Contacts of the helix formed by residues 349 - 374 (chain A) in PDB entry 1XB7
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 SER 349 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A SER 3.8 1.8 + - - -
348A LEU* 1.3 74.0 - - - +
350A LEU* 1.3 59.8 + - - +
351A SER* 3.7 8.4 + - - -
352A ASP* 3.1 29.9 + - - +
353A GLN* 2.9 23.9 + - - +
439A GLU* 5.4 2.6 - - - +
440A ASP* 5.9 1.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A LEU 3.6 1.0 + - - -
349A SER* 1.3 73.5 - - - +
351A SER* 1.3 58.5 + - - +
353A GLN* 3.2 28.9 + - - +
354A MET* 2.9 32.1 + - - +
211P LEU* 4.0 15.3 - - + -
214P LEU* 4.3 14.5 - - + +
215P THR* 3.6 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A SER* 3.1 8.9 + - - -
350A LEU* 1.3 79.3 - - - +
352A ASP* 1.3 65.1 + - - +
354A MET* 3.3 13.6 + - - +
355A SER* 2.9 30.7 + - - -
437A HIS 5.6 0.5 + - - -
439A GLU* 4.3 12.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 352 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A LEU* 4.3 16.3 - - + +
349A SER* 3.1 21.3 + - - +
351A SER* 1.3 79.4 + - - +
353A GLN* 1.3 63.5 + - - +
354A MET 3.1 2.0 - - - -
355A SER* 3.8 3.7 - - - -
356A VAL* 3.1 29.0 + - - +
437A HIS 4.0 1.9 - - - +
438A ILE* 3.5 14.5 - - + +
439A GLU* 2.9 34.9 + - - +
440A ASP* 3.1 34.8 + - - +
443A ALA* 5.6 0.7 - - - +
444A VAL* 4.7 5.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A LYS* 5.0 1.6 - - - +
345A PHE* 3.6 44.5 - - + +
346A SER* 3.4 22.9 + - - +
348A LEU* 2.7 27.9 + - + +
349A SER 2.9 12.6 + - - +
350A LEU* 3.2 29.4 + - - +
352A ASP* 1.3 75.8 - - - +
354A MET* 1.3 62.3 + - - +
356A VAL* 3.9 0.2 - - - +
357A LEU* 3.2 30.3 + - - +
214P LEU* 3.1 31.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A LEU* 2.9 15.8 + - - +
351A SER* 3.4 17.7 - - - +
353A GLN* 1.3 77.5 - - - +
355A SER* 1.3 57.3 + - - +
357A LEU* 3.4 2.9 + - - +
358A GLN* 3.0 43.1 + - - +
101P IOD 3.9 20.0 - - + -
208P SER 3.8 24.5 - - - +
210P LEU* 4.0 21.3 - - + +
211P LEU* 4.0 28.9 - - - -
214P LEU* 3.5 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A SER 2.9 18.0 + - - -
352A ASP* 3.3 6.2 + - - -
354A MET* 1.3 73.6 - - - +
356A VAL* 1.3 65.1 + - - +
358A GLN* 3.5 16.2 + - - +
359A SER* 3.2 24.6 + - - -
435A SER* 3.7 24.6 + - - -
437A HIS* 3.6 23.8 + - - +
438A ILE* 4.2 11.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A PHE* 4.0 11.9 - - + -
348A LEU* 4.3 15.9 - - + -
352A ASP 3.1 17.1 + - - +
353A GLN 3.9 2.9 - - - +
355A SER* 1.3 72.5 - - - +
357A LEU* 1.3 67.2 + - - +
359A SER* 3.0 6.2 + - - -
360A VAL* 2.9 25.0 + - + +
430A LEU* 3.4 43.7 - - + +
431A ALA* 5.5 1.8 - - - -
433A SER* 3.7 18.6 - - - -
438A ILE* 4.4 12.8 - - + -
444A VAL* 4.5 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A THR* 4.6 19.3 - - + +
336A ILE* 4.5 12.8 - - + -
339A ALA* 3.8 22.4 - - + -
345A PHE* 3.7 21.8 - - + -
353A GLN 3.2 19.3 + - - +
354A MET 3.8 3.1 - - - +
356A VAL* 1.3 80.5 - - - +
358A GLN* 1.3 58.0 + - - +
360A VAL* 4.2 4.3 - - + -
361A TRP* 3.0 37.9 + - + +
430A LEU* 4.2 11.9 - - + -
513A MET* 3.9 10.9 - - + +
