Contacts of the helix formed by residues 475 - 486 (chain M) in PDB entry 6QX2
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 ASN 475 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461M ILE* 5.9 0.2 - - - +
462M LEU* 3.4 32.8 + - + +
471M ARG 2.9 11.5 + - - +
472M ILE 3.3 15.5 + - - +
473M LEU 4.3 0.5 - - - +
474M ASN* 1.3 76.3 - - - +
476M ASN* 1.3 58.1 + - - +
477M GLU* 2.9 34.8 + - - +
478M ILE* 3.1 21.6 + - + +
479M ARG* 3.1 27.9 + - - +
2014N T 4.1 21.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 476 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474M ASN 3.5 4.7 + - - +
475M ASN* 1.3 72.0 + - - +
477M GLU* 1.3 69.9 + - - +
479M ARG* 3.4 6.9 + - - +
480M GLN* 3.0 35.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 477 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456M PRO 5.0 1.9 - - - +
457M LEU* 4.4 19.6 - - + +
458M ARG* 3.3 58.7 + - + +
460M LYS 6.1 0.4 - - - +
461M ILE* 5.0 17.9 - - + -
475M ASN* 2.9 10.4 + - - +
476M ASN* 1.3 84.6 + - - +
478M ILE* 1.3 64.6 + - + +
480M GLN* 3.5 14.5 + - - +
481M MET* 3.3 30.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 478 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461M ILE* 4.2 13.9 - - + -
462M LEU* 4.7 8.5 - - + +
464M VAL* 4.2 11.9 - - + -
472M ILE* 3.5 32.1 - - + +
473M LEU* 5.3 1.6 - - + -
475M ASN* 3.1 25.0 + - + +
477M GLU* 1.3 73.8 - - + +
479M ARG* 1.3 64.2 + - - +
481M MET* 3.3 18.8 + - + +
482M ILE* 3.1 34.5 + - + +
523M PHE* 3.7 42.7 - - + -
527M PHE* 6.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 479 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473M LEU* 3.2 49.5 + - - +
474M ASN 5.7 0.4 - - - +
475M ASN 3.1 18.9 + - - +
476M ASN* 3.6 9.0 - - - +
477M GLU 3.3 0.2 - - - -
478M ILE* 1.3 76.5 - - - +
480M GLN* 1.3 56.7 + - + +
482M ILE* 3.3 39.1 + - - +
483M THR* 2.9 41.9 + - - +
489M ILE* 5.3 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 480 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417M LYS* 3.3 37.0 + - - +
418M LEU* 4.6 1.6 + - - -
455M LEU* 3.7 21.3 - - + +
456M PRO 5.2 0.3 - - - +
457M LEU* 6.3 0.9 - - + -
476M ASN* 3.0 24.1 + - + +
477M GLU* 3.9 15.5 - - - +
478M ILE 3.4 0.4 - - - -
479M ARG* 1.3 75.9 - - + +
481M MET* 1.3 57.8 + - - +
483M THR* 3.5 7.1 + - - -
484M ALA* 3.0 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 481 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433M LEU* 4.5 6.5 - - + -
455M LEU* 3.7 23.3 - - + -
457M LEU* 4.2 13.5 - - + -
461M ILE* 4.4 6.3 - - + -
477M GLU 3.3 18.3 + - - +
478M ILE* 3.7 19.5 - - + +
479M ARG 3.2 0.6 - - - -
480M GLN* 1.3 75.6 - - - +
482M ILE* 1.3 65.6 + - - +
484M ALA* 3.3 2.1 + - - +
485M PHE* 3.1 43.3 + - + -
520M LEU* 3.6 30.1 - - + -
523M PHE* 3.6 32.8 - - + -
524M PHE* 4.4 12.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 482 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473M LEU* 5.3 0.9 - - + -
478M ILE* 3.1 32.9 + - + +
479M ARG* 3.3 41.3 + - - +
481M MET* 1.3 76.8 - - - +
483M THR* 1.3 58.5 + - - +
485M PHE* 4.0 1.4 - - - +
486M GLY* 2.9 28.2 + - - -
487M THR 4.2 2.3 + - - -
488M GLY* 4.4 21.9 + - - +
489M ILE* 3.7 36.1 - - + -
523M PHE* 4.0 4.9 - - + -
527M PHE* 6.0 0.2 - - + -
528M MET* 3.9 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 483 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479M ARG* 2.9 30.7 + - - +
480M GLN* 3.7 7.6 - - - -
482M ILE* 1.3 77.5 - - - +
484M ALA* 1.3 62.2 + - - +
486M GLY* 3.4 12.1 + - - -
499M ARG* 4.6 6.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 484 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418M LEU* 4.4 16.4 - - + -
431M ILE* 3.9 25.6 - - + -
455M LEU* 4.2 10.5 - - + -
480M GLN 3.0 18.4 + - - +
481M MET 3.3 5.3 + - - +
483M THR* 1.3 76.1 - - - +
485M PHE* 1.3 58.1 + - + +
499M ARG* 3.0 31.4 + - - +
500M TYR* 3.1 14.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 485 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431M ILE* 3.9 22.0 - - + -
433M LEU* 4.4 9.0 - - + -
455M LEU* 5.6 0.2 - - + -
481M MET* 3.1 32.8 + - + +
482M ILE 4.1 2.5 - - - +
484M ALA* 1.3 79.7 - - + +
486M GLY* 1.3 63.6 + - - +
487M THR* 3.3 16.8 + - + +
498M ALA* 3.5 5.1 - - - -
499M ARG* 3.0 28.3 + - - +
500M TYR* 4.6 7.2 - + - +
503M ILE* 3.6 47.3 - - + -
524M PHE* 3.4 29.6 - + - -
528M MET* 3.7 24.5 - - + -
531M LEU* 4.5 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 486 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482M ILE 2.9 14.4 + - - -
483M THR* 3.8 9.9 - - - -
484M ALA 3.4 2.4 - - - -
485M PHE* 1.3 75.3 - - - +
487M THR* 1.3 58.6 + - - +
488M GLY 3.6 1.6 - - - -
497M LYS* 3.3 26.9 - - - +
499M ARG* 4.5 7.9 - - - -
----------------------------------------------------------
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