Contacts of the helix formed by residues 278 - 293 (chain A) in PDB entry 2P2B
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 278 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 3.7 30.1 - - + +
77A LEU* 4.6 22.0 - - + +
253A MET* 4.7 7.8 - - + +
254A ASN 4.0 9.0 + - - +
255A ALA 3.2 5.3 + - - -
257A ASP* 2.9 21.1 + - - +
258A PRO 4.3 1.2 + - - -
259A LEU* 3.8 20.1 + - + +
277A THR* 1.3 80.7 - - - +
279A GLY* 1.3 59.7 + - - +
280A GLY 3.8 0.4 - - - -
281A TYR* 3.9 1.6 - - - +
282A LEU* 3.1 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 279 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 4.1 1.0 - - - +
48A TRP* 3.9 21.3 - - - -
70A TYR* 4.3 5.6 - - - -
75A LEU* 4.0 11.7 - - - -
255A ALA* 2.9 21.8 + - - +
278A THR* 1.3 69.2 - - - +
280A GLY* 1.3 64.6 + - - +
282A LEU* 3.2 3.3 + - - +
283A VAL* 2.9 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A TRP* 4.4 2.5 + - - -
70A TYR* 3.9 17.3 - - - -
255A ALA 4.6 1.0 + - - -
277A THR* 5.3 0.2 + - - -
278A THR 5.2 0.2 - - - +
279A GLY* 1.3 73.3 - - - +
281A TYR* 1.3 62.3 + - - +
284A TYR* 2.9 27.4 + - - +
471A PRO* 3.1 33.0 - - - +
475A ARG* 4.1 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A LEU* 3.5 29.4 - - + -
260A PHE* 3.5 22.3 - + - -
276A HIS* 3.7 25.4 - + + +
277A THR* 3.2 22.8 - - - +
278A THR 3.8 1.3 + - - +
279A GLY 3.2 0.4 - - - -
280A GLY* 1.3 76.2 - - - +
282A LEU* 1.3 65.5 + - + +
284A TYR* 3.7 2.1 - - - +
285A ALA* 2.9 32.3 + - + +
310A VAL* 5.6 0.2 - - + -
313A HIS* 3.6 6.1 - - - +
314A SER* 2.8 46.1 + - - -
318A TYR* 3.7 20.6 - + + -
419A GLY* 3.6 19.0 - - - -
471A PRO 3.5 3.2 + - - -
472A GLY* 4.0 9.6 - - - -
475A ARG* 4.8 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 3.9 31.1 - - + +
75A LEU* 4.7 3.1 - - + -
77A LEU* 3.8 42.0 - - + +
80A ASN* 3.9 20.0 - - + +
81A CYS* 4.6 1.3 - - - -
278A THR 3.1 17.4 + - - +
281A TYR* 1.3 83.6 - - + +
283A VAL* 1.3 66.0 + - - +
285A ALA* 4.4 2.9 - - + +
286A ALA* 3.1 24.4 + - - +
318A TYR* 4.1 31.4 - - + +
322A ALA* 4.3 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A TRP* 4.0 15.0 - - + -
42A GLN 4.1 2.9 - - - +
43A GLY* 3.9 22.9 - - - -
45A ILE* 4.4 2.5 - - + -
46A LEU* 3.6 22.4 - - + +
48A TRP* 3.9 7.6 - - + -
70A TYR* 3.5 36.8 - - + +
279A GLY 2.9 20.2 + - - +
280A GLY 3.8 3.6 - - - +
282A LEU* 1.3 74.5 - - - +
284A TYR* 1.3 57.9 + - - +
286A ALA* 4.0 1.0 - - - +
287A THR* 2.6 46.7 + - - +
471A PRO* 4.9 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A TRP* 3.6 35.0 - + - -
280A GLY 2.9 19.3 + - - +
281A TYR 3.7 1.6 - - - +
283A VAL* 1.3 80.2 - - - +
285A ALA* 1.3 49.9 + - - +
287A THR* 4.0 2.4 - - - -
288A THR* 2.6 49.3 + - + +
419A GLY 5.9 0.2 - - - -
420A GLY* 3.7 29.2 - - - -
421A PHE 2.7 29.6 + - - -
422A MET* 3.9 0.9 - - - -
441A PHE* 3.6 13.0 - + - -
442A PHE 4.0 2.2 - - - -
444A VAL* 3.3 23.2 - - - +
470A TRP* 3.8 20.2 - + + -
471A PRO* 3.9 13.5 - - + -
472A GLY* 3.5 21.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A TYR* 2.9 32.3 + - + +
282A LEU* 4.1 6.5 - - + +
283A VAL 3.5 0.2 - - - -
284A TYR* 1.3 70.8 - - - +
