Contacts of the helix formed by residues 244 - 261 (chain D) in PDB entry 5DO7
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 244 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C SER* 4.8 16.2 - - - +
308C ASP* 2.7 32.0 - - - +
309C THR* 5.5 1.7 - - - +
243D LEU* 1.3 74.6 - - - +
245D SER* 1.3 67.9 + - - +
247D THR* 2.5 43.2 + - - -
248D ALA* 2.8 11.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 245 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C ASP* 4.9 1.5 + - - -
303C ASP* 3.9 20.0 + - - -
243D LEU 4.2 0.2 + - - -
244D ASP* 1.3 71.5 - - - +
246D PHE* 1.3 65.4 + - - +
248D ALA* 3.0 20.1 + - - +
249D HIS* 3.2 14.4 + - - +
273D ARG* 3.6 30.9 - - - +
275D ASP* 4.0 12.1 - - - +
276D ILE* 3.7 11.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 246 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C ASP* 5.4 6.1 + - - -
306C SER 4.7 8.5 - - - -
308C ASP* 3.1 64.4 - - + +
310C GLN* 3.8 23.6 - - + -
314C ARG* 3.6 50.1 + - + -
318C THR* 4.4 14.8 - - + -
321C ARG* 6.0 2.5 - - - -
245D SER* 1.3 78.6 - - - +
247D THR* 1.3 57.3 + - - +
249D HIS* 3.7 8.8 - - - +
250D ASN* 3.1 22.1 + - - -
275D ASP* 5.5 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 247 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C ASP* 4.5 1.7 + - - -
310C GLN* 3.2 28.6 + - - +
216D GLY* 4.4 8.7 - - - -
220D ARG* 4.0 18.2 - - - +
243D LEU* 4.0 21.5 - - + -
244D ASP* 2.5 33.7 + - - -
246D PHE* 1.3 71.6 - - - +
248D ALA* 1.3 63.7 + - - -
249D HIS 3.2 2.0 - - - -
250D ASN* 2.8 10.0 + - + +
251D LEU* 2.8 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 248 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240D THR* 3.9 29.6 - - + +
243D LEU* 4.5 9.5 - - + +
244D ASP 2.8 16.0 + - - +
245D SER* 3.0 16.4 + - - +
247D THR* 1.3 69.7 - - - +
249D HIS* 1.3 54.8 + - - +
251D LEU* 3.1 7.7 + - - +
252D VAL* 2.8 39.1 + - - +
273D ARG* 6.2 0.4 - - - -
276D ILE* 4.1 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 249 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C ARG* 4.4 17.1 + - - -
245D SER 3.2 2.9 + - - +
246D PHE 3.7 12.6 - - - +
248D ALA* 1.3 76.6 - - - +
250D ASN* 1.3 76.1 + - - +
251D LEU 3.2 0.2 + - - -
252D VAL* 3.4 8.9 - - - +
253D LYS* 2.8 61.5 + - - +
275D ASP* 3.0 37.3 + - - +
276D ILE* 4.6 0.2 - - - +
279D LEU* 3.1 30.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 250 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310C GLN* 3.7 29.2 - - - +
314C ARG* 4.0 17.0 + - - +
196D ARG* 4.6 4.8 + - - +
220D ARG* 3.0 16.2 + - - +
246D PHE* 3.1 23.8 + - - -
247D THR* 2.8 17.3 + - + +
249D HIS* 1.3 89.1 - - - +
251D LEU* 1.3 50.5 + - - +
253D LYS* 4.3 9.1 + - - +
254D THR* 2.6 28.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 251 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D LEU* 6.4 0.2 - - + -
216D GLY 5.6 0.7 - - - +
219D ARG* 4.1 12.6 - - + -
220D ARG* 3.7 33.2 - - + +
223D ILE* 4.1 18.4 - - + -
239D PRO* 3.9 40.6 - - + +
240D THR* 4.5 6.1 - - + +
243D LEU* 4.2 18.4 - - + -
247D THR 2.8 10.3 + - - +
248D ALA 3.5 6.3 - - - +
250D ASN* 1.3 75.6 - - - +
252D VAL* 1.3 63.5 + - - +
253D LYS 3.1 1.6 - - - -
254D THR* 2.8 24.7 + - + -
255D LEU* 2.8 20.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 252 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D MET* 4.4 7.7 - - - +
239D PRO* 6.3 0.9 - - + -
240D THR* 5.0 9.0 - - + -
248D ALA 2.8 17.9 + - - +
249D HIS* 3.4 12.3 - - - +
251D LEU* 1.3 73.9 - - - +
253D LYS* 1.3 58.8 + - - +
255D LEU* 3.2 14.6 + - + +
256D SER* 2.8 27.2 + - - -
267D ILE* 4.2 24.7 - - + -
269D LEU* 5.6 2.0 - - + -
276D ILE* 4.2 26.2 - - + -
