Contacts of the helix formed by residues 233 - 247 (chain D) in PDB entry 3KDO
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 233 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232D ALA* 1.3 80.5 - - - +
234D LEU* 1.3 68.4 + - - +
235D LEU 3.3 1.1 - - - +
236D GLU* 3.1 20.5 + - - +
237D MET* 3.0 15.6 + - - +
99J ALA 3.4 24.1 - - - +
100J ASN* 4.2 2.9 + - - -
101J LEU* 4.5 3.3 + - - +
102J PRO* 3.7 19.8 - - - +
261J TRP 4.1 6.1 - - - +
262J GLY 3.8 3.7 - - - +
265J ARG* 4.0 38.1 + - + +
266J TYR 6.1 0.7 - - - +
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Residues in contact with LEU 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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233D ASP* 1.3 72.0 - - - +
235D LEU* 1.3 66.9 + - + +
237D MET* 3.1 10.8 + - + +
238D GLU* 3.0 28.0 + - + +
263D ALA* 4.5 11.2 - - + -
266D TYR* 3.9 29.4 - - + -
267D ILE* 3.9 15.0 - - + -
234J LEU* 3.4 27.4 - - + -
262J GLY 2.9 18.7 + - - +
263J ALA* 4.3 3.3 - - + +
266J TYR* 3.5 47.2 - - + +
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Residues in contact with LEU 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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233D ASP* 3.3 1.6 - - + +
234D LEU* 1.3 77.4 - - + +
236D GLU* 1.3 70.9 + - - +
238D GLU* 3.2 26.5 + - - +
239D GLN* 3.1 35.0 + - - +
266J TYR* 4.2 34.5 - - + -
269J ASP* 6.0 1.8 - - - +
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Residues in contact with GLU 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 ALA* 3.6 17.3 - - + -
233D ASP* 3.1 31.7 + - - +
235D LEU* 1.3 81.5 + - - +
237D MET* 1.3 63.4 + - - +
239D GLN* 3.1 22.8 + - - +
240D ARG* 2.9 49.3 + - - +
97J GLU* 4.8 3.1 - - - +
99J ALA 5.3 5.5 - - - +
100J ASN* 6.5 0.2 - - + -
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Residues in contact with MET 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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230D ILE* 3.1 43.5 - - + +
231D THR* 4.2 4.0 - - - -
232D ALA 3.2 34.8 - - - +
233D ASP 3.0 6.4 + - - +
234D LEU* 3.4 15.0 - - + +
236D GLU* 1.3 76.9 - - - +
238D GLU* 1.3 57.1 + - - +
240D ARG* 3.3 2.0 + - - +
241D LEU* 2.9 35.4 + - - +
254D VAL* 4.8 2.7 - - - -
259D THR* 4.1 20.6 - - + -
263D ALA* 5.4 0.4 - - + -
267D ILE* 4.1 27.1 - - + -
262J GLY* 3.9 25.1 - - - +
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Residues in contact with GLU 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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234D LEU* 3.0 22.1 + - + +
235D LEU* 3.4 32.5 - - - +
236D GLU 3.2 0.2 - - - -
237D MET* 1.3 77.9 - - - +
239D GLN* 1.3 63.9 + - + +
241D LEU* 3.4 3.6 + - - +
242D GLU* 3.0 22.5 + - - +
266D TYR* 2.4 38.2 + - + +
267D ILE* 5.3 1.3 - - + +
270D LEU* 4.0 23.5 - - + +
274D TYR* 4.9 2.8 + - - -
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Residues in contact with GLN 239 (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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235D LEU* 3.1 24.1 + - - +
236D GLU* 3.1 24.2 + - - +
238D GLU* 1.3 75.2 - - + +
240D ARG* 1.3 62.1 + - + +
242D GLU* 3.2 14.3 + - - +
243D VAL* 3.0 32.7 + - + +
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Residues in contact with ARG 240 (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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195D THR* 4.2 4.2 - - - +
196D SER* 3.6 21.4 + - - +
202D PHE* 3.5 43.4 - - + +
