Contacts of the helix formed by residues 260 - 274 (chain I) 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 I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258E ILE 4.5 0.7 - - - -
260E GLY* 3.7 17.0 - - - -
256I VAL 3.2 10.7 + - - -
257I VAL 3.5 9.2 + - - -
258I ILE 3.2 1.4 - - - -
259I THR* 1.3 82.6 - - - +
261I TRP* 1.3 69.1 + - - -
262I GLY 3.3 2.9 + - - -
263I ALA 3.8 0.5 + - - -
264I LEU* 3.3 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 261 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233E ASP* 4.1 6.9 - - - +
257E VAL 5.3 1.3 - - - -
258E ILE* 3.3 29.9 + - + +
284E MET* 4.5 16.4 - - + +
101I LEU* 3.9 16.8 - - + -
102I PRO* 3.9 24.8 - - + +
105I LEU* 3.5 28.2 - - + +
260I GLY* 1.3 74.3 - - - -
262I GLY* 1.3 64.5 + - - +
263I ALA 3.2 1.3 + - - -
264I LEU* 3.8 10.8 + - + +
265I ARG* 4.7 1.7 + - - +
288I PHE* 6.4 0.7 - + - -
301I LEU* 4.2 18.8 - - + -
304I LEU* 3.7 30.7 - - + -
305I TYR* 3.7 41.7 - + - -
308I ILE* 3.8 21.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 262 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232E ALA 4.1 7.0 - - - -
233E ASP* 3.6 3.1 - - - +
234E LEU* 2.9 33.3 + - - +
237E MET* 3.7 15.6 - - - +
258E ILE 3.8 0.6 + - - -
259E THR* 2.8 28.6 + - - +
263E ALA* 5.1 2.0 - - - -
102I PRO* 4.7 2.2 - - - +
261I TRP* 1.3 78.6 - - - +
263I ALA* 1.3 59.6 + - - +
265I ARG* 5.4 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 263 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234E LEU* 4.4 15.9 - - + -
259E THR 4.3 1.6 + - - -
262E GLY* 4.9 0.9 - - - -
263E ALA* 3.5 32.8 - - + +
234I LEU* 4.5 9.4 - - + -
237I MET* 5.3 0.4 - - + -
259I THR* 4.8 8.7 - - + +
260I GLY 3.8 2.2 + - - -
262I GLY* 1.3 77.6 - - - +
264I LEU* 1.3 67.4 + - - +
265I ARG* 3.2 3.6 - - - -
266I TYR* 3.1 5.5 + - - +
267I ILE* 2.9 27.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 264 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254I VAL* 4.4 14.1 - - + -
256I VAL* 4.0 32.8 - - + +
259I THR* 4.4 8.9 - - + +
260I GLY 3.3 17.2 + - - +
261I TRP* 3.8 9.5 + - + +
263I ALA* 1.3 78.3 - - - +
265I ARG* 1.3 57.1 + - - +
267I ILE* 3.5 7.6 + - + +
268I ARG* 2.9 30.5 + - + +
305I TYR* 3.4 39.9 - - + -
308I ILE* 3.7 24.7 - - + -
310I ILE* 4.4 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 265 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233E ASP* 3.8 37.5 + - + +
99I ALA* 5.3 9.1 + - - +
101I LEU* 5.9 1.8 - - - +
135I GLU 2.9 26.1 + - - -
136I PHE* 3.5 36.6 - - - +
137I ASP* 4.8 12.6 + - - +
261I TRP 4.7 1.8 + - - +
262I GLY 6.0 0.7 - - - +
263I ALA 3.2 0.8 - - - -
264I LEU* 1.3 76.4 - - - +
266I TYR* 1.3 66.1 + - - +
268I ARG* 3.2 3.1 + - - +
269I ASP* 2.9 45.6 + - - +
308I ILE* 4.3 28.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 266 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233E ASP* 6.2 0.2 - - - +
234E LEU* 3.5 37.8 - - + +
235E LEU* 3.9 34.5 - - + +
234I LEU* 4.0 11.0 - - + -
238I GLU* 2.7 39.6 + - + -
263I ALA* 3.1 8.7 + - - +
265I ARG* 1.3 79.7 - - - +
267I ILE* 1.3 61.0 + - + +