279D LEU* 3.8 28.7 - - + +
280D PHE* 5.2 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 253 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C ARG* 5.9 1.8 - - - +
196D ARG* 5.4 7.4 - - - +
249D HIS* 2.8 53.1 + - - +
250D ASN* 4.6 7.1 + - - -
252D VAL* 1.3 76.4 - - - +
254D THR* 1.3 54.5 + - - +
256D SER* 3.4 8.8 + - - -
257D ARG* 2.8 43.1 + - + +
279D LEU* 4.3 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 254 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194D GLU* 4.1 2.2 - - - +
195D LEU* 3.6 36.7 + - + +
196D ARG* 3.6 10.9 + - - +
220D ARG* 3.8 9.4 + - + -
250D ASN 2.6 25.2 + - - -
251D LEU* 2.8 15.3 + - + -
253D LYS* 1.3 74.3 - - - +
255D LEU* 1.3 60.8 + - - +
257D ARG* 3.7 28.4 - - - +
258D LEU* 2.8 30.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 255 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D MET* 4.6 2.5 - - - -
195D LEU* 6.2 0.4 - - + -
223D ILE* 4.0 21.8 - - + -
234D LEU* 5.0 1.1 - - + -
236D LEU* 3.2 39.0 - - + -
239D PRO* 4.0 19.3 - - + -
240D THR* 6.5 0.2 - - + -
251D LEU* 2.8 24.5 + - + +
252D VAL* 3.2 23.1 + - + +
254D THR* 1.3 74.1 - - + +
256D SER* 1.3 60.3 + - - +
258D LEU* 3.1 21.5 - - + +
259D ALA* 2.8 27.1 + - - +
265D VAL* 4.0 11.6 - - + +
267D ILE* 4.1 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 256 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D MET* 3.4 27.9 - - - +
252D VAL 2.8 11.5 + - - -
253D LYS* 3.5 15.0 - - - -
255D LEU* 1.3 74.5 - - - +
257D ARG* 1.3 54.8 + - - +
259D ALA* 2.9 6.5 + - - +
260D LYS* 2.8 40.4 + - - +
279D LEU* 4.7 10.7 + - - +
281D ASP* 5.7 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 257 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D GLN 4.8 3.4 - - - +
25D ASP* 3.3 16.8 + - - +
26D ARG 2.9 28.9 + - - +
27D LEU* 3.5 12.0 - - + +
28D PHE* 4.5 6.9 - - - -
194D GLU* 2.4 50.7 + - - +
196D ARG* 2.9 56.9 - - - +
253D LYS* 2.8 33.2 + - + +
254D THR* 3.2 16.3 + - - +
256D SER* 1.3 68.2 - - - +
258D LEU* 1.3 69.4 + - - +
260D LYS* 2.9 22.4 + - - +
261D GLY 3.3 6.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 258 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D SER* 5.1 0.2 - - - -
194D GLU* 4.0 20.9 + - + +
195D LEU* 4.3 15.0 - - + -
223D ILE* 4.4 4.0 - - + -
227D LEU* 3.9 34.1 - - + -
234D LEU* 3.8 23.3 - - + -
254D THR 2.8 17.3 + - - +
255D LEU* 3.1 26.2 - - + +
257D ARG* 1.3 70.4 - - - +
259D ALA* 1.3 53.4 + - - +
261D GLY* 2.8 23.4 + - - -
263D ARG* 3.1 50.4 - - + +
265D VAL* 5.1 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 259 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D SER 3.8 0.9 - - - +
98D GLY* 3.6 20.6 - - - +
100D MET* 4.1 14.4 - - + +
255D LEU 2.8 14.7 + - - +
256D SER* 2.9 19.5 + - - +
258D LEU* 1.3 73.3 - - - +
260D LYS* 1.3 61.4 + - + +
261D GLY 3.2 0.7 + - - -
262D ASN 3.5 4.3 + - - -
263D ARG 3.3 17.1 - - - +
265D VAL* 3.4 29.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 260 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D LEU* 3.9 17.7 - - + -
98D GLY* 5.0 3.9 - - - -
256D SER* 2.8 25.0 + - - +
257D ARG* 2.9 12.6 + - - +
259D ALA* 1.3 71.0 - - - +
261D GLY* 1.3 57.6 + - - +
262D ASN* 3.0 6.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 261 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D LEU* 3.9 9.5 - - - +
29D SER 3.7 14.1 - - - -
30D SER* 3.1 29.7 - - - -
31D GLU 3.4 0.5 + - - -
257D ARG 3.3 3.2 + - - -
258D LEU* 2.8 12.3 + - - -
260D LYS* 1.3 75.6 - - - +
262D ASN* 1.3 65.8 + - - +
263D ARG* 3.1 10.3 + - - -
----------------------------------------------------------
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