Contacts of the helix formed by residues 244 - 260 (chain D) in PDB entry 1XDM
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 THR 244 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243D TYR* 1.3 73.1 - - - +
245D PRO* 1.3 65.2 - - - +
246D GLU* 2.7 21.2 + - - +
247D GLN* 2.7 43.8 + - - +
248D VAL* 2.9 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 245 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243D TYR 4.3 2.0 - - - +
244D THR* 1.3 87.4 - - - +
246D GLU* 1.3 67.4 + - - +
248D VAL* 3.1 4.9 + - + +
249D ALA* 2.6 37.6 + - - +
281D LEU* 4.5 17.5 - - + +
282D ASN* 3.9 23.6 - - - +
285D ALA* 3.8 17.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 246 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244D THR* 2.7 28.7 + - - +
245D PRO* 1.3 89.3 - - - +
247D GLN* 1.3 51.1 + - + +
249D ALA* 3.6 7.0 - - - +
250D MET* 2.6 38.5 + - - +
285D ALA* 4.7 6.6 - - + +
289D CYS* 4.7 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 247 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198D LEU* 4.1 9.9 - - + +
243D TYR* 3.2 23.0 - - + +
244D THR* 2.7 56.4 + - - +
246D GLU* 1.3 77.2 - - + +
248D VAL* 1.3 65.0 + - - +
250D MET* 3.4 6.2 - - - +
251D ALA* 2.9 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 248 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198D LEU* 4.9 2.5 - - - -
232D MET* 4.6 6.3 - - + -
233D VAL 3.2 13.5 - - - +
234D THR* 3.1 37.2 - - + -
243D TYR* 3.5 24.9 - - + +
244D THR 2.9 17.9 + - - +
245D PRO* 3.4 9.4 - - + +
247D GLN* 1.3 77.4 - - - +
249D ALA* 1.3 53.7 + - - +
251D ALA* 4.1 0.2 - - - -
252D THR* 2.2 42.3 + - - +
282D ASN* 4.1 21.8 - - + +
286D ILE* 6.0 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 249 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245D PRO 2.6 21.4 + - - +
246D GLU* 3.7 6.1 - - - +
248D VAL* 1.3 74.3 - - - +
250D MET* 1.3 56.7 + - - +
252D THR* 4.0 0.4 - - - -
253D VAL* 2.8 36.4 + - - +
282D ASN 4.6 0.6 + - - +
285D ALA* 3.7 7.0 - - + -
286D ILE* 3.3 48.0 - - + +
289D CYS* 3.9 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 250 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C SO4 5.3 7.2 - - - +
246D GLU 2.6 24.2 + - - +
247D GLN* 3.4 9.9 - - - +
249D ALA* 1.3 70.7 - - - +
251D ALA* 1.3 58.2 + - - +
253D VAL* 4.0 0.5 - - - +
254D THR* 2.5 62.7 + - + +
289D CYS* 3.5 19.1 - - - -
290D PRO* 5.4 6.1 - - - -
291D LEU* 3.4 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 251 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198D LEU* 4.3 14.4 - - + -
202D GLN* 3.1 31.8 + - + +
233D VAL* 3.4 22.1 - - + +
247D GLN 2.9 18.2 + - - +
248D VAL 4.1 0.7 - - - +
250D MET* 1.3 74.7 - - - +
252D THR* 1.3 63.7 + - - +
254D THR* 3.3 3.1 - - - -
255D ALA* 3.0 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 252 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231D ASN 4.9 0.4 - - - +
232D MET* 4.1 1.5 - - - +
233D VAL* 3.0 39.0 + - + +
248D VAL* 2.2 30.9 + - - +
249D ALA* 3.5 7.4 - - - -
251D ALA* 1.3 79.8 - - - +
253D VAL* 1.3 63.1 + - - +
255D ALA* 3.9 2.1 - - - +
256D LEU* 3.3 23.8 + - + +
269D PHE* 3.4 39.0 - - + -
286D ILE* 4.0 10.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 253 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D ALA 2.8 23.1 + - - +
252D THR* 1.3 71.5 - - + +
254D THR* 1.3 69.1 + - - +
256D LEU* 3.2 7.3 + - - -
