Contacts of the helix formed by residues 460 - 474 (chain B) in PDB entry 3MBK
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 460 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B ASP* 3.4 12.1 + - - -
458B SER* 3.1 7.6 + - - -
459B PRO* 1.3 79.8 - - - +
461B LEU* 1.3 66.7 + - - +
462B ARG* 4.0 16.2 + - - -
463B CYS* 2.9 27.0 + - - +
464B VAL* 3.1 10.4 + - - +
489B PHE* 3.2 30.3 - - - -
503B TRP* 3.9 5.1 + - - +
565B HIS* 3.3 9.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 461 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B PRO* 5.0 5.2 - - + -
417B ARG* 4.0 6.5 - - - +
424B TYR* 3.5 34.5 - - + +
427B ASP* 2.9 28.5 + - - +
428B ALA 4.3 0.4 - - - +
429B PRO* 4.0 16.6 - - + -
459B PRO 3.3 4.4 + - - -
460B SER* 1.3 71.4 - - - +
462B ARG* 1.3 63.1 + - - +
464B VAL* 3.1 5.1 + - + +
465B GLN* 2.9 47.9 + - + +
504B ILE* 4.3 12.6 - - + -
509B LEU* 3.9 26.7 - - + -
514B LEU* 4.1 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 462 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B HIS* 3.5 30.4 + - + +
383B ARG* 3.5 36.4 - - + +
426B LYS 4.9 4.2 + - - -
427B ASP* 4.4 11.3 + - - +
428B ALA 3.6 26.6 + - - +
429B PRO 4.6 0.9 - - - -
430B ILE* 3.5 23.9 - - + +
460B SER* 4.0 18.0 + - - -
461B LEU* 1.3 77.8 - - - +
463B CYS* 1.3 59.8 + - - +
465B GLN* 4.1 2.9 - - - -
466B THR* 2.7 36.0 + - - -
489B PHE* 4.8 3.2 - - - -
490B GLU* 3.0 21.4 + - - -
565B HIS* 3.6 9.2 + - - -
700B SO4 2.9 28.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 463 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B HIS* 4.1 7.2 - - - -
457B CYS* 4.2 2.9 - - - -
458B SER* 3.5 31.6 - - - +
460B SER* 2.9 12.8 + - - +
462B ARG* 1.3 82.0 - - - +
464B VAL* 1.3 65.2 + - - +
466B THR* 3.3 1.8 + - - -
467B ALA* 2.9 24.1 + - - +
563B VAL* 3.6 20.0 - - - +
564B ALA* 3.4 26.9 - - - -
565B HIS* 3.7 16.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 464 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B CYS* 3.7 16.2 - - - -
458B SER 3.7 12.3 + - - +
459B PRO 4.0 7.6 - - - +
460B SER 3.1 14.4 + - - +
461B LEU* 3.7 6.3 - - + +
463B CYS* 1.3 76.4 - - - +
465B GLN* 1.3 63.5 + - - +
467B ALA* 3.2 3.3 + - - +
468B HIS* 3.0 21.5 + - - +
482B ILE* 4.2 1.2 - - + +
484B VAL* 4.5 3.1 - - + -
509B LEU* 3.8 33.0 - - + -
514B LEU* 4.1 17.3 - - + +
516B VAL* 3.7 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 465 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B PRO* 6.1 0.4 - - - +
414B LEU* 4.4 10.9 - - - +
415B PRO* 4.9 6.5 - - - +
429B PRO* 3.2 20.1 - - - +
430B ILE* 2.8 49.7 + - + +
435B CYS* 5.9 0.2 - - - -
461B LEU* 2.9 42.6 + - + +
462B ARG* 4.1 1.0 - - - +
464B VAL* 1.3 75.3 - - - +
466B THR* 1.3 62.9 + - - +
468B HIS* 3.4 6.6 + - - +
469B ASN* 2.9 32.3 + - - +
514B LEU* 4.2 19.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 466 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B HIS* 3.5 5.1 - - - -
381B GLY* 2.8 31.9 + - - +
430B ILE* 3.7 9.4 - - - +
438B ALA* 3.5 21.0 - - + +
462B ARG 2.7 23.5 + - - -
463B CYS 3.7 4.7 - - - -
464B VAL 3.3 0.2 - - - -
465B GLN* 1.3 77.0 - - - +
467B ALA* 1.3 56.5 + - - +
469B ASN 3.1 1.6 + - - -
470B ILE* 2.8 36.5 + - + +
563B VAL* 3.6 18.6 - - + -
