Contacts of the helix formed by residues 280 - 296 (chain D) in PDB entry 1OJ7
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 280 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D PRO* 5.6 5.2 - - - +
68D ASN* 5.3 6.2 + - - +
186D ARG* 2.9 44.2 + - - +
187D GLN* 3.6 7.8 + - - -
190D ASN* 2.9 31.6 + - - +
278D GLY 4.6 3.3 - - - +
279D LEU* 1.3 74.5 - - - +
281D HIS* 1.3 68.6 + - - +
283D GLN* 3.0 33.2 + - + +
284D THR* 3.2 8.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 281 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D ASN* 4.8 12.7 + - - +
142D THR* 5.6 3.1 - - + -
160D LYS* 4.9 7.1 - - - +
194D ASP* 3.2 39.5 + - - -
198D HIS* 4.6 1.0 + - - -
267D HIS* 3.2 31.8 + + - -
271D HIS* 3.9 25.7 - + - -
274D THR* 3.8 11.6 + - - +
279D LEU 3.5 1.8 + - - -
280D ASP* 1.3 70.4 - - - +
282D ALA* 1.3 61.8 + - - +
284D THR* 2.6 27.4 + - - -
285D LEU* 3.3 20.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 282 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190D ASN* 3.2 49.8 - - + +
193D VAL* 3.7 14.9 - - + +
194D ASP* 4.3 8.1 - - + +
280D ASP* 3.2 2.0 - - - +
281D HIS* 1.3 77.0 - - - +
283D GLN* 1.3 64.6 + - - +
285D LEU* 3.2 13.4 + - - +
286D ALA* 3.0 23.2 + - - +
339D VAL* 4.6 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 283 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186D ARG* 3.9 21.0 + - - +
190D ASN* 4.0 9.1 + - - +
279D LEU* 3.8 14.3 - - + +
280D ASP* 3.0 49.1 + - + +
282D ALA* 1.3 78.8 - - - +
284D THR* 1.3 60.6 + - - +
286D ALA* 3.4 3.1 + - - +
287D ILE* 3.2 29.3 + - - +
338D GLY 6.0 0.4 + - - -
339D VAL* 4.0 13.4 - - + +
340D PRO* 5.9 1.4 - - - +
346D TYR* 3.6 37.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 284 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270D GLY* 3.3 34.6 + - - +
273D LEU* 3.6 19.1 - - + -
274D THR* 3.3 24.2 - - - +
279D LEU* 3.7 13.7 - - + -
280D ASP 3.5 8.1 - - - +
281D HIS* 2.6 21.7 + - - -
283D GLN* 1.3 76.7 - - - +
285D LEU* 1.3 58.6 + - - +
287D ILE* 3.5 9.6 + - - +
288D VAL* 3.1 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 285 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193D VAL* 4.6 0.7 - - + -
194D ASP* 3.3 33.2 - - - +
197D VAL* 3.9 26.7 - - + -
266D THR* 3.9 15.0 - - + +
267D HIS* 3.6 43.3 - - + +
281D HIS* 3.5 31.6 - - + +
282D ALA* 3.2 10.0 + - - +
284D THR* 1.3 80.1 - - - +
286D ALA* 1.3 58.7 + - - +
289D LEU* 2.9 36.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 286 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193D VAL* 4.5 3.7 - - + +
282D ALA 3.0 8.8 + - - +
283D GLN 3.7 3.4 - - - +
285D LEU* 1.3 76.6 - - - +
287D ILE* 1.3 57.0 + - - +
290D PRO* 3.1 20.3 - - - +
334D PHE* 3.7 27.1 - - + -
339D VAL* 3.5 35.7 - - + +
340D PRO 3.9 7.0 - - - +
341D THR* 3.3 17.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 287 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273D LEU* 4.6 2.7 - - + -
279D LEU* 3.7 23.6 - - + -
283D GLN 3.2 18.2 + - - +
284D THR* 3.6 7.9 - - - +
285D LEU 3.2 0.2 - - - -
286D ALA* 1.3 77.5 - - - +
288D VAL* 1.3 69.7 + - + +
290D PRO* 3.5 9.4 - - - +
291D ALA* 4.2 3.1 - - - +
331D ARG* 5.1 0.7 + - - -
340D PRO 4.1 0.4 - - - +
341D THR 3.6 21.8 - - - +
342D HIS 4.1 2.0 - - - +
343D LEU* 4.0 26.0 - - + -
346D TYR* 3.5 33.0 - - + -
383D TYR* 6.4 0.2 - - + -
386D ALA* 3.6 34.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 288 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266D THR* 3.9 31.4 - - + +
269D LEU* 3.9 33.2 - - + -
270D GLY 4.5 3.4 - - - +
273D LEU* 3.9 21.8 - - + -
284D THR 3.1 19.4 + - - +
