Contacts of the helix formed by residues 260 - 274 (chain G) 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 GLY 260 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B VAL 5.8 0.2 - - - -
258B ILE 4.6 0.2 - - - -
260B GLY* 3.7 16.4 - - - -
256G VAL 3.1 14.3 + - - +
257G VAL 3.4 10.1 + - - -
258G ILE 3.2 1.8 - - - -
259G THR* 1.3 82.2 - - - +
261G TRP* 1.3 69.1 + - - -
262G GLY 3.4 3.3 + - - -
263G ALA 3.8 0.3 + - - -
264G LEU* 3.4 23.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 261 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B ASP* 4.3 6.6 - - - +
257B VAL 5.3 1.3 - - - -
258B ILE* 3.4 33.9 + - + +
284B MET* 4.5 16.7 - - + +
101G LEU* 4.1 10.3 - - + -
102G PRO* 4.2 16.7 - - + +
105G LEU* 3.5 27.6 - - + +
260G GLY* 1.3 74.2 - - - -
262G GLY* 1.3 65.6 + - - +
263G ALA 3.2 1.0 + - - -
264G LEU* 3.6 11.1 + - + +
265G ARG 4.6 1.9 + - - -
288G PHE* 6.4 0.2 - + - -
301G LEU* 3.7 23.6 - - + -
304G LEU* 3.7 39.0 - - + -
305G TYR* 3.5 39.9 - + - -
308G ILE* 3.9 22.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 262 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B ALA 4.1 14.4 - - - -
233B ASP* 3.6 4.0 - - - +
234B LEU* 2.8 31.7 + - - -
237B MET* 4.7 3.6 - - - -
258B ILE 3.7 0.6 + - - -
259B THR* 2.9 30.3 + - - -
263B ALA* 5.1 1.1 - - - -
102G PRO* 4.5 4.0 - - - +
261G TRP* 1.3 80.0 - - - +
263G ALA* 1.3 58.5 + - - +
265G ARG 5.4 0.3 + - - -
266G TYR 5.7 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 263 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B LEU* 4.4 9.6 - - + -
259B THR 4.2 1.8 + - - -
262B GLY 4.7 0.7 - - - -
263B ALA* 3.3 34.8 - - + +
234G LEU* 4.5 15.5 - - + -
259G THR* 4.6 14.1 - - + +
260G GLY 3.8 2.0 + - - -
261G TRP 3.2 0.4 - - - -
262G GLY* 1.3 75.7 - - - +
264G LEU* 1.3 64.1 + - - +
265G ARG 3.4 2.5 - - - -
266G TYR* 3.5 5.1 + - - +
267G ILE* 3.1 26.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 264 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254G VAL* 4.4 7.6 - - + -
256G VAL* 3.9 27.1 - - + +
259G THR* 4.2 17.5 - - + -
260G GLY 3.4 17.5 + - - +
261G TRP* 3.6 10.7 + - + +
263G ALA* 1.3 78.3 - - - +
265G ARG* 1.3 59.3 + - - +
267G ILE* 3.4 7.8 + - + +
268G ARG* 2.9 29.7 + - + +
305G TYR* 3.3 40.4 - - + -
308G ILE* 3.8 26.0 - - + -
310G ILE* 4.6 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 265 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B ASP* 4.1 34.1 + - + +
99G ALA* 4.3 18.9 - - - +
135G GLU 2.8 32.1 + - - -
136G PHE* 3.8 29.6 - - - +
137G ASP* 3.9 18.5 + - - +
261G TRP 4.6 2.8 + - - -
262G GLY 5.4 0.2 + - - -
263G ALA 3.4 0.6 - - - -
264G LEU* 1.3 74.5 - - - +
266G TYR* 1.3 56.4 + - - +
268G ARG* 3.1 11.2 + - - +
269G ASP* 2.7 52.0 + - - +
308G ILE* 4.3 16.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 266 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B ASP* 6.2 0.4 - - - +
234B LEU* 3.5 39.9 - - + +
235B LEU* 4.1 33.7 - - + -
234G LEU* 4.1 15.7 - - + -
238G GLU* 2.3 37.5 + - + -
262G GLY 5.7 0.2 + - - -
263G ALA 3.5 7.1 + - - +
264G LEU 3.4 0.4 - - - -
265G ARG* 1.3 78.4 - - - +
267G ILE* 1.3 59.9 + - + +