210P LEU* 4.2 17.5 - - + -
214P LEU* 4.2 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A MET* 3.0 32.2 + - - +
355A SER* 3.5 19.4 + - - +
357A LEU* 1.3 77.1 - - - +
359A SER* 1.3 57.7 + - - +
361A TRP* 3.4 21.2 + - - +
435A SER* 5.6 1.5 + - - +
437A HIS* 4.3 20.8 - - - -
513A MET* 4.0 13.6 - - + +
516A ALA* 3.8 41.8 - - + +
210P LEU* 3.8 13.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A SER 3.2 10.6 + - - -
356A VAL 3.0 6.2 + - - -
358A GLN* 1.3 80.9 - - - +
360A VAL* 1.3 59.0 + - - +
361A TRP* 3.8 1.6 - - - -
362A MET 5.5 0.2 - - - -
363A GLU* 4.1 9.0 - - - +
433A SER* 2.3 37.0 + - - +
434A ASP 5.3 0.4 - - - -
435A SER* 3.9 15.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A VAL 2.9 16.6 + - - +
357A LEU* 4.2 3.1 - - + -
359A SER* 1.3 79.6 - - - +
361A TRP* 1.3 71.2 + - - +
362A MET 3.1 3.6 - - - -
363A GLU* 2.8 32.5 + - + +
364A VAL* 3.1 14.2 + - + +
429A ALA 3.8 12.1 - - - +
430A LEU* 3.4 42.2 - - + +
433A SER* 3.6 36.8 - - - +
485A ARG* 5.8 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 361 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A ILE* 3.6 30.1 - - + -
335A THR* 4.9 13.1 - - + +
357A LEU* 3.0 30.1 + - + +
358A GLN* 3.4 17.2 + - - -
359A SER 4.9 0.4 - - - -
360A VAL* 1.3 79.3 - - - +
362A MET* 1.3 94.0 + - + +
364A VAL* 3.2 9.4 + - - +
365A LEU* 3.1 50.9 + - + +
492A LEU* 3.6 27.5 - - + +
510A PHE* 3.7 24.5 - + - -
513A MET* 3.5 54.0 + - + +
514A LEU* 4.3 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A PHE* 4.5 16.2 - - + -
359A SER 5.5 0.2 + - - -
360A VAL 3.1 0.4 - - - -
361A TRP* 1.3 114.3 - - + +
363A GLU* 1.3 61.1 + - - +
365A LEU* 4.3 13.5 - - - -
366A VAL* 2.9 36.5 + - - +
488A ALA* 3.4 32.1 - - + +
491A VAL* 3.6 29.8 - - + +
492A LEU* 4.0 30.1 - - + +
495A PHE* 5.2 3.8 - - + -
510A PHE* 5.1 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A SER 4.1 13.6 - - - +
360A VAL* 2.8 22.9 + - + +
362A MET* 1.3 79.6 - - - +
364A VAL* 1.3 56.9 + - + +
367A LEU* 3.0 29.5 + - - +
429A ALA* 4.5 17.3 - - + +
433A SER 5.4 0.3 - - - +
481A LEU* 5.1 2.3 - - - +
484A LEU* 3.5 25.2 - - + +
485A ARG* 2.9 57.5 + - - +
488A ALA* 3.7 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A THR* 4.1 27.1 - - + +
338A TRP* 3.9 24.9 - - + -
360A VAL* 3.1 26.3 + - + +
361A TRP 3.2 6.9 + - - +
363A GLU* 1.3 75.1 - - + +
365A LEU* 1.3 65.3 + - - +
367A LEU* 3.4 5.7 + - - +
368A GLY* 3.0 19.6 + - - -
426A LYS* 3.8 40.8 + - + +
429A ALA* 5.6 2.5 - - + -
430A LEU* 4.9 4.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A PHE* 4.1 34.5 - - + +
331A GLU* 3.6 33.7 - - + +
332A ILE* 4.4 1.3 - - + +
335A THR* 3.4 26.2 - - - +
361A TRP* 3.1 50.8 + - + +
362A MET* 3.8 14.4 - - - +
364A VAL* 1.3 75.8 - - + +
366A VAL* 1.3 62.0 + - - +
368A GLY* 3.1 4.4 + - - -
369A VAL* 3.1 26.5 + - + +
372A ARG* 4.9 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A MET* 2.9 38.5 + - - +
363A GLU 4.0 2.5 - - - +
365A LEU* 1.3 74.3 - - + +
367A LEU* 1.3 58.5 + - - +
369A VAL* 3.3 9.7 + - - +
370A ALA* 3.0 25.5 + - - +
