Contacts of the helix formed by residues 226 - 234 (chain D) in PDB entry 3JXI
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 226 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213D ILE 4.1 9.6 - - - -
214D ASN* 4.1 29.1 + - + +
215D SER 4.1 6.1 - - - -
216D PRO* 4.4 6.7 - - + -
217D PHE* 4.6 6.6 - - - -
224D GLY 4.0 5.6 - - - +
225D GLN* 1.3 79.8 - - - +
227D ALA* 1.3 64.8 + - - +
228D LEU* 3.7 16.8 + - - +
229D HIS* 3.1 26.8 + - - +
230D ILE* 4.1 1.9 + - - +
249D ASP 4.8 1.9 + - - -
252D ALA* 3.3 33.1 - - + +
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Residues in contact with ALA 227 (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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181D LEU* 3.8 29.4 - - + -
182D PRO* 4.7 12.4 - - + +
185D LEU* 4.3 8.9 - - + +
212D PHE 5.3 0.9 - - - +
213D ILE 3.6 17.7 + - - +
215D SER 4.7 2.4 + - - +
226D THR* 1.3 75.6 - - - +
228D LEU* 1.3 61.9 + - - +
229D HIS 3.2 0.4 + - - -
230D ILE* 3.4 14.9 + - - +
231D ALA* 3.2 17.7 + - - +
243D LEU* 3.6 15.0 - - + +
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Residues in contact with LEU 228 (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 ILE* 4.9 2.1 + - + +
214D ASN* 6.1 0.2 - - - +
226D THR* 3.2 11.2 + - - +
227D ALA* 1.3 79.4 - - - +
229D HIS* 1.3 56.0 + - - +
231D ALA 4.0 0.2 - - - -
232D ILE* 3.1 42.7 + - + +
240D VAL* 3.4 45.3 - - + +
243D LEU* 3.8 14.8 - - + +
244D VAL* 4.2 10.1 - - + -
248D ALA* 4.1 19.3 - - + -
249D ASP 3.6 23.1 - - - +
250D VAL* 4.1 9.2 - - + -
274D PRO* 4.1 18.8 - - + -
290D LEU* 4.7 3.6 - - + -
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Residues in contact with HIS 229 (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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225D GLN* 3.7 10.5 - - + -
226D THR* 3.1 37.9 + - - +
228D LEU* 1.3 75.8 - - - +
230D ILE* 1.3 56.0 + - + +
232D ILE* 3.4 1.0 + - - -
233D GLU* 2.8 37.0 + - - +
252D ALA* 3.2 30.1 + - + -
253D GLN 4.3 0.2 - - - -
254D ALA* 3.5 27.4 - - + +
270D PHE* 4.2 3.4 - + + -
272D GLU 3.0 25.4 + - - -
274D PRO* 4.4 12.2 - - + -
277D LEU* 3.5 27.7 - - + +
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Residues in contact with ILE 230 (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* 3.6 43.7 - - + +
185D LEU* 3.6 22.7 - - + -
186D LEU* 4.0 26.7 - - + -
217D PHE* 4.2 20.9 - - + -
225D GLN* 6.2 0.2 - - + -
226D THR 4.6 2.2 - - - +
227D ALA* 3.4 11.1 + - - +
229D HIS* 1.3 73.8 - - + +
231D ALA* 1.3 58.0 + - - +
233D GLU* 4.3 5.2 - - - +
234D ARG* 2.8 51.0 + - + +
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Residues in contact with ALA 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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185D LEU* 4.5 8.0 - - + +
227D ALA 3.2 3.0 + - - +
228D LEU 3.7 5.2 - - - +
229D HIS 3.4 0.2 - - - -
230D ILE* 1.3 78.8 - - - +
232D ILE* 1.3 58.7 + - - +
234D ARG* 3.8 0.4 - - - -
235D ARG 3.2 3.8 + - - -
236D CYS* 2.9 36.3 + - - +
239D TYR* 4.1 7.9 - - + -
240D VAL* 3.6 26.2 - - + +
243D LEU* 3.6 29.8 - - + -
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Residues in contact with ILE 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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228D LEU* 3.1 27.3 + - + +
229D HIS 3.6 3.8 - - - +
230D ILE 3.2 0.2 - - - -
231D ALA* 1.3 73.3 - - - +
233D GLU* 1.3 57.1 + - - +
235D ARG* 2.7 22.2 + - - -
240D VAL* 4.1 17.3 - - + -
274D PRO* 3.3 45.8 - - + +
277D LEU* 3.5 24.0 - - + -
278D ALA* 3.9 14.8 - - + -
281D THR* 4.3 0.7 - - - +
283D GLN* 2.8 33.2 + - - +
286D ILE* 4.3 12.1 - - + -
290D LEU* 4.4 9.0 - - + -
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Residues in contact with GLU 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 HIS 2.8 22.8 + - - +
230D ILE* 3.9 5.5 - - - +
232D ILE* 1.3 75.8 - - - +
234D ARG* 1.3 85.3 + - - +
235D ARG* 3.3 12.1 + - - +
268D PHE* 6.5 0.7 - - + -
277D LEU* 4.7 16.2 - - + -
281D THR* 5.5 8.0 - - + +
283D GLN* 4.7 2.3 + - - +
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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
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185D LEU 3.3 23.1 + - - +
186D LEU* 3.4 46.1 + - - +
188D LEU* 4.2 18.7 - - + +
230D ILE* 2.8 33.2 + - + +
233D GLU* 1.3 84.9 + - - +
235D ARG* 1.3 70.4 + - - +
236D CYS* 3.5 19.7 + - - -
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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