269I ASP* 3.2 8.5 + - + +
270I LEU* 2.9 52.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 267 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230I ILE* 4.2 9.4 - - + -
234I LEU* 4.2 14.1 - - + -
237I MET* 3.9 44.4 - - + -
238I GLU 5.1 0.7 - - - +
241I LEU* 4.2 14.2 - - + +
254I VAL* 4.2 28.9 - - + -
259I THR* 4.8 3.6 - - + -
263I ALA* 2.9 22.3 + - + +
264I LEU* 3.7 9.9 - - + +
266I TYR* 1.3 81.9 - - + +
268I ARG* 1.3 58.1 + - - +
270I LEU* 3.3 7.5 + - + +
271I ALA* 2.8 31.5 + - + +
278I ILE* 6.0 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 268 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137I ASP* 3.6 26.1 + - - +
138I GLY 2.9 24.6 + - - -
140I ALA* 4.0 20.0 - - - +
264I LEU* 2.9 19.1 + - + +
265I ARG* 3.5 5.6 - - - +
267I ILE* 1.3 77.4 - - - +
269I ASP* 1.3 89.7 + - - +
271I ALA* 3.4 2.6 + - - +
272I ALA* 2.9 45.6 + - - +
278I ILE* 3.7 26.9 - - + +
308I ILE* 3.3 33.2 + - + +
309I GLY* 4.0 10.6 + - - +
310I ILE* 5.3 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 269 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137I ASP* 4.2 7.4 - - - +
265I ARG* 2.9 40.0 + - - +
266I TYR* 3.7 7.9 + - + +
268I ARG* 1.3 109.2 + - - +
270I LEU* 1.3 61.6 + - - +
272I ALA* 3.3 1.6 + - - +
273I ASP* 2.8 39.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 270 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238I GLU* 4.0 31.0 - - + +
241I LEU* 3.6 20.6 - - + -
266I TYR* 2.9 41.5 + - + +
267I ILE* 3.5 6.7 - - + +
269I ASP* 1.3 74.2 - - - +
271I ALA* 1.3 66.2 + - - +
273I ASP* 3.1 14.7 + - + +
274I TYR* 3.0 51.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 271 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241I LEU* 4.2 22.3 - - + +
252I ALA* 4.9 2.2 - - + -
267I ILE* 2.8 19.6 + - + +
268I ARG 3.7 4.5 - - - +
270I LEU* 1.3 76.2 - - - +
272I ALA* 1.3 60.8 + - - +
274I TYR* 3.2 6.8 + - - +
275I GLY 3.0 4.2 + - - -
276I LEU* 2.8 38.4 + - + +
278I ILE* 3.9 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 272 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140I ALA* 4.5 17.5 - - + -
141I PHE* 6.2 0.7 - - - -
268I ARG* 2.9 41.3 + - - +
269I ASP 3.5 4.9 - - - +
271I ALA* 1.3 74.0 - - - +
273I ASP* 1.3 60.7 + - - +
275I GLY* 2.8 24.4 + - - +
276I LEU 4.4 5.6 + - - +
278I ILE* 5.2 1.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 273 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269I ASP* 2.8 23.1 + - - +
270I LEU* 3.1 17.9 + - + +
272I ALA* 1.3 77.3 - - - +
274I TYR* 1.3 64.0 + - + +
275I GLY 3.4 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 274 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238I GLU 5.0 1.5 + - - -
241I LEU* 3.9 19.7 - - + -
242I GLU* 3.9 40.2 + - + +
245I ALA* 3.5 26.7 - - + +
246I ASP* 6.0 0.7 - - - -
270I LEU* 3.0 46.5 + - + +
271I ALA 3.6 7.4 - - - +
273I ASP* 1.3 78.4 - - + +
275I GLY* 1.3 62.7 + - - +
276I LEU* 3.7 19.7 - - + +
----------------------------------------------------------
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