Contacts of the helix formed by residues 226 - 237 (chain D) in PDB entry 1JPM
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 226 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198D PRO* 3.3 28.6 - - - +
222D VAL* 3.6 7.7 - - + +
223D HIS* 2.9 26.5 + - + +
224D LYS 4.9 0.2 - - - -
225D ASP* 1.3 77.2 - - - +
227D LEU* 1.3 56.7 + - - +
228D ALA* 3.9 5.7 + - - +
229D GLY* 3.0 21.6 + - - -
230D LEU* 2.9 26.9 + - - +
246D SER* 5.5 0.2 - - - -
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Residues in contact with LEU 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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224D LYS 4.2 5.8 - - - +
225D ASP 3.1 9.9 + - - +
226D ASP* 1.3 69.8 - - - +
228D ALA* 1.3 61.9 + - - +
230D LEU* 3.1 8.9 + - + +
231D LYS* 2.8 31.2 + - - +
246D SER* 4.1 23.8 - - - +
255D GLU* 3.4 39.0 - - + +
256D VAL* 4.0 26.0 - - + -
259D THR* 5.3 4.0 - - + +
261D SER* 3.7 12.6 + - - +
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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
----------------------------------------------------------
226D ASP* 3.4 5.1 + - - +
227D LEU* 1.3 78.0 - - - +
229D GLY* 1.3 58.1 + - - +
231D LYS* 3.4 8.5 + - - +
232D LYS* 3.0 25.7 + - - +
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Residues in contact with GLY 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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198D PRO* 3.5 27.8 - - - +
222D VAL* 4.0 5.4 - - - -
226D ASP* 3.0 18.7 + - - -
228D ALA* 1.3 76.2 - - - +
230D LEU* 1.3 64.9 + - - +
232D LYS* 3.1 14.8 + - - +
233D VAL* 3.1 17.3 + - - +
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Residues in contact with LEU 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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220D GLN* 3.9 16.8 - - - +
221D PRO* 3.7 31.2 - - + -
222D VAL* 3.5 11.8 - - + +
226D ASP 2.9 15.1 + - - +
227D LEU* 3.1 13.9 + - + +
229D GLY* 1.3 74.3 - - - +
231D LYS* 1.3 63.0 + - - +
233D VAL* 3.2 7.1 + - - +
234D THR* 3.0 23.0 + - - -
241D ILE* 4.0 10.8 - - + -
242D MET 5.1 1.8 - - - +
243D ALA* 4.1 22.0 - - + -
246D SER* 3.9 20.0 - - - +
256D VAL* 5.0 2.2 - - + -
261D SER* 3.5 23.3 - - - +
262D ALA* 4.2 3.8 - - + -
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Residues in contact with LYS 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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227D LEU 2.8 15.4 + - - +
228D ALA* 3.6 7.9 - - - +
230D LEU* 1.3 74.3 - - - +
232D LYS* 1.3 66.3 + - - +
234D THR* 3.1 1.9 + - - -
235D ASP* 2.9 41.9 + - - +
259D THR* 2.9 32.3 + - - +
260D ARG* 3.7 22.0 - - - +
261D SER* 3.4 20.8 + - - +
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Residues in contact with LYS 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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198D PRO* 3.6 33.0 - - + -
199D LYS* 4.3 17.1 - - - +
202D VAL* 4.3 10.2 - - + +
228D ALA 3.0 14.4 + - - +
229D GLY* 3.1 8.9 + - - +
231D LYS* 1.3 76.5 - - - +
233D VAL* 1.3 64.9 + - - +
235D ASP* 3.4 5.0 + - - +
236D ALA* 3.1 25.4 + - + +
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Residues in contact with VAL 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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198D PRO* 3.7 23.8 - - + +
201D ALA* 3.8 13.9 - - + -
202D VAL* 3.9 10.3 - - + +
205D ILE* 3.8 29.2 - - + -
221D PRO* 4.0 11.9 - - + -
222D VAL* 4.1 12.3 - - + -
229D GLY 3.1 14.2 + - - +
230D LEU 3.6 6.5 - - - +
232D LYS* 1.3 75.8 - - - +
234D THR* 1.3 62.8 + - - +
236D ALA 3.3 7.4 + - - -
237D THR* 2.9 27.6 + - + +
241D ILE* 3.8 12.6 - - + -
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Residues in contact with THR 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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230D LEU 3.0 7.1 + - - -
231D LYS* 3.1 8.9 + - - -
233D VAL* 1.3 77.2 - - - +
235D ASP* 1.3 66.7 + - - +
237D THR* 3.3 22.0 + - - +
241D ILE* 3.5 18.9 - - - +
260D ARG 4.4 4.7 - - - +
261D SER 2.6 30.8 + - - +
262D ALA* 3.5 11.4 - - - -
263D ASP* 3.6 31.7 - - - +
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Residues in contact with ASP 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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231D LYS* 2.9 45.9 + - - +
232D LYS* 4.1 4.4 - - - +
234D THR* 1.3 84.7 - - - +
236D ALA* 1.3 58.1 + - - +
237D THR 3.5 1.9 + - - +
260D ARG* 4.5 4.0 - - - +
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Residues in contact with ALA 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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202D VAL* 3.8 22.9 - - + -
206D ARG* 3.1 42.8 + - - +
232D LYS* 3.1 20.4 + - + +
233D VAL 3.3 1.5 + - - +
235D ASP* 1.3 76.8 - - - +
237D THR* 1.3 60.4 + - - +
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Residues in contact with THR 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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202D VAL* 4.4 14.6 - - - +
205D ILE* 3.7 37.0 - - + -
206D ARG* 4.7 3.8 - - + +
209D GLU* 4.0 5.6 - - - +
233D VAL* 2.9 24.3 + - + +
234D THR 3.3 13.3 + - - +
235D ASP 4.7 1.6 - - - +
236D ALA* 1.3 86.2 + - + +
238D ASP* 1.3 64.6 + - - +
239D THR 3.1 22.0 + - - +
241D ILE* 3.9 6.4 - - - +
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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