286A ALA* 1.3 60.7 + - - +
288A THR* 3.2 5.5 + - - -
289A PHE* 3.0 32.7 + - - +
314A SER* 4.1 30.3 - - - +
315A TYR* 3.8 6.2 - - - -
319A GLY* 3.7 11.4 - - - +
419A GLY 5.0 2.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ILE* 3.8 17.2 - - + +
46A LEU* 4.3 10.1 - - + -
84A ARG* 5.7 0.2 - - - +
282A LEU 3.1 17.3 + - - +
283A VAL 4.0 2.0 - - - +
285A ALA* 1.3 77.1 - - - +
287A THR* 1.3 58.7 + - - +
289A PHE* 4.5 0.2 - - - -
290A LYS* 3.1 31.0 + - - +
319A GLY* 4.1 7.3 - - - -
322A ALA* 3.8 23.8 - - + -
323A CYS* 3.5 14.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A PHE* 5.8 0.7 - - + -
39A TRP* 4.2 9.6 - - + -
42A GLN* 3.0 44.5 + - + +
45A ILE* 3.9 12.1 - - - +
283A VAL* 2.6 26.1 + - - +
284A TYR* 4.0 2.5 - - - -
286A ALA* 1.3 78.3 - - - +
288A THR* 1.3 61.2 + - - +
290A LYS* 3.8 0.4 - - - +
291A TYR* 3.2 43.7 + - + +
441A PHE* 4.0 17.9 - - + -
442A PHE* 5.3 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A TYR* 2.6 43.7 + - + +
285A ALA 3.2 3.5 + - - -
287A THR* 1.3 71.3 - - - +
289A PHE* 1.3 67.0 + - - +
292A VAL* 3.0 31.0 + - - +
315A TYR* 2.6 25.1 + - - +
421A PHE* 3.7 23.3 - - + +
441A PHE* 3.4 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A ALA 3.0 21.1 + - - +
286A ALA 3.9 1.6 - - - +
288A THR* 1.3 76.3 + - - +
290A LYS* 1.3 68.0 + - - +
293A PHE* 3.2 47.5 + + + +
295A TYR* 3.5 37.0 - + + +
301A TYR* 3.7 42.8 - + - -
315A TYR* 3.9 11.3 - + + -
319A GLY 3.8 12.6 - - - -
320A PRO* 3.8 17.9 - - + -
323A CYS* 3.8 26.5 - - + -
325A ALA* 3.8 20.9 - - + -
353A ILE* 5.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 3.5 20.5 - - + +
42A GLN* 5.7 0.2 + - - -
45A ILE* 4.1 25.0 - - + +
286A ALA 3.1 19.7 + - - +
287A THR 3.8 3.6 - - - +
288A THR 3.3 0.2 - - - -
289A PHE* 1.3 83.0 - - - +
291A TYR* 1.3 85.7 + - + +
294A ASP* 3.1 5.0 + - - -
295A TYR* 2.9 40.1 + - + +
323A CYS* 4.0 12.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 3.8 28.0 - - + -
19A ILE* 3.6 32.8 - - + +
27A LYS* 4.3 11.5 + - - -
38A PHE* 6.6 0.2 - + - -
42A GLN* 3.9 24.3 + - - -
287A THR* 3.2 42.9 + - + +
290A LYS* 1.3 103.3 + - + +
292A VAL* 1.3 65.5 + - - +
294A ASP* 3.5 9.2 + - - +
426A LEU* 3.9 23.5 - - + +
427A PRO* 3.5 15.6 - - - +
441A PHE* 4.4 10.5 - + + -
442A PHE* 4.7 3.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A THR 3.0 18.8 + - - +
291A TYR* 1.3 76.7 - - - +
293A PHE* 1.3 59.0 - - + +
382A ILE* 4.6 0.3 - - - +
410A VAL* 3.6 26.1 - - + +
412A THR* 3.9 1.3 - - + -
421A PHE* 3.6 25.8 - - + -
424A THR* 3.5 42.0 - - + +
425A PRO 3.9 6.5 - - - +
426A LEU* 4.2 2.9 - - + -
427A PRO* 3.2 25.4 - - - +
441A PHE* 3.9 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A PHE* 3.2 44.4 + + + +
292A VAL* 1.3 75.1 - - + +
294A ASP* 1.3 71.5 + - - +
295A TYR* 3.3 2.2 + - + +
301A TYR* 3.5 17.9 - + + -
315A TYR* 4.3 1.8 - + - -
353A ILE* 3.5 41.6 - - + +
355A TYR* 3.4 43.5 - + + -
382A ILE* 3.8 22.6 - - + +
384A GLY* 4.6 2.5 - - - -
410A VAL* 3.8 26.5 - - + -
421A PHE* 3.5 31.4 - + - -
----------------------------------------------------------
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