Contacts of the helix formed by residues 463 - 486 (chain B) in PDB entry 1MWT
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 463 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B LYS* 3.4 0.9 - - - -
427B ILE* 3.4 9.7 - - - +
445B ARG* 2.8 49.5 + - - -
447B GLU 3.8 8.9 - - - +
449B VAL* 4.0 8.3 - - - +
453B ILE* 4.5 4.3 - - - -
458B ALA* 2.9 20.2 + - + -
461B SER* 3.4 5.7 + - - +
462B SER* 1.3 73.3 - - - +
464B ASN* 1.3 67.2 + - - +
465B ILE* 3.3 2.0 + - - +
466B PHE* 3.3 33.5 + - + -
467B PHE* 3.4 19.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 464 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B LYS* 2.8 21.6 + - - +
443B VAL* 4.2 2.9 - - + -
444B THR 3.2 25.8 + - - +
445B ARG* 4.1 9.5 - - - +
446B TYR 4.8 0.2 - - - +
462B SER 3.2 2.1 + - - -
463B ASP* 1.3 72.9 - - - +
465B ILE* 1.3 52.3 + - - +
467B PHE* 3.3 1.4 + - - +
468B ALA* 2.7 38.2 + - - +
519B TYR* 3.2 34.2 - - + -
708B PNM 2.7 51.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 465 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B ILE* 3.8 26.0 - - + -
429B GLY 5.2 0.7 - - - +
430B LYS 3.5 18.6 - - - +
431B GLY 3.8 4.3 - - - +
432B TRP* 3.6 40.8 - - + -
443B VAL* 3.1 31.6 - - + +
445B ARG* 3.8 23.1 - - + +
463B ASP* 3.3 7.5 + - - +
464B ASN* 1.3 75.5 - - - +
466B PHE* 1.3 65.3 + - - +
468B ALA* 3.6 6.4 - - - +
469B ARG* 3.0 30.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 466 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B LEU* 3.9 17.0 - - + -
423B THR* 4.8 1.3 - - + -
424B SER* 4.7 2.5 - - - -
425B TYR* 3.9 22.9 - + - -
427B ILE* 3.8 9.8 - - + +
453B ILE* 3.1 33.7 - - + -
454B ASP* 3.4 11.4 - - - -
455B LEU* 3.5 35.9 - - + -
458B ALA* 3.3 29.4 - - + -
463B ASP* 3.3 17.4 + - + +
464B ASN 3.3 0.2 - - - -
465B ILE* 1.3 80.7 - - - +
467B PHE* 1.3 67.9 + + - +
469B ARG* 3.2 6.9 + - - +
470B VAL* 3.0 43.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 467 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B LYS* 3.4 57.2 - - + -
409B THR* 4.0 13.8 - - + +
410B ALA* 4.2 6.7 - - + -
419B LEU* 5.4 0.2 - - + -
455B LEU* 3.6 32.5 - - + -
458B ALA* 3.5 28.5 - - + -
459B ILE* 4.0 13.7 - - + -
463B ASP 3.4 13.5 - - - -
464B ASN 3.3 4.5 + - - +
466B PHE* 1.3 83.9 - + - +
468B ALA* 1.3 68.3 + - - +
469B ARG 2.9 1.8 - - - -
470B VAL* 2.9 8.1 + - + +
471B ALA* 2.9 24.9 + - - +
518B GLY* 3.8 19.5 - - - +
519B TYR* 4.6 1.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 468 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B TRP* 5.6 2.5 - - + -
443B VAL* 3.7 27.8 - - + -
464B ASN 2.7 22.8 + - - +
465B ILE* 3.2 5.4 + - - +
467B PHE* 1.3 74.6 - - - +
469B ARG* 1.3 60.7 + - + +
471B ALA* 3.6 4.3 - - - +
472B LEU* 3.2 26.5 + - - +
515B ALA* 3.2 32.7 - - + +
519B TYR* 3.8 2.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 469 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B TYR* 3.4 50.1 + - + +
426B LYS 4.1 17.0 + - - +
427B ILE* 5.4 0.4 - - - +
432B TRP* 3.4 59.6 - - + +
465B ILE* 3.0 23.8 + - + +
466B PHE 3.4 8.1 - - - +
467B PHE 2.9 0.6 - - - -
468B ALA* 1.3 77.7 - - - +
470B VAL* 1.3 60.1 + - - +
471B ALA 2.9 2.0 - - - -
472B LEU* 3.0 7.6 + - + +