257D HIS* 2.8 24.8 + - + +
286D ILE* 3.4 41.5 - - + +
289D CYS* 4.0 11.2 - - + -
291D LEU* 4.0 16.8 - - + -
292D PRO 3.9 10.8 - - - +
293D LYS* 3.8 23.1 - - + -
295D TRP* 5.0 4.0 - - + -
297D LEU* 4.5 6.7 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
224C GLU* 4.7 4.0 - - - +
365C SO4 3.7 5.5 + - - +
202D GLN* 3.0 15.3 - - - +
250D MET* 2.5 51.4 + - + +
251D ALA* 3.3 7.4 - - - -
253D VAL* 1.3 75.3 - - - +
255D ALA* 1.3 65.2 + - - +
257D HIS* 2.5 24.8 + - - -
258D ARG* 3.0 39.9 - - - +
291D LEU* 3.3 11.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 255 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202D GLN* 4.2 8.5 - - + +
205D THR* 4.6 12.6 - - + -
206D GLU* 3.3 40.2 - - + +
233D VAL* 5.0 2.2 - - + -
251D ALA 3.0 12.9 + - - +
252D THR 3.9 4.0 - - - +
254D THR* 1.3 79.2 - - - +
256D LEU* 1.3 55.2 + - - +
258D ARG* 2.8 32.4 + - - +
259D THR* 3.0 13.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 256 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D THR* 5.9 0.9 - - + -
209D LEU* 4.0 14.1 - - + -
228D LEU* 4.0 10.3 - - + -
230D PRO* 4.7 4.9 - - + -
231D ASN 5.7 0.2 - - - +
233D VAL* 6.4 0.2 - - + -
252D THR* 3.3 20.8 + - + +
253D VAL* 3.2 4.9 + - - +
255D ALA* 1.3 80.3 - - + +
257D HIS* 1.3 57.1 + - - +
259D THR* 3.0 7.6 + - - -
260D VAL* 2.8 63.0 + - + +
267D ILE* 3.9 18.2 - - + -
269D PHE* 3.4 38.1 - - + -
295D TRP* 3.5 11.4 - - + -
297D LEU* 4.4 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 257 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C GLU* 3.6 23.6 + - + +
262C ALA* 2.7 42.6 + - + +
263C ALA* 2.7 55.1 + - + +
253D VAL 2.8 15.9 + - - +
254D THR* 2.5 36.6 + - + -
255D ALA 2.9 0.6 + - - -
256D LEU* 1.3 74.0 - - - +
258D ARG* 1.3 51.8 + - + +
259D THR 3.6 0.2 - - - -
260D VAL 4.4 1.3 - - - -
291D LEU* 4.3 13.0 - - + +
292D PRO* 3.6 42.6 - - + +
295D TRP* 3.7 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 258 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C ASN* 4.8 6.2 + - - +
221C VAL 5.9 0.4 + - - -
222C TYR* 4.5 13.9 - - - +
223C LEU* 3.4 28.4 - - + +
224C GLU* 2.7 43.3 + - - -
261C PRO* 3.3 28.1 - - - +
263C ALA* 3.4 9.6 - - + -
365C SO4 2.5 30.9 + - - -
202D GLN* 2.9 14.8 + - - -
206D GLU* 3.4 26.8 + - - +
210D ALA* 5.2 0.3 - - - +
254D THR* 3.0 18.3 + - - +
255D ALA* 2.8 18.8 + - - +
257D HIS* 1.3 76.9 - - - +
259D THR* 1.3 61.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 259 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C ASN* 4.5 1.8 - - - +
259C THR 5.7 0.2 - - - +
261C PRO* 4.9 5.4 - - - +
206D GLU* 3.3 47.3 - - + +
209D LEU* 3.6 20.1 - - + +
210D ALA* 4.1 16.6 - - + +
213D TYR* 4.1 9.2 - - - +
255D ALA 3.0 18.2 + - - +
256D LEU* 3.0 12.8 - - - -
258D ARG* 1.3 86.1 - - + +
260D VAL* 1.3 73.8 + - - +
261D PRO* 3.5 10.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 260 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261C PRO* 5.3 2.0 - - - -
262C ALA* 4.4 5.5 + - - +
209D LEU* 3.7 4.5 - - + -
213D TYR* 3.5 29.4 - - + +
228D LEU* 3.7 5.6 - - + -
256D LEU* 2.8 46.6 + - + +
257D HIS 4.4 6.9 - - - +
259D THR* 1.3 82.3 + - - +
261D PRO* 1.4 70.5 - - + +
262D ALA 4.0 0.7 + - - -
264D VAL* 4.4 5.6 - - + -
267D ILE* 3.8 14.6 - - + -
295D TRP* 3.3 33.0 + - + +
----------------------------------------------------------
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