405A LEU* 3.8 18.0 - - + +
408A LEU* 3.7 23.6 - - + -
484A LEU* 3.8 9.0 - - + -
487A THR* 4.1 10.8 - - + -
488A ALA* 4.0 16.4 - - + +
491A VAL* 4.1 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A GLU 3.0 20.0 + - - +
364A VAL* 3.4 5.6 + - - +
366A VAL* 1.3 75.2 - - - +
368A GLY* 1.3 59.4 + - - +
370A ALA* 3.3 4.3 + - + +
371A GLN 3.0 23.0 + - - -
408A LEU* 5.2 0.7 - - + -
412A LEU* 4.0 26.2 - - + -
417A LEU* 5.5 1.3 - - + -
422A TYR* 3.5 23.1 - - + +
425A LEU* 4.4 18.2 - - + +
426A LYS* 3.5 43.5 - - + +
429A ALA* 5.2 2.0 - - + -
484A LEU* 3.9 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A VAL 3.0 14.0 + - - -
365A LEU* 3.1 4.4 + - - -
367A LEU* 1.3 74.1 - - - +
369A VAL* 1.3 64.4 + - - +
371A GLN* 3.4 1.9 + - - +
372A ARG* 3.2 43.6 + - - +
422A TYR* 3.6 19.9 + - - -
426A LYS* 5.2 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A PHE* 5.5 6.5 - - + -
331A GLU* 5.6 2.5 - - - +
365A LEU* 3.1 17.3 + - + +
366A VAL* 3.3 9.1 + - - +
368A GLY* 1.3 75.6 - - - +
370A ALA* 1.3 59.7 + - - +
372A ARG* 3.4 21.8 + - - +
373A SER* 2.7 39.4 + - - +
380A LEU* 4.4 13.9 - - + -
381A ALA 3.8 18.4 - - - +
382A PHE* 4.0 33.0 - - + +
405A LEU* 4.9 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A VAL 3.0 13.6 + - - +
367A LEU* 3.6 9.2 - - - +
368A GLY 3.2 0.2 - - - -
369A VAL* 1.3 76.9 - - - +
371A GLN* 1.4 62.2 + - - +
373A SER* 3.0 12.8 + - - -
374A LEU* 3.1 19.4 + - - +
405A LEU* 5.9 1.3 - - + +
408A LEU* 3.9 14.6 - - + -
409A VAL* 3.9 19.1 - - + +
412A LEU* 3.7 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A LEU* 3.0 8.2 + - - +
368A GLY 3.4 2.7 + - - +
370A ALA* 1.4 73.1 - - - +
372A ARG* 1.3 62.8 + - + +
374A LEU* 3.0 45.7 + - - +
375A PRO* 3.9 4.3 - - - +
412A LEU* 5.3 1.2 - - - +
417A LEU* 3.7 17.1 + - - +
418A GLU 4.3 2.2 + - - -
419A ARG* 3.8 44.5 - - - +
422A TYR* 3.5 47.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A LYS* 5.4 17.9 - - - +
305A LEU 6.2 0.9 - - - +
331A GLU* 3.5 18.8 + - - -
365A LEU 4.9 1.2 + - - -
368A GLY* 3.2 29.5 + - - +
369A VAL* 3.6 26.8 - - - +
370A ALA 3.2 0.2 - - - -
371A GLN* 1.3 77.8 - - + +
373A SER* 1.3 59.7 + - - +
374A LEU 3.4 0.2 - - - -
375A PRO* 3.7 10.7 - - - +
376A LEU* 4.3 5.5 - - - +
381A ALA* 3.0 38.6 + - + +
382A PHE 3.1 24.3 + - - -
383A ALA* 4.5 7.7 - - - +
384A GLU* 5.6 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A VAL* 2.7 23.4 + - - +
370A ALA 3.0 6.1 + - - -
372A ARG* 1.3 77.3 - - - +
374A LEU* 1.3 63.7 + - - +
375A PRO* 3.4 2.7 - - - -
376A LEU* 3.2 26.3 + - - +
379A GLU 3.5 18.2 - - - +
380A LEU* 3.3 4.5 - - - -
381A ALA 2.8 22.3 + - - -
409A VAL* 3.9 18.4 - - - +
413A GLN* 3.8 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A ALA 3.1 22.1 + - - +
371A GLN* 3.0 35.2 + - - +
373A SER* 1.3 76.4 - - - +
375A PRO* 1.3 63.3 - - + +
409A VAL* 3.9 15.9 - - + +
412A LEU* 3.7 29.4 - - + +
413A GLN* 2.5 38.6 + - + +
416A ARG* 6.2 0.7 - - - -
417A LEU* 4.0 30.7 - - + +
----------------------------------------------------------
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