229D ASN 5.1 0.6 + - - -
230D ILE* 3.8 26.8 + - + +
231D THR 3.9 6.9 + - - -
232D ALA* 3.8 13.9 - - - +
236D GLU* 2.9 43.3 + - - +
237D MET 3.9 1.8 - - - +
239D GLN* 1.3 79.4 + - + +
241D LEU* 1.3 64.0 + - - +
243D VAL* 3.2 4.9 + - + -
244D LEU* 3.1 26.7 + - - +
97J GLU* 2.6 43.0 + - - -
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Residues in contact with LEU 241 (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 ILE* 3.6 28.9 - - + +
237D MET 2.9 21.2 + - - +
238D GLU 3.6 4.7 - - - +
240D ARG* 1.3 74.4 - - - +
242D GLU* 1.3 62.7 + - - +
244D LEU* 3.3 6.8 + - - +
245D ALA* 3.1 22.9 + - - +
252D ALA* 3.7 24.5 - - + -
267D ILE* 4.2 20.0 - - + +
270D LEU* 3.8 34.8 - - + -
271D ALA* 4.3 11.0 - - + +
274D TYR* 3.9 15.9 - - + -
276D LEU* 4.0 11.5 - - + +
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Residues in contact with GLU 242 (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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238D GLU 3.0 14.0 + - - +
239D GLN* 3.4 16.9 - - - +
240D ARG 3.2 0.2 - - - -
241D LEU* 1.3 77.2 - - - +
243D VAL* 1.3 57.5 + - + +
245D ALA* 3.4 0.9 + - - +
246D ASP* 2.9 49.3 + - - +
274D TYR* 3.9 25.9 + - + +
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Residues in contact with VAL 243 (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 PHE* 4.2 10.8 - - + -
203D GLU* 4.4 32.5 - - + +
206D ALA* 3.9 27.1 - - + -
239D GLN* 3.0 21.6 + - + +
240D ARG* 3.2 10.5 + - + +
242D GLU* 1.3 74.6 - - + +
244D LEU* 1.3 66.0 + - - +
246D ASP* 3.4 6.8 + - - +
247D LEU* 3.1 31.5 + - + +
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Residues in contact with LEU 244 (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 PHE* 3.6 11.4 - - + -
206D ALA* 4.9 1.1 - - + -
226D TRP* 3.7 4.0 - - + -
228D ALA* 3.6 24.0 - - + -
230D ILE* 4.1 13.9 - - + -
240D ARG 3.1 15.2 + - - +
241D LEU* 3.6 6.5 - - - +
243D VAL* 1.3 77.4 - - - +
245D ALA* 1.3 62.7 + - - +
247D LEU 3.2 2.8 + - - -
248D GLY 3.1 3.5 + - - -
249D LEU* 3.0 56.3 + - + +
251D HIS 3.4 21.5 - - - +
252D ALA* 3.8 21.5 - - + -
276D LEU* 3.9 16.6 - - + -
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Residues in contact with ALA 245 (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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241D LEU 3.1 7.7 + - - +
242D GLU 3.8 4.0 - - - +
244D LEU* 1.3 78.8 - - - +
246D ASP* 1.3 66.0 + - - +
248D GLY* 3.0 15.5 + - - -
249D LEU 5.1 0.4 - - - -
274D TYR* 3.4 50.3 - - + +
276D LEU* 4.5 6.4 - - - +
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Residues in contact with ASP 246 (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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242D GLU* 2.9 41.6 + - - +
243D VAL* 3.8 7.0 - - - +
244D LEU 3.3 0.2 - - - -
245D ALA* 1.3 77.5 - - - +
247D LEU* 1.3 63.4 + - + +
248D GLY 3.3 0.6 + - - -
274D TYR* 6.1 0.2 - - - -
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Residues in contact with LEU 247 (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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206D ALA* 3.5 43.5 - - + +
207D GLU* 3.4 29.8 - - + +
210D ALA* 4.3 22.2 - - + +
243D VAL* 3.1 25.4 + - + +
244D LEU 3.2 3.8 + - - +
245D ALA 3.1 0.4 - - - -
246D ASP* 1.3 79.3 - - + +
248D GLY* 1.3 59.2 + - - +
249D LEU* 3.1 15.5 + - + +
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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