Contacts of the helix formed by residues 286 - 300 (chain D) in PDB entry 2ABJ
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 286 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D ARG* 3.7 1.3 - - - -
260D ASN* 3.2 22.5 - - - +
284D LEU* 2.8 11.5 + - - -
285D PRO* 1.3 74.1 - - - +
287D VAL* 1.3 61.8 + - - -
288D THR 3.4 1.3 - - - -
289D ARG* 3.4 6.7 + - - +
290D ARG* 3.1 25.1 + - - +
420D PLP 3.4 18.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 287 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D PHE* 4.3 9.6 - - + -
110D GLN* 3.8 30.7 - - + -
113D LEU* 3.7 33.2 - - + +
114D ASN* 4.2 20.2 - - - +
117D ARG* 3.6 10.3 - - - +
285D PRO 5.1 0.9 - - - +
286D GLY* 1.3 69.0 - - - -
288D THR* 1.3 60.6 + - - +
290D ARG* 3.2 8.4 + - - +
291D CYS* 2.9 31.4 + - - -
331D THR* 5.3 3.8 - - - +
420D PLP 2.8 19.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 288 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D PHE* 5.8 3.5 - - + -
287D VAL* 1.3 78.1 - - - +
289D ARG* 1.3 57.3 + - - +
291D CYS* 3.3 6.9 + - - +
292D ILE* 2.9 38.2 + - + +
329D SER* 3.9 13.7 - - - -
330D GLY 3.4 14.9 - - - -
331D THR* 3.6 6.2 + - - -
334D VAL* 3.4 32.3 - - + +
367D LEU* 4.0 22.2 - - + -
420D PLP 2.7 16.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 289 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260D ASN* 3.4 40.1 - - + +
262D PHE* 3.7 25.8 - - + -
276D THR* 3.8 10.0 + - - +
277D PRO 3.0 26.7 + - - -
278D PRO* 4.1 0.2 - - - +
279D LEU* 3.5 35.8 - - - +
283D ILE* 4.3 3.4 - - - +
284D LEU 4.3 2.2 - - - -
285D PRO* 5.2 1.0 - - - +
286D GLY 3.4 15.3 + - - +
288D THR* 1.3 77.2 - - - +
290D ARG* 1.3 68.4 + - - +
292D ILE* 3.3 3.6 + - - +
293D LEU* 2.9 49.5 + - + +
306D GLU* 2.7 29.1 + - - -
329D SER* 3.7 4.8 + - - -
420D PLP 4.3 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 290 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D GLN* 5.2 3.6 - - - +
113D LEU* 4.5 18.4 - - + -
279D LEU* 5.2 5.9 - - - +
286D GLY 3.1 11.5 + - - +
287D VAL* 3.4 11.2 - - - +
289D ARG* 1.3 98.2 - - - +
291D CYS* 1.3 58.1 + - - +
293D LEU* 3.3 32.9 + - - +
294D ASP* 2.9 60.3 + - - +
297D HIS* 5.2 5.5 + - - -
306D GLU* 4.3 9.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 291 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D PHE* 3.6 32.5 - - - -
110D GLN* 3.7 23.6 - - - -
287D VAL* 2.9 18.1 + - - +
288D THR* 3.6 9.6 - - - +
290D ARG* 1.3 76.9 - - - +
292D ILE* 1.3 57.8 + - - +
294D ASP* 3.4 2.5 + - - +
295D LEU* 2.9 34.5 + - - +
367D LEU* 3.9 11.4 - - + -
379D TRP* 3.5 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 292 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262D PHE* 3.7 28.9 - - + -
274D LEU* 4.0 10.5 - - + -
288D THR* 2.9 20.6 + - + +
289D ARG 3.7 4.3 - - - +
291D CYS* 1.3 72.3 - - - +
293D LEU* 1.3 61.1 + - - +
295D LEU* 3.5 8.4 + - - +
296D ALA* 2.9 28.6 + - + +
299D TRP* 5.7 0.5 - - - -
327D PHE* 4.2 3.8 - - + -
329D SER* 3.6 30.5 - - - -
335D VAL* 4.1 8.7 - - + -
