Contacts of the helix formed by residues 222 - 233 (chain D) in PDB entry 3J82
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 ASP 222 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220D ALA* 3.8 2.9 - - - -
221D LEU* 1.3 82.5 - - + +
223D PHE* 1.3 64.3 + - - +
224D GLU* 4.2 12.2 - - + +
225D GLN* 3.7 26.2 - - + +
226D GLU* 3.1 24.7 + - - +
312D ARG* 5.6 0.7 - - - -
315D LYS* 3.9 17.4 + - - +
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Residues in contact with PHE 223 (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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220D ALA* 4.2 8.9 - - + +
222D ASP* 1.3 73.9 + - - +
224D GLU* 1.3 83.4 + - + +
226D GLU* 3.2 7.8 + - - +
227D MET* 3.2 47.8 + - + +
255D PHE* 4.4 14.6 - + - -
256D ARG* 4.8 5.2 - - + -
259D GLU* 2.8 43.3 - - + +
263D GLN* 3.7 14.1 - - - +
266D PHE* 3.5 26.9 - + - -
312D ARG* 4.6 13.0 - - - +
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Residues in contact with GLU 224 (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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222D ASP* 3.2 14.1 - - + +
223D PHE* 1.3 100.6 + - + +
225D GLN* 1.3 65.9 - - - +
226D GLU 3.3 0.3 + - - -
227D MET* 3.3 8.3 + - - +
228D ALA* 3.3 18.0 + - - +
263D GLN* 4.4 6.1 + - - -
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Residues in contact with GLN 225 (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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222D ASP* 3.5 24.0 + - + +
223D PHE 3.3 0.4 - - - -
224D GLU* 1.3 78.6 - - - +
226D GLU* 1.3 57.2 + - + +
228D ALA* 2.9 15.7 + - - +
229D THR* 2.7 47.2 + - - +
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Residues in contact with GLU 226 (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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218D TYR* 2.7 33.0 + - - -
220D ALA* 3.0 32.1 - - + -
221D LEU* 4.2 17.6 - - + +
222D ASP 3.1 13.9 + - - +
223D PHE 3.6 4.7 - - - +
225D GLN* 1.3 77.0 - - + +
227D MET* 1.3 66.1 + - - +
229D THR* 3.4 15.1 + - - +
230D ALA* 3.1 21.0 + - - +
255D PHE* 3.6 20.6 - - + -
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Residues in contact with MET 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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223D PHE* 3.2 46.0 + - + +
224D GLU* 3.8 7.4 - - - +
225D GLN 3.2 0.2 - - - -
226D GLU* 1.3 77.3 - - - +
228D ALA* 1.3 57.7 + - - +
230D ALA* 2.7 30.8 + - + +
231D ALA* 3.5 3.5 + - - +
252D ASN* 5.4 10.5 - - + +
255D PHE* 3.5 23.5 - - + -
256D ARG* 5.6 4.5 - - - -
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Residues in contact with ALA 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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224D GLU 3.3 8.8 + - - +
225D GLN* 2.9 22.3 + - - +
227D MET* 1.3 80.8 - - - +
229D THR* 1.3 62.4 + - - +
230D ALA 3.3 0.2 + - - -
231D ALA* 3.4 16.3 + - - +
232D SER* 4.3 1.4 + - - -
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Residues in contact with THR 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* 2.7 37.2 + - - +
226D GLU* 3.7 17.7 + - - +
228D ALA* 1.3 72.2 - - - +
230D ALA* 1.3 61.0 + - - +
231D ALA 2.9 2.7 - - - -
232D SER* 2.8 13.5 + - - -
233D SER* 2.6 35.3 + - - +
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Residues in contact with ALA 230 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A GLU* 3.6 9.0 - - - +
226D GLU 3.1 13.4 + - - +
227D MET* 2.7 20.7 + - + +
229D THR* 1.3 75.7 - - - +
231D ALA* 1.3 64.5 + - - +
233D SER* 2.8 23.1 + - - -
236D LEU* 3.5 25.1 - - + +
252D ASN* 4.5 6.5 - - + -
255D PHE* 4.1 10.1 - - + -
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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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152A PHE* 3.7 6.4 - - - -
153A GLU* 4.5 1.6 - - - +
154A ARG* 2.7 62.1 + - - +
227D MET 3.5 2.3 + - - +
228D ALA* 3.4 12.9 + - - +
229D THR 2.9 0.2 + - - -
230D ALA* 1.3 83.7 - - - +
232D SER* 1.3 62.2 + - - +
233D SER 4.4 1.6 - - - +
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Residues in contact with SER 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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152A PHE* 3.3 23.6 - - - -
154A ARG* 3.5 6.9 - - - +
156A GLU* 5.6 0.8 + - - -
164A SER* 5.1 4.3 + - - -
167A LYS* 4.8 11.5 + - - -
228D ALA 4.3 1.0 + - - -
229D THR* 2.8 16.1 + - - -
231D ALA* 1.3 78.5 - - - +
233D SER* 1.3 65.8 + - - +
234D SER* 3.0 4.7 + - - -
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Residues in contact with SER 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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152A PHE* 5.3 0.3 - - - -
153A GLU* 2.7 29.6 - - - +
229D THR* 2.6 35.3 + - - +
230D ALA* 2.8 17.0 + - - -
232D SER* 1.3 75.2 - - - +
234D SER* 1.3 63.1 + - - +
235D SER* 4.1 4.0 - - - +
236D LEU* 3.3 30.5 - - - +
237D GLU* 4.3 0.9 - - - +
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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