473B GLU* 2.8 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 470 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B THR* 4.1 20.0 - - + +
413B GLY* 4.5 4.3 - - - -
418B THR* 5.2 3.1 - - - +
419B LEU* 4.1 33.0 - - + -
425B TYR* 4.1 14.6 + - + +
466B PHE* 3.0 47.0 + - + +
467B PHE* 2.9 12.6 + - + +
469B ARG* 1.3 76.0 - - - +
471B ALA* 1.3 60.8 + - - +
473B GLU* 3.6 3.6 + - + +
474B LEU* 3.3 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 471 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B THR* 4.7 1.3 - - + +
467B PHE 2.9 13.7 + - - +
468B ALA 3.6 5.6 - - - +
470B VAL* 1.3 77.4 - - - +
472B LEU* 1.3 60.6 + - - +
474B LEU* 3.3 11.3 + - - +
475B GLY 2.9 23.6 + - - +
479B PHE* 4.5 8.0 - - + +
514B LEU* 3.4 43.5 - - + +
518B GLY* 3.8 13.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 472 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B TRP* 3.9 33.4 - - + -
434B LYS* 5.0 7.9 - - + -
438B TRP* 4.1 14.6 - - + -
468B ALA 3.2 15.9 - - - +
469B ARG* 3.0 10.6 + - + +
471B ALA* 1.3 73.1 - - - +
473B GLU* 1.3 66.8 + - - +
475B GLY* 3.4 9.7 + - - -
511B GLU* 3.7 41.5 - - + +
514B LEU* 4.1 15.7 - - + -
515B ALA* 4.2 5.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 473 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B THR* 4.0 31.1 - - + +
425B TYR* 3.9 23.8 + - + +
469B ARG 2.8 15.0 + - - +
470B VAL* 3.6 7.6 - - + +
471B ALA 3.2 0.2 - - - -
472B LEU* 1.3 78.8 - - - +
474B LEU* 1.3 62.3 + - - +
475B GLY* 3.4 0.5 + - - -
478B LYS* 5.3 2.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 474 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B THR* 4.4 2.5 - - + +
412B ILE* 3.9 19.5 - - + +
413B GLY* 3.9 18.6 - - - +
416B ASN* 3.4 35.7 - - + +
418B THR* 3.2 26.7 - - + +
470B VAL* 3.3 21.9 + - + +
471B ALA* 3.5 7.2 - - - +
473B GLU* 1.3 80.3 - - - +
475B GLY* 1.3 68.0 + - - +
477B LYS* 4.9 0.5 + - - +
478B LYS* 3.3 37.2 + - + +
479B PHE* 4.4 15.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 475 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B ALA 2.9 12.0 + - - -
472B LEU 3.4 6.9 + - - -
473B GLU 3.3 3.5 - - - -
474B LEU* 1.3 82.6 - - - +
476B SER* 1.3 65.9 + - - -
477B LYS* 3.2 2.4 + - - -
479B PHE* 3.1 19.2 + - - +
514B LEU* 3.7 11.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 476 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475B GLY* 1.3 72.4 - - - -
477B LYS* 1.3 65.5 + - - +
479B PHE* 4.1 2.4 - - - +
480B GLU* 3.2 27.7 + - - +
508B LEU* 2.9 39.1 + - - +
509B ASP* 4.1 10.8 + - - -
514B LEU* 3.5 20.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 477 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474B LEU 5.5 0.2 - - - +
475B GLY 3.2 1.4 - - - -
476B SER* 1.3 85.3 + - - +
478B LYS* 1.3 77.1 + - + +
480B GLU* 4.2 2.2 - - - +
481B LYS* 3.4 41.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 478 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B ILE* 3.9 5.7 - - - +
416B ASN* 3.5 36.9 + - + +
418B THR* 5.1 8.1 - - + -
473B GLU 5.3 2.7 - - - -
474B LEU* 3.3 32.7 + - + +
475B GLY 3.4 1.2 + - - -
477B LYS* 1.3 89.5 - - + +
479B PHE* 1.3 60.4 + - - +
481B LYS* 4.0 8.8 - - - +
482B GLY* 2.8 27.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 479 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B GLN* 3.9 20.6 - - - -