363D ILE* 3.7 46.4 - - + -
367D LEU* 4.3 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 293 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262D PHE* 3.7 23.8 - - + -
274D LEU* 5.0 5.4 - - + +
275D ALA 6.3 0.2 - - - -
276D THR* 4.0 15.3 - - + -
289D ARG* 2.9 56.4 + - + +
290D ARG* 3.4 25.8 - - - +
292D ILE* 1.3 74.1 - - - +
294D ASP* 1.3 58.7 + - - +
296D ALA* 3.4 2.7 + - - +
297D HIS* 2.9 42.8 + - + +
304D VAL* 3.8 23.8 - - + -
305D SER 5.9 0.9 - - - +
306D GLU* 4.1 13.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 294 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D GLN* 5.2 1.0 - - - +
290D ARG* 2.9 48.6 + - - +
291D CYS 3.5 5.4 - - - +
293D LEU* 1.3 75.4 - - - +
295D LEU* 1.3 57.4 + - + +
297D HIS* 3.4 8.0 + - - +
298D GLN* 2.9 29.8 + - - +
379D TRP* 3.8 27.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 295 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291D CYS 2.9 22.4 + - - +
292D ILE* 3.7 7.6 - - - +
294D ASP* 1.3 77.2 - - - +
296D ALA* 1.3 57.2 + - - +
298D GLN* 3.0 27.0 + - - +
299D TRP* 2.9 58.5 + - + -
363D ILE* 5.7 4.0 - - + +
366D LYS* 3.9 25.6 - - + -
367D LEU* 3.8 30.1 - - + -
370D ILE* 5.1 2.5 - - + -
379D TRP* 3.7 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 296 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274D LEU* 3.9 14.8 - - + -
292D ILE* 2.9 18.8 + - + +
293D LEU 3.9 2.2 - - - +
295D LEU* 1.3 75.4 - - - +
297D HIS* 1.3 62.5 + - - +
299D TRP* 3.7 15.3 + - + +
300D GLY* 3.4 16.8 + - - -
301D GLU 4.8 0.9 + - - -
302D PHE* 3.8 23.3 - - + +
304D VAL* 3.6 26.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 297 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290D ARG* 5.2 5.0 + - - -
293D LEU* 2.9 34.6 + - + +
294D ASP* 3.6 8.4 + - - +
296D ALA* 1.3 76.5 - - - +
298D GLN* 1.3 63.1 + - - +
300D GLY* 3.4 13.0 + - - -
304D VAL* 3.6 40.1 + - + +
306D GLU* 5.5 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 298 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294D ASP 2.9 14.5 + - - +
295D LEU* 3.0 32.3 + - - +
297D HIS* 1.3 74.1 - - - +
299D TRP* 1.3 80.1 + - + +
300D GLY* 3.4 1.0 + - - -
366D LYS* 5.7 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 299 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292D ILE* 5.7 0.4 - - + -
295D LEU* 2.9 39.5 + - + +
296D ALA* 3.9 21.5 - - + +
297D HIS 3.4 0.2 - - - -
298D GLN* 1.3 95.8 - - + +
300D GLY* 1.3 66.2 + - - +
301D GLU* 3.3 25.8 + - + +
302D PHE* 4.2 11.0 - + + -
359D LEU* 3.8 24.2 - - + -
362D ARG* 3.3 53.3 - - + +
363D ILE* 4.2 21.1 - - + -
366D LYS* 4.3 20.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 300 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296D ALA 3.4 10.6 + - - -
297D HIS 3.9 10.1 - - - -
298D GLN 3.3 3.0 - - - -
299D TRP* 1.3 78.6 - - - +
301D GLU* 1.3 60.0 + - - +
302D PHE 3.6 5.4 - - - -
----------------------------------------------------------
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