Contacts of the helix formed by residues 489 - 498 (chain A) in PDB entry 1MWH
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 489 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A THR 4.0 3.4 - - - -
458A ALA* 3.2 27.8 - - - +
459A ARG 3.7 5.4 - - - -
460A GLY* 4.6 0.2 - - - -
461A GLY 5.0 1.1 - - - -
486A LYS* 3.0 40.0 + - + +
487A ALA 2.7 7.7 + - - +
488A ALA* 1.3 78.5 - - - +
490A LYS* 1.3 63.8 + - - +
491A ILE* 3.7 8.4 + - - +
492A PHE* 3.1 18.9 + - - +
493A GLN* 3.0 23.0 + - - +
1020A ALA* 4.2 7.6 - - - +
1023A ALA* 4.3 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 490 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A TYR* 2.9 47.9 + - + +
456A VAL* 4.7 1.4 - - - +
457A THR* 3.3 24.2 + - - +
459A ARG* 3.1 14.3 + - - +
460A GLY 3.7 15.3 - - - -
461A GLY* 3.5 25.6 - - - -
489A THR* 1.3 70.5 - - - +
491A ILE* 1.3 54.8 + - - +
493A GLN* 3.1 13.4 + - - +
494A ALA* 2.8 33.8 + - - +
530A PRO* 6.0 0.4 - - - -
531A LEU 4.0 11.0 - - - +
532A ASN 5.0 0.7 - - - -
533A VAL* 3.9 17.5 - - + +
536A GLN* 4.5 9.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 491 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A VAL* 4.0 15.9 - - + +
457A THR* 3.1 36.0 + - - +
458A ALA* 3.8 7.6 - - + +
489A THR* 3.9 5.8 - - - +
490A LYS* 1.3 77.5 - - - +
492A PHE* 1.3 63.3 + - - +
494A ALA* 3.2 1.7 + - - +
495A ALA* 3.1 18.0 + - - +
970A PHE* 4.6 2.7 - - + -
974A LEU* 3.4 19.5 - - + +
1016A TRP* 3.4 53.2 - - + +
1019A GLY* 4.4 4.3 - - - -
1020A ALA* 4.0 19.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 492 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A ARG* 5.0 6.1 - - - -
479A ASP* 3.6 20.2 - - - -
480A PHE* 3.8 26.9 - + + -
483A LEU* 5.8 0.2 - - + -
485A VAL* 4.0 13.7 - - + -
486A LYS 4.1 0.4 - - - +
487A ALA* 3.2 52.9 - - + +
489A THR* 3.1 15.0 + - - +
491A ILE* 1.3 78.0 - - - +
493A GLN* 1.3 64.4 + - + +
495A ALA* 3.1 4.9 + - - +
496A GLN* 3.0 55.3 + - + +
970A PHE* 3.6 24.5 - + + -
1020A ALA* 5.7 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 493 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A GLY* 2.9 40.4 + - - +
463A GLY* 3.5 22.1 - - - +
466A LEU* 3.8 21.7 - - + +
487A ALA 5.7 0.7 - - - +
488A ALA 6.3 0.2 - - - -
489A THR 3.0 11.6 + - - +
490A LYS* 3.1 14.1 + - - +
492A PHE* 1.3 78.4 - - + +
494A ALA* 1.3 62.8 + - - +
496A GLN* 3.1 13.8 + - - +
497A LEU* 3.0 32.3 + - + +
532A ASN* 3.4 9.1 - - - +
533A VAL* 3.2 35.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 494 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A VAL* 4.2 16.4 - - + -
490A LYS 2.8 15.7 + - - +
491A ILE 3.2 9.4 + - - +
493A GLN* 1.3 72.4 - - - +
495A ALA* 1.3 55.3 + - - +
497A LEU* 3.2 3.2 + - - +
498A ALA* 2.7 37.2 + - - +
533A VAL* 4.3 6.0 - - + +
974A LEU* 4.1 11.0 - - + -
977A TYR* 4.1 33.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 495 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A PRO* 5.3 0.9 - - - +
480A PHE* 3.7 14.2 - - + -
491A ILE 3.1 7.5 + - - +
492A PHE 3.4 4.7 - - - +
494A ALA* 1.3 81.4 - - - +
496A GLN* 1.3 62.0 + - - +
498A ALA* 3.6 5.0 - - - +
499A ASN* 5.2 1.0 + - - -
970A PHE* 3.3 37.9 - - + -
973A ALA* 3.2 28.7 - - + +
974A LEU* 3.8 13.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 496 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A LEU* 5.1 1.2 - - - +
467A ARG* 3.7 23.6 + - - +
477A LEU* 3.7 43.1 - - + +
478A PRO* 2.7 48.6 + - - +
480A PHE* 4.0 8.1 - - + -
492A PHE* 3.0 47.8 + - + +
493A GLN* 3.1 16.1 + - - +
495A ALA* 1.3 77.8 - - - +
497A LEU* 1.3 59.8 + - - +
499A ASN 5.0 1.0 + - - -
500A LEU* 3.9 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 497 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A LEU* 4.4 11.0 - - + -
470A LEU* 4.1 5.8 - - + -
477A LEU* 3.7 32.1 - - + -
493A GLN* 3.0 19.7 + - + +
494A ALA* 4.1 2.7 - - - +
496A GLN* 1.3 76.8 - - + +
498A ALA* 1.3 55.8 + - - +
499A ASN 2.7 17.1 + - - -
500A LEU* 2.8 24.1 + - - +
505A THR* 3.7 24.5 - - + -
533A VAL* 4.0 16.4 - - + -
534A PRO* 3.7 33.0 - - + -
977A TYR* 5.5 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 498 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A ARG* 5.8 0.7 + - - -
494A ALA 2.7 21.6 + - - +
495A ALA 3.6 11.2 - - - +
496A GLN 3.5 0.4 - - - -
497A LEU* 1.3 69.8 - - - +
499A ASN* 1.3 65.2 + - - +
500A LEU 3.5 2.6 + - - +
973A ALA* 3.0 33.9 - - + +
976A ASP* 4.5 6.7 - - + +
977A TYR* 4.1 22.6 + - + +
980A GLN* 5.5 6.4 - - - +
----------------------------------------------------------
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