269G ASP* 3.2 8.5 + - + +
270G LEU* 2.8 55.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 267 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230G ILE* 4.1 22.0 - - + -
234G LEU* 3.6 27.6 - - + +
237G MET* 4.2 30.1 - - + -
238G GLU* 5.2 1.6 - - + -
241G LEU* 4.2 14.2 - - + +
254G VAL* 4.3 17.5 - - + -
259G THR* 5.0 3.6 - - + -
263G ALA 3.1 20.3 + - - +
264G LEU* 3.7 10.3 - - + +
265G ARG 3.3 0.2 - - - -
266G TYR* 1.3 82.8 - - + +
268G ARG* 1.3 56.8 + - - +
270G LEU* 3.6 6.4 - - + +
271G ALA* 2.9 29.0 + - + +
278G ILE* 5.9 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 268 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137G ASP* 3.4 23.6 + - - +
138G GLY 3.1 21.6 + - - -
140G ALA* 4.3 17.8 - - - +
264G LEU* 2.9 18.8 + - + +
265G ARG* 3.1 8.2 + - - +
267G ILE* 1.3 75.6 - - - +
269G ASP* 1.3 100.3 + - - +
271G ALA* 3.3 2.8 + - - +
272G ALA* 3.0 46.2 + - - +
278G ILE* 3.6 27.0 - - + +
308G ILE* 3.0 36.1 + - + +
309G GLY* 4.1 8.5 + - - +
310G ILE* 5.2 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 269 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B LEU* 6.1 0.7 - - - +
137G ASP* 4.2 9.3 - - - +
265G ARG* 2.7 38.8 + - - +
266G TYR* 3.7 8.4 + - + +
268G ARG* 1.3 109.1 + - - +
270G LEU* 1.3 62.7 + - - +
272G ALA* 3.2 2.4 + - - +
273G ASP* 3.0 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 270 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238G GLU* 4.0 29.6 - - + +
241G LEU* 3.7 21.1 - - + -
266G TYR* 2.8 43.4 + - + +
267G ILE* 3.6 7.4 - - + +
269G ASP* 1.3 74.4 - - - +
271G ALA* 1.3 61.4 + - - +
273G ASP* 3.4 12.5 + - + +
274G TYR* 3.2 59.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 271 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241G LEU* 4.3 15.5 - - + +
252G ALA* 5.1 1.6 - - + -
267G ILE* 2.9 19.4 + - + +
268G ARG 3.6 4.7 - - - +
270G LEU* 1.3 76.4 - - - +
272G ALA* 1.3 56.6 + - - +
274G TYR* 3.2 8.4 + - - +
275G GLY 3.1 3.8 + - - -
276G LEU* 2.7 45.1 + - + +
278G ILE* 3.8 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 272 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140G ALA* 4.4 18.2 - - + -
141G PHE* 5.8 0.9 - - - -
268G ARG* 3.0 40.8 + - + +
269G ASP 3.5 3.1 - - - +
270G LEU 3.2 0.2 - - - -
271G ALA* 1.3 72.9 - - - +
273G ASP* 1.3 61.6 + - - +
274G TYR 3.0 1.3 - - - -
275G GLY* 2.6 26.1 + - - +
276G LEU 4.5 5.8 - - - +
278G ILE* 5.4 0.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 273 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269G ASP* 3.0 22.0 + - - +
270G LEU* 3.4 13.3 + - + +
272G ALA* 1.3 77.2 - - - +
274G TYR* 1.3 64.0 + - + +
275G GLY 3.4 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 274 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238G GLU 5.0 1.8 + - - -
241G LEU* 3.8 30.3 - - + -
242G GLU* 4.0 27.8 + - + +
245G ALA* 3.5 28.1 - - + +
270G LEU* 3.2 47.7 + - + +
271G ALA* 3.2 10.2 + - - +
272G ALA 3.0 0.8 - - - -
273G ASP* 1.3 77.7 - - + +
275G GLY* 1.3 62.9 + - - +
276G LEU* 3.9 17.6 - - + +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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