Contacts of the helix formed by residues 369 - 387 (chain B) in PDB entry 2XLR
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 369 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B VAL* 1.3 82.2 - - + +
370B ALA* 1.3 66.1 + - - +
371B GLU* 3.6 10.1 + - - +
372B GLU* 2.7 58.6 + - - +
373B MET* 3.1 17.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 370 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B TRP* 4.1 27.1 - - + -
368B VAL 4.1 0.8 + - - -
369B THR* 1.3 71.9 - - - +
371B GLU* 1.3 64.1 + - - +
373B MET* 3.2 6.4 + - - +
374B TYR* 3.2 23.8 + - - +
403B LEU* 6.4 0.9 - - + -
406B LYS* 4.8 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 371 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B THR* 3.0 9.7 + - - +
370B ALA* 1.3 79.0 - - - +
372B GLU* 1.3 57.4 + - + +
374B TYR* 3.7 4.5 + - - +
375B THR* 2.5 40.0 + - - +
400B LYS* 5.6 7.7 - - - +
403B LEU* 4.3 33.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 372 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B THR* 4.6 10.7 - - - +
367B LEU* 4.2 18.9 - - + +
368B VAL* 3.1 18.2 + - - +
369B THR* 2.7 53.6 + - - +
371B GLU* 1.3 78.1 - - + +
373B MET* 1.3 53.0 + - - +
375B THR* 3.4 6.2 + - - -
376B TYR* 2.8 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 373 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B LEU* 3.7 28.2 - - + +
324B TRP* 3.7 34.3 - - + -
367B LEU* 4.0 23.6 - - + +
368B VAL 3.6 29.8 - - - +
369B THR 3.1 8.8 + - - +
370B ALA* 3.2 8.7 + - - +
372B GLU* 1.3 72.2 - - - +
374B TYR* 1.3 65.7 + - - +
375B THR 3.0 0.4 - - - -
376B TYR* 3.0 6.2 + - - +
377B GLN* 2.9 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 374 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B TRP* 4.3 25.1 - - + -
325B TYR* 3.6 9.0 - - + -
370B ALA 3.2 12.7 + - - +
371B GLU* 4.3 5.2 - - - +
373B MET* 1.3 75.3 - - - +
375B THR* 1.3 57.7 + - - +
377B GLN* 3.4 1.0 + - - +
378B GLY* 2.8 26.9 + - - -
399B ASN* 3.7 16.4 - - + +
402B PHE* 4.5 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 375 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B GLU* 2.5 30.8 + - - +
372B GLU* 3.5 7.3 - - - -
373B MET 3.0 0.6 - - - -
374B TYR* 1.3 78.6 - - - +
376B TYR* 1.3 57.0 + - - +
378B GLY* 3.3 0.7 + - - -
379B ASP* 2.9 48.1 + - - +
399B ASN* 3.9 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 376 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B LEU* 3.9 38.4 - - + -
299B TRP* 3.4 20.5 - + + +
360B TRP* 2.9 53.9 + + - -
363B LYS* 3.7 32.8 - - + -
364B GLU* 3.9 9.6 - - + -
367B LEU* 3.7 20.0 - - + -
372B GLU 2.8 15.1 + - - +
373B MET 3.4 6.5 - - - +
375B THR* 1.3 76.0 - - - +
377B GLN* 1.3 68.2 + - + +
379B ASP* 3.0 11.8 + - + +
380B TYR* 2.9 22.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 377 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B LEU* 3.6 21.6 + - + +
321B GLN* 4.1 7.3 - - - +
322B ASP 3.0 22.0 + - - -
324B TRP* 2.7 36.2 + - + +
325B TYR* 2.9 22.7 + - + +
329B MET* 3.5 30.7 - - - -
373B MET 2.9 14.6 + - - +
374B TYR 4.0 3.1 - - - +
376B TYR* 1.3 79.3 - - + +
378B GLY* 1.4 53.4 + - - +
380B TYR* 3.1 11.7 + - + +
381B ILE* 2.8 42.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 378 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B TYR* 3.8 12.6 - - - -
374B TYR 2.8 19.2 + - - -
375B THR* 3.5 4.7 - - - -
377B GLN* 1.4 70.6 - - - +
379B ASP* 1.3 56.7 + - - +
381B ILE* 3.4 4.7 + - - +
382B GLN* 2.9 29.6 + - - +
395B ILE* 3.8 29.5 - - - +
