Contacts of the helix formed by residues 478 - 489 (chain G) in PDB entry 5K5L
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 GLU 478 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441G HIS* 4.8 5.7 - - - +
459G GLN 3.2 17.3 - - - +
460G HIS* 2.5 46.8 + - - +
461G SER 4.0 5.4 - - - +
462G TYR* 5.6 0.2 - - - -
463G ILE* 4.6 3.6 - - - +
476G PHE* 3.5 6.2 - - - +
477G HIS* 1.3 78.9 - - - +
479G ARG* 