75.9 - - - +
237A GLY* 1.3 61.8 + - - +
239A LEU* 3.3 13.5 + - + +
240A GLU* 3.0 37.0 + - + +
243A ARG* 6.2 1.3 - - - +
260A ILE* 5.2 2.2 - - + -
262A GLU* 3.6 38.6 - - + +
263A ALA* 4.3 6.1 - - - -
266A ARG* 3.8 38.1 - - + -
272A MSE 4.5 3.6 - - - +
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Residues in contact with GLY 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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205A ARG* 3.7 26.0 - - - +
209A LEU* 3.7 15.8 - - - +
233A ASP 3.5 4.9 + - - -
234A MSE 3.0 7.8 + - - -
236A MSE 1.3 80.9 - - - +
238A ALA* 1.3 56.4 + - - +
240A GLU* 3.2 12.5 + - - +
241A ALA* 2.9 26.9 + - - +
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Residues in contact with ALA 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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166A ILE* 6.3 0.2 - - + -
208A ALA* 4.4 1.6 - - + +
212A THR* 3.7 31.1 - - + +
227A ILE* 4.2 8.1 - - + -
229A CYS* 3.7 29.8 - - - -
234A MSE 2.9 8.1 + - - +
235A ALA 3.2 3.1 + - - +
237A GLY* 1.3 72.1 - - - +
239A LEU* 1.3 67.4 + - - +
241A ALA* 3.2 2.9 + - - +
242A VAL* 2.9 28.4 + - - +
254A VAL* 4.5 6.5 - - + -
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Residues in contact with LEU 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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235A ALA 2.8 16.3 + - - +
236A MSE 3.6 14.8 - - + +
238A ALA* 1.3 76.2 - - - +
240A GLU* 1.3 60.8 + - - +
242A VAL* 3.3 6.5 + - + +
243A ARG* 3.0 30.7 + - - +
249A SER* 4.8 7.4 - - - -
254A VAL* 3.8 25.7 - - + +
266A ARG* 3.9 22.2 - - + -
271A GLU* 3.4 48.0 - - + +
272A MSE 3.6 31.2 - - + -
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Residues in contact with GLU 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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205A ARG* 4.6 16.8 + - - +
209A LEU* 4.0 20.6 - - + +
236A MSE 3.0 24.9 + - + +
237A GLY* 3.5 14.6 - - - +
238A ALA 3.2 0.2 - - - -
239A LEU* 1.3 74.8 - - - +
241A ALA* 1.3 53.2 + - - +
243A ARG* 3.2 33.1 + - - +
244A ALA* 2.7 36.0 + - - +
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Residues in contact with ALA 241 (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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209A LEU* 3.5 11.1 - - + +
212A THR* 3.6 27.4 - - + -
213A GLN* 3.6 27.4 - - + +
216A LEU* 3.7 4.6 - - + +
237A GLY 2.9 12.2 + - - +
238A ALA 3.2 7.6 + - - +
240A GLU* 1.3 76.6 - - - +
242A VAL* 1.3 56.7 + - - +
244A ALA* 3.3 3.3 + - - +
245A ALA* 3.0 31.5 + - - +
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Residues in contact with VAL 242 (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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216A LEU* 4.1 11.9 - - + -
227A ILE* 3.8 26.0 - - + -
238A ALA 2.9 19.4 + - - +
239A LEU* 3.5 10.3 - - + +
241A ALA* 1.3 75.7 - - - +
243A ARG* 1.3 61.6 + - + +
245A ALA* 3.3 5.2 + - - +
247A LEU* 3.0 53.8 + - + +
249A SER* 4.4 16.2 - - - +
252A VAL* 3.8 24.0 - - + +
254A VAL* 4.5 7.0 - - + -
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Residues in contact with ARG 243 (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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236A MSE 6.2 1.2 - - - +
239A LEU* 3.0 22.3 + - - +
240A GLU* 3.4 35.8 + - - +
242A VAL* 1.3 73.8 - - + +
244A ALA* 1.3 65.2 + - - +
245A ALA 3.1 2.0 - - - -
246A GLY* 3.0 15.2 + - - -
247A LEU 4.5 7.6 - - - +
249A SER* 6.0 4.7 - - - -
266A ARG* 5.4 1.6 - - - +
271A GLU* 2.2 44.6 + - + +
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Residues in contact with ALA 244 (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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209A LEU* 5.2 1.8 - - + -
213A GLN* 3.6 26.7 - - - +
240A GLU 2.7 21.7 + - - +
241A ALA* 3.3 3.6 + - - +
243A ARG* 1.3 72.9 - - - +
245A ALA* 1.3 59.0 + - - +
246A GLY 3.2 0.7 + - - -
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Residues in contact with ALA 245 (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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213A GLN* 6.4 0.7 - - + -
216A LEU* 4.2 12.6 - - + -
241A ALA 3.0 17.0 + - - +
242A VAL 3.8 4.7 - - - +
243A ARG 3.1 0.6 - - - -
244A ALA* 1.3 75.8 - - - +
246A GLY* 1.3 62.8 + - - +
247A LEU* 3.4 24.0 + - + +
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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