409B THR* 3.9 25.8 - - + -
412B ILE* 4.0 17.0 - - + +
471B ALA* 4.5 9.2 - - + -
474B LEU* 4.4 19.4 - - + +
475B GLY 3.1 19.5 + - - +
476B SER* 4.1 3.8 - - - +
477B LYS 3.4 0.2 - - - -
478B LYS* 1.3 75.4 - - - +
480B GLU* 1.3 60.5 + - - +
482B GLY* 3.2 1.0 + - - -
483B MET* 3.0 51.7 + - + +
503B ILE* 5.9 1.6 - - + -
508B LEU* 3.6 21.8 - - + -
514B LEU* 4.1 18.8 - - + -
517B SER* 4.0 29.6 - - - -
518B GLY* 4.6 0.4 - - - -
524B ILE* 5.8 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 480 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476B SER 3.2 14.2 + - - +
477B LYS* 4.2 2.7 - - - +
479B PHE* 1.3 74.9 - - - +
481B LYS* 1.3 68.0 + - - +
483B MET* 3.3 7.2 + - - +
484B LYS* 3.1 38.5 + - - +
503B ILE* 4.9 16.6 - - + +
508B LEU* 3.8 32.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 481 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477B LYS* 3.4 36.4 + - - +
478B LYS* 4.0 7.9 - - - +
479B PHE 3.4 0.4 - - - -
480B GLU* 1.3 79.1 - - - +
482B GLY* 1.3 57.9 + - - +
484B LYS* 3.3 12.5 + - + +
485B LYS* 2.8 37.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 482 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B ILE* 3.5 24.0 - - - +
415B ASN* 6.0 0.9 - - - -
416B ASN* 5.4 1.6 - - - -
478B LYS 2.8 19.4 + - - -
479B PHE 3.6 1.6 - - - -
480B GLU 3.2 0.2 - - - -
481B LYS* 1.3 75.5 - - - +
483B MET* 1.3 63.8 + - - +
485B LYS* 3.3 12.0 + - - +
486B LEU* 3.2 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 483 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B GLN* 3.1 42.6 - - - +
408B LEU* 3.9 17.0 - - + -
412B ILE* 3.5 15.7 - - + -
479B PHE* 3.0 36.3 + - + +
480B GLU* 3.3 6.5 + - - +
482B GLY* 1.3 74.6 - - - +
484B LYS* 1.3 58.4 + - - +
486B LEU* 2.9 22.0 + - - +
488B VAL* 3.2 41.5 + - + +
503B ILE* 4.8 10.1 - - + -
508B LEU* 6.1 0.2 - - + -
524B ILE* 3.6 22.7 - - + -
526B ILE* 4.5 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 484 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B GLU* 3.1 28.5 + - - +
481B LYS* 3.7 11.6 - - + +
483B MET* 1.3 79.2 - - - +
485B LYS* 1.3 57.9 + - - +
487B GLY* 2.9 16.6 + - - -
488B VAL 3.5 16.5 + - - +
489B GLY* 6.2 0.7 - - - -
490B GLU* 3.4 24.8 - - + +
559B LYS* 4.2 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 485 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B ASN* 3.3 39.9 + - - +
481B LYS* 2.8 25.3 + - + +
482B GLY* 3.4 11.9 - - - +
483B MET 3.2 0.2 - - - -
484B LYS* 1.3 78.2 - - - +
486B LEU* 1.3 61.7 + - + +
487B GLY 3.3 0.9 + - - -
559B LYS* 3.9 18.0 + - - +
560B LYS 5.2 1.4 + - - -
561B ASN 3.7 19.2 + - - -
562B ILE* 4.3 18.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 486 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B LEU* 3.8 38.4 - - + +
411B MET* 4.1 13.0 - - + -
412B ILE* 4.0 24.7 - - + +
482B GLY 3.2 11.0 + - - +
483B MET* 2.9 11.5 + - - +
485B LYS* 1.3 81.0 - - + +
487B GLY* 1.3 58.2 + - - +
488B VAL* 3.4 1.2 + - + -
530B GLN* 4.9 0.9 + - - -
534B ILE* 3.7 27.2 - - + +
544B ILE* 3.8 9.5 - - - +
558B TRP* 5.5 1.7 - - - -
559B LYS* 4.3 5.5 - - - +
562B ILE* 3.5 46.4 - - + +
----------------------------------------------------------
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