Contacts of the helix formed by residues 226 - 238 (chain D) in PDB entry 4IRQ
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 ARG 226 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196D TYR* 3.7 16.4 + - - -
221D PHE* 3.7 7.9 - - + -
224D TRP* 3.3 34.0 - - - -
225D GLY* 1.3 71.0 - - - +
227D GLU* 1.3 57.8 + - - +
228D ASP* 3.3 11.0 + - - -
229D ASP* 2.6 42.1 + - + +
230D GLU* 2.9 28.9 + - - +
278D GLN* 3.3 55.1 + - + +
279D PHE* 4.3 19.1 - - + -
403D TRS 4.2 0.6 + - - -
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Residues in contact with GLU 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141D ARG* 2.9 27.1 + - + +
142D ALA* 3.6 34.0 - - + +
217D MET* 3.9 8.5 - - + +
218D SER* 5.7 1.6 + - - -
221D PHE* 3.6 36.1 - - + -
223D GLY 5.2 1.6 - - - +
225D GLY 3.0 10.4 + - - +
226D ARG* 1.3 69.9 - - - +
228D ASP* 1.3 73.9 + - - +
230D GLU* 3.5 3.6 + - - +
231D PHE* 3.1 22.2 + - - +
403D TRS 2.9 45.0 + - - -
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Residues in contact with ASP 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141D ARG* 4.6 3.6 - - - +
196D TYR* 4.5 1.7 + - - -
199D TYR* 3.4 24.1 - - - -
200D VAL* 3.2 19.7 - - + +
201D GLY* 3.6 19.8 - - - +
217D MET* 4.6 4.0 - - + -
226D ARG* 3.5 10.2 + - - -
227D GLU* 1.3 87.9 + - - +
229D ASP* 1.3 73.8 + - - +
231D PHE* 3.0 7.3 + - - +
232D TYR 2.9 25.3 + - - -
403D TRS 2.9 28.9 + - - -
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Residues in contact with ASP 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196D TYR* 2.4 33.9 + - - -
198D THR* 4.3 7.2 + - - +
199D TYR* 4.7 1.2 - - - -
200D VAL* 5.2 0.4 - - - -
226D ARG* 2.6 52.1 + - - +
228D ASP* 1.3 87.0 + - - +
230D GLU* 1.3 62.4 + - - +
232D TYR* 3.3 16.7 + - - +
233D ARG* 3.4 16.4 + - - +
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Residues in contact with GLU 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218D SER* 3.8 14.8 + - - -
221D PHE* 3.7 26.9 - - + -
226D ARG 2.9 16.1 + - - +
227D GLU 3.8 3.9 - - - +
228D ASP 3.3 0.2 - - - -
229D ASP* 1.3 75.6 - - - +
231D PHE* 1.3 59.9 + - - +
233D ARG* 3.1 29.7 + - - +
234D ARG* 3.0 36.0 + - - +
278D GLN 5.6 0.4 - - - +
280D LYS 3.9 14.1 - - - +
281D VAL* 4.1 7.1 - - + +
282D ASP* 3.0 33.4 + - - +
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Residues in contact with PHE 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D MET* 4.1 3.8 - - + -
200D VAL* 5.0 2.0 - - + -
204D LEU* 3.6 33.0 - - + -
206D LEU* 3.7 27.8 - - + -
211D TYR* 4.3 11.2 - + - -
214D CYS* 4.0 13.7 - - + -
216D GLY* 3.1 34.3 - - - -
217D MET* 3.6 26.0 - - + -
227D GLU 3.1 13.6 + - - +
228D ASP* 3.0 10.1 + - - +
230D GLU* 1.3 76.7 + - - +
232D TYR* 1.3 65.0 + - - +
233D ARG 3.1 1.6 - - - -
234D ARG* 3.2 9.6 + - - +
235D ILE* 3.1 40.9 + - + +
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Residues in contact with TYR 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197D LYS 5.2 0.6 + - - -
198D THR* 3.5 53.9 - - + +
200D VAL* 3.6 24.6 - - + +
228D ASP 2.9 11.2 + - - +
229D ASP* 3.5 11.0 - - - +
231D PHE* 1.3 76.8 - - - +
233D ARG* 1.3 68.7 + - + +
235D ILE* 3.6 8.7 + - + +
236D LYS* 2.4 67.1 + - + +
242D LEU* 3.9 20.4 - - + -
244D ARG* 4.8 0.7 - - - -
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Residues in contact with ARG 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229D ASP 3.4 13.1 + - - +
230D GLU* 3.1 15.4 + - - +
231D PHE 3.1 0.6 - - - -
232D TYR* 1.3 85.0 - - + +
234D ARG* 1.3 56.5 + - - +
236D LYS* 3.9 3.1 - - - +
237D GLY* 2.8 29.1 + - - -
279D PHE* 3.0 28.1 + - - +
280D LYS* 4.1 0.8 - - - +
281D VAL* 3.6 32.1 - - + +
283D ARG* 3.9 14.5 + - - +
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Residues in contact with ARG 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214D CYS* 3.2 27.8 + - + +
215D ASN* 3.1 29.9 + - - +
216D GLY 3.2 16.7 + - - -
217D MET 3.8 1.8 - - - -
218D SER* 3.6 14.6 - - - +
230D GLU* 3.0 31.7 + - - +
231D PHE* 3.2 14.9 + - + +
233D ARG* 1.3 76.3 - - - +
235D ILE* 1.3 56.4 + - - +
237D GLY* 3.7 0.5 - - - -
238D ALA* 2.9 31.9 + - - +
281D VAL* 5.6 0.2 - - + -
282D ASP* 2.7 41.7 + - - -
283D ARG* 4.1 22.8 + - - +
285D GLY 2.8 18.7 + - - -
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Residues in contact with ILE 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182D PRO* 4.2 30.1 - - + -
200D VAL* 5.2 4.0 - - + -
204D LEU* 4.5 9.9 - - + -
214D CYS* 4.0 16.8 - - - -
231D PHE* 3.1 41.5 + - + +
232D TYR* 3.7 14.4 - - + +
234D ARG* 1.3 75.3 - - - +
236D LYS* 1.3 73.2 + - - +
238D ALA* 3.2 12.6 + - - +
240D LEU* 3.2 40.8 + - + +
242D LEU* 4.9 15.0 - - + -
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Residues in contact with LYS 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D TYR* 2.4 64.6 + - + +
233D ARG* 4.0 3.8 - - - +
235D ILE* 1.3 80.2 - - - +
237D GLY* 1.3 59.1 + - - +
239D GLY* 2.9 21.0 + - - -
240D LEU 4.0 15.9 - - - +
241D GLN* 5.4 0.7 - - - +
242D LEU* 4.2 22.6 - - - +
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Residues in contact with GLY 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233D ARG 2.8 21.7 + - - -
234D ARG 3.7 2.0 - - - -
236D LYS* 1.3 73.2 - - - +
238D ALA* 1.3 56.3 + - - +
239D GLY 3.0 4.7 + - - -
283D ARG* 4.8 14.4 - - - -
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Residues in contact with ALA 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213D LEU* 4.0 43.7 - - + +
214D CYS* 4.7 4.3 - - - -
234D ARG 2.9 18.2 + - - +
235D ILE 3.2 5.1 + - - +
237D GLY* 1.3 72.9 - - - +
239D GLY* 1.3 60.9 + - - +
240D LEU* 3.6 9.5 + - + +
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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