287D ILE* 1.3 80.1 - - + +
289D LEU* 1.3 67.4 + - - +
291D ALA* 3.2 7.8 + - - +
292D LEU* 2.9 22.7 + - + -
382D ILE* 4.1 7.6 - - + -
383D TYR* 4.4 9.9 - - + -
386D ALA* 5.0 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 289 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196D PHE* 5.0 1.6 - - + -
197D VAL* 4.3 8.3 - - + -
200D VAL* 4.0 20.6 - - + -
201D GLU* 5.7 2.0 - - - +
263D ASP* 6.2 0.2 - - - +
266D THR* 3.6 29.3 - - + +
285D LEU 2.9 23.4 + - - +
288D VAL* 1.3 72.4 - - - +
290D PRO* 1.3 59.7 - - + +
292D LEU* 3.3 2.1 + - + +
293D TRP* 3.0 78.6 + - + +
330D THR* 4.2 6.7 - - + -
334D PHE* 4.0 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 290 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286D ALA* 3.1 25.4 - - - +
287D ILE 3.5 8.3 - - - +
289D LEU* 1.3 97.8 - - + +
291D ALA* 1.3 59.8 + - - +
293D TRP* 3.9 5.0 - - + +
294D ASN* 3.2 22.7 + - - +
327D ILE* 3.9 25.1 - - + +
330D THR* 5.9 2.2 - - + -
331D ARG* 3.4 53.2 + - + +
334D PHE* 5.1 4.9 - - + -
341D THR* 4.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 291 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287D ILE 4.2 2.4 + - - +
288D VAL 3.2 8.0 + - - +
290D PRO* 1.3 80.5 - - - +
292D LEU* 1.3 62.6 + - - +
294D ASN* 3.4 7.0 + - - +
295D GLU* 3.1 21.7 + - - +
331D ARG* 4.4 5.5 - - - +
382D ILE* 3.6 29.1 - - + +
385D ALA* 4.3 12.9 - - + +
386D ALA* 4.1 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 292 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263D ASP* 3.7 21.1 - - - +
265D ALA* 3.6 30.5 - - + -
266D THR* 3.7 23.3 - - - +
269D LEU* 4.5 6.3 - - + -
288D VAL* 2.9 19.9 + - + +
289D LEU* 3.8 3.1 - - + +
291D ALA* 1.3 72.9 - - - +
293D TRP* 1.3 65.6 + - + +
295D GLU* 3.2 1.4 + - - +
296D LYS* 2.8 40.6 + - + +
300D LYS* 3.8 15.9 - - - -
374D ILE* 4.0 3.8 - - + -
382D ILE* 3.9 33.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 293 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200D VAL* 3.7 31.2 + - + +
204D VAL* 3.8 24.6 + - + +
263D ASP* 5.4 0.8 + - - -
289D LEU* 3.0 42.5 + - + +
290D PRO* 3.9 6.5 - - + +
292D LEU* 1.3 81.2 - - + +
294D ASN* 1.3 58.7 + - - +
296D LYS* 3.4 2.9 - - - +
297D ARG* 2.9 31.4 + - - +
300D LYS* 3.7 27.1 - - + +
304D LEU* 3.8 19.9 - - + +
307D TYR* 3.6 36.1 - + - -
326D ALA 4.9 0.4 - - - -
327D ILE* 4.0 26.0 - - + -
330D THR* 3.5 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 294 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290D PRO 3.2 15.0 + - - +
291D ALA* 3.7 6.7 + - - +
292D LEU 3.3 0.2 - - - -
293D TRP* 1.3 78.4 - - - +
295D GLU* 1.3 64.3 + - - +
297D ARG* 3.0 51.3 + - - +
327D ILE* 3.8 13.6 - - + +
385D ALA* 5.8 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 295 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291D ALA 3.1 15.0 + - - +
292D LEU 3.5 7.6 - - - +
294D ASN* 1.3 78.7 - - - +
296D LYS* 1.3 66.0 + - + +
297D ARG* 3.4 1.5 + - - +
298D ASP* 3.7 8.8 - - - +
378D VAL* 3.7 26.2 - - + +
381D ARG* 2.8 53.1 + - - +
382D ILE* 3.8 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 296 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292D LEU* 2.8 28.6 + - + +
293D TRP 3.4 2.7 - - - -
295D GLU* 1.3 88.4 - - + +
297D ARG* 1.3 58.5 + - - +
298D ASP* 3.1 9.4 + - - +
299D THR* 3.4 25.1 + - - +
300D LYS* 2.9 47.2 + - + +
369D GLY* 6.3 0.2 - - - -
370D GLU* 6.1 1.1 - - - -
371D ASN* 5.1 2.2 - - - +
373D ASP* 2.7 44.3 + - - -
374D ILE* 3.9 31.1 - - + +
378D VAL* 4.8 4.5 - - + +
382D ILE* 5.2 0.2 - - + -
----------------------------------------------------------
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