Contacts of the helix formed by residues 461 - 473 (chain H) in PDB entry 1MKD
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 461 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459H ASN 4.1 5.0 + - - -
460H ALA* 1.3 75.4 + - - +
462H VAL* 1.3 67.2 + - - +
463H GLU* 3.1 7.0 - - - -
464H LYS* 2.8 50.0 + - - +
465H SER* 2.9 18.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 462 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430H THR* 3.8 27.1 - - + -
431H ASP* 5.7 2.9 - - - +
434H MET* 3.8 35.2 - - + -
438H PHE* 4.8 5.2 - - + -
460H ALA* 3.6 8.4 - - + +
461H SER* 1.3 73.7 - - - +
463H GLU* 1.3 78.0 + - - +
465H SER* 3.4 7.5 + - - -
466H GLN* 3.1 23.2 + - - +
503H TYR* 4.7 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 463 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461H SER* 2.9 5.4 + - - -
462H VAL* 1.3 89.8 + - - +
464H LYS* 1.3 64.3 + - - +
466H GLN* 3.2 4.7 + - - +
467H VAL* 3.1 25.3 + - - +
503H TYR* 3.6 21.7 - - + +
506H THR* 3.4 43.5 - - + +
507H ILE* 3.5 22.2 - - + -
508H PRO* 3.9 16.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 464 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461H SER* 2.8 34.0 + - - +
463H GLU* 1.3 75.2 - - + +
465H SER* 1.3 58.1 + - - +
467H VAL* 3.2 3.4 + - - +
468H GLY* 2.8 27.2 + - - -
507H ILE* 3.7 43.3 - - + -
508H PRO* 5.2 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 465 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434H MET* 5.2 1.4 - - - +
454H MET* 3.5 46.0 - - - +
460H ALA* 5.9 0.2 - - - +
461H SER* 2.9 21.0 + - - -
462H VAL* 3.5 12.7 + - - -
464H LYS* 1.3 76.7 - - - +
466H GLN* 1.3 60.0 + - - +
468H GLY* 3.3 1.6 + - - -
469H PHE* 2.8 31.1 + - - +
3008H ZAR 4.1 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 466 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426H TYR* 2.7 32.0 + - - +
430H THR* 3.4 32.1 - - + +
433H ILE* 4.6 3.4 - - - +
434H MET* 4.8 5.5 - - - -
462H VAL 3.1 19.1 + - - +
463H GLU 3.2 7.2 + - - +
465H SER* 1.3 73.4 - - - +
467H VAL* 1.3 61.0 + - - +
469H PHE* 3.2 7.5 + - - +
470H ILE* 2.9 36.7 + - + +
503H TYR* 3.9 22.4 - - + -
3008H ZAR 3.0 46.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 467 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463H GLU 3.1 16.0 + - - +
464H LYS* 3.6 6.5 - - - +
466H GLN* 1.3 75.6 - - - +
468H GLY* 1.3 58.8 + - - +
470H ILE* 3.5 6.4 + - - +
471H ASP* 2.9 37.9 + - - +
500H ARG* 3.2 46.2 - - + +
503H TYR* 4.0 5.4 - - + -
504H GLN* 3.8 37.5 - - - +
507H ILE* 3.8 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 468 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464H LYS 2.8 15.7 + - - -
465H SER* 3.7 1.8 - - - -
467H VAL* 1.3 74.9 - - - +
469H PHE* 1.3 58.7 + - - +
471H ASP* 3.1 3.1 + - - -
472H TYR* 2.8 60.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 469 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370H MET* 5.5 3.4 - - + -
416H LEU* 3.7 26.0 - - + -
419H PRO* 4.1 15.3 - - + -
465H SER 2.8 21.5 + - - +
466H GLN* 3.5 13.5 - - - +
468H GLY* 1.3 71.1 - - - +
470H ILE* 1.3 57.4 + - - +
472H TYR* 5.4 0.2 - - - -
473H ILE* 3.0 49.9 + - + +
474H VAL* 3.1 34.2 + - + -
3008H ZAR 3.6 68.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 470 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419H PRO* 4.0 22.2 - - + -
426H TYR* 3.4 27.8 - - + +
466H GLN* 2.9 20.6 + - + +
467H VAL* 3.7 4.3 - - - +
469H PHE* 1.3 79.0 - - + +
471H ASP* 1.3 61.9 + - - +
474H VAL* 3.9 5.8 - - - -
475H HIS* 2.7 46.0 + - + +
476H PRO* 3.4 0.9 - - - +
496H LEU* 3.9 22.0 - - + -
497H GLU* 6.1 0.2 - - - -
499H ASN 4.8 0.2 - - - +
500H ARG* 3.9 44.4 - - + +
503H TYR* 5.6 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 471 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A HIS* 3.5 26.3 - - + +
487A PRO* 5.3 2.4 - - - +
467H VAL* 2.9 26.3 + - - +
468H GLY* 3.1 6.8 + - - +
470H ILE* 1.3 78.1 - - - +
472H TYR* 1.3 70.9 + - + +
475H HIS* 4.7 4.5 - - - +
476H PRO* 3.2 18.9 - - - +
500H ARG* 2.7 45.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 472 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A LYS* 4.4 20.9 - - + -
389A VAL* 4.8 22.4 - - + -
390A THR 5.7 0.7 - - - -
391A SER 5.4 6.3 - - - -
392A SER 5.4 1.3 - - - -
393A GLY* 4.5 26.6 + - - -
486A HIS* 3.1 31.6 + + + -
487A PRO* 4.3 6.1 - - - +
373H HIS* 4.6 2.6 + - - -
374H MET* 4.7 8.4 - - + +
468H GLY* 2.8 41.8 + - - +
471H ASP* 1.3 87.5 + - + +
473H ILE* 1.3 76.5 + - + +
476H PRO* 3.5 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 473 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370H MET* 3.8 26.0 - - + -
373H HIS* 3.6 35.1 + - + +
374H MET* 4.5 10.3 - - + -
416H LEU* 3.9 14.6 - - + -
469H PHE* 3.0 33.3 + - + +
472H TYR* 1.3 96.0 - - + +
474H VAL* 1.3 66.6 + - - +
475H HIS 3.5 0.9 - - - -
476H PRO* 3.3 3.9 - - - +
477H LEU* 3.2 23.3 + - - +
----------------------------------------------------------
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