597B LEU* 4.0 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 467 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B VAL* 4.3 5.6 - - + +
457B CYS* 4.2 11.0 - - + -
463B CYS 2.9 16.5 + - - +
464B VAL 3.2 2.4 + - - +
466B THR* 1.3 76.2 - - - +
468B HIS* 1.3 63.6 + - - +
470B ILE* 3.3 5.0 + - - +
471B LEU* 3.0 26.3 + - - +
482B ILE* 3.6 24.0 - - + -
563B VAL* 3.8 27.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 468 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B VAL 3.0 11.3 + - - +
465B GLN 3.6 7.4 - - - +
467B ALA* 1.3 75.7 - - - +
469B ASN* 1.3 65.1 + - - +
471B LEU* 3.2 7.2 + - - +
472B LYS* 3.0 51.2 + - + +
477B ASP* 4.5 10.8 - - + -
482B ILE* 3.5 7.7 - - - +
513B ASN 3.4 23.0 + - - -
514B LEU* 3.6 29.2 - - + +
515B SER* 2.8 36.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 469 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B ILE* 4.2 1.2 - - - +
435B CYS* 3.7 33.0 - - - +
438B ALA* 3.5 23.3 - - + -
439B ARG* 2.7 48.9 + - + +
465B GLN* 2.9 30.1 + - - +
468B HIS* 1.3 83.8 - - - +
470B ILE* 1.3 63.8 + - - +
472B LYS* 3.3 11.3 + - - +
473B GLY 3.1 17.7 + - - -
514B LEU* 5.7 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 470 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B CYS* 3.9 18.2 - - - -
438B ALA* 3.4 24.7 - - + +
441B VAL* 4.5 6.1 - - + -
442B GLY* 3.4 16.3 - - - +
445B LEU* 4.3 6.7 - - + -
466B THR* 2.8 25.7 + - + +
467B ALA* 3.7 7.2 - - - +
469B ASN* 1.3 71.4 - - - +
471B LEU* 1.3 59.1 + - + +
473B GLY 3.1 1.9 + - - -
474B LEU* 2.9 36.5 + - + +
561B LEU* 3.9 21.1 - - + -
563B VAL* 3.9 25.8 - - + -
597B LEU* 4.0 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 471 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B ILE* 5.8 0.2 - - + -
455B VAL* 4.0 16.6 - - + -
467B ALA 3.0 14.9 + - - +
468B HIS* 3.2 8.3 + - - +
470B ILE* 1.3 79.0 - - + +
472B LYS* 1.3 62.6 + - - +
474B LEU* 3.2 15.9 + - + -
475B GLN 3.0 3.8 + - - -
476B GLN* 2.9 33.0 + - + +
477B ASP* 3.8 13.0 - - + -
480B LEU* 3.8 51.6 - - + +
482B ILE* 3.7 31.0 - - + -
515B SER* 4.1 10.5 - - - -
561B LEU* 6.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 472 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B ARG* 4.2 27.2 - - + +
468B HIS* 3.0 38.8 + - + +
469B ASN* 3.6 27.8 - - - +
470B ILE 3.2 0.4 - - - -
471B LEU* 1.3 74.5 - - - +
473B GLY* 1.3 64.1 + - - +
475B GLN* 3.0 18.7 + - - +
477B ASP* 3.7 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 473 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B ARG* 3.5 28.1 - - - +
442B GLY 3.4 7.0 - - - -
443B GLU* 3.5 26.6 - - - +
446B LEU* 3.8 11.1 - - - +
469B ASN 3.1 11.3 + - - -
470B ILE 3.1 2.7 + - - -
472B LYS* 1.3 77.0 - - - +
474B LEU* 1.3 59.7 + - - +
475B GLN* 3.3 3.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
442B GLY* 3.6 11.4 - - - +
445B LEU* 3.5 29.6 - - + -
446B LEU* 3.9 25.2 - - + +
450B THR 4.2 9.9 - - - +
452B ILE* 3.9 29.2 - - + +
470B ILE* 2.9 29.2 + - + +
471B LEU* 3.2 26.0 + - + +
473B GLY* 1.3 75.5 - - - +
475B GLN* 1.3 67.6 + - - +
476B GLN* 3.4 23.8 + - + +
480B LEU* 5.1 0.4 - - + -
561B LEU* 5.4 1.3 - - + -
----------------------------------------------------------
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