399B ASN* 4.7 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 379 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B TRP* 4.2 11.4 - - + -
363B LYS* 5.7 3.1 + - - -
375B THR* 2.9 32.2 + - - +
376B TYR* 3.3 11.8 - - + +
378B GLY* 1.3 73.3 - - - +
380B TYR* 1.3 60.4 - - - +
382B GLN* 3.4 7.7 + - - +
383B ASN* 2.9 29.6 + - - +
395B ILE* 5.8 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 380 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B LEU 6.0 0.4 - - - -
299B TRP* 3.6 29.6 - + + -
305B LYS* 2.5 34.9 + - + -
306B GLY* 3.4 5.7 - - - -
321B GLN* 4.6 8.7 - - + -
329B MET* 4.0 23.8 - - + -
333B GLN* 3.0 29.8 + - - +
360B TRP* 3.7 25.0 - + + -
376B TYR* 2.9 16.1 + - + +
377B GLN* 3.3 15.3 - - + +
379B ASP* 1.3 73.4 - - - +
381B ILE* 1.4 68.2 + - + +
383B ASN* 3.3 6.1 + - + +
384B LEU* 3.1 43.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 381 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B TYR* 3.4 48.9 - - + -
328B ASN* 4.6 4.5 - - + +
329B MET* 3.9 28.0 - - + +
332B ALA* 4.0 10.8 - - + -
377B GLN* 2.8 26.0 + - + +
378B GLY* 3.7 3.6 - - - +
380B TYR* 1.4 75.7 - - + +
382B GLN* 1.3 58.1 + - - +
384B LEU* 2.8 25.7 + - - +
385B ILE* 2.9 29.7 + - + +
393B PHE* 4.4 11.4 - - + -
395B ILE* 4.2 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 382 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B GLY 2.9 18.7 + - - +
379B ASP* 3.5 9.9 - - - +
381B ILE* 1.3 75.9 - - - +
383B ASN* 1.3 64.0 + - - +
384B LEU 3.2 0.2 + - - -
385B ILE* 3.3 24.4 + - - +
386B ASP* 2.9 59.7 + - - +
392B SER* 3.7 8.6 + - - -
393B PHE 4.6 5.4 - - - +
395B ILE* 3.6 24.7 + - + +
396B PRO* 5.5 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 383 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B LYS* 3.0 32.9 + - - +
360B TRP* 4.5 20.6 - - + +
379B ASP 2.9 13.1 + - - +
380B TYR* 3.5 10.4 - - + +
381B ILE 3.3 0.2 - - - -
382B GLN* 1.3 77.2 - - - +
384B LEU* 1.3 64.8 + - - +
386B ASP* 3.6 12.8 + - - +
387B MET* 3.5 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 384 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B LYS* 3.9 26.9 - - + +
307B VAL* 5.0 1.1 - - + -
329B MET 4.9 0.7 - - - +
332B ALA* 3.9 19.0 - - + +
333B GLN* 3.9 24.2 - - + +
336B TYR* 4.0 29.0 - - + +
380B TYR* 3.1 50.2 + - + +
381B ILE* 2.8 16.2 + - + +
383B ASN* 1.3 72.0 - - - +
385B ILE* 1.3 61.9 + - - +
387B MET* 3.2 26.6 + - + +
388B THR* 3.9 9.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 385 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B ALA* 3.7 22.0 - - + -
381B ILE* 2.9 25.4 + - + +
382B GLN* 3.5 33.2 - - - +
384B LEU* 1.3 73.1 - - - +
386B ASP* 1.3 58.9 + - - +
388B THR* 2.8 34.6 + - - +
390B TYR* 3.8 31.0 - - + +
391B PRO 4.4 0.2 - - - +
392B SER* 3.6 31.8 + - - +
393B PHE* 4.3 17.9 - - + +
395B ILE* 4.3 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 386 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B GLN* 2.9 50.2 + - - +
383B ASN* 3.9 8.7 - - - +
384B LEU 3.2 0.6 - - - -
385B ILE* 1.3 76.3 - - - +
387B MET* 1.3 61.8 + - + +
388B THR 3.4 1.1 - - - +
392B SER* 4.3 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 387 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B LYS* 3.7 37.0 - - + -
336B TYR* 3.8 27.1 - - + -
339B ASP* 4.1 2.8 - - - +
345B LEU* 4.1 31.9 - - + +
383B ASN* 3.5 25.8 + - - +
384B LEU* 3.2 13.8 + - + +
385B ILE 3.2 1.2 - - - -
386B ASP* 1.3 82.2 - - + +
388B THR* 1.3 63.2 + - + +
----------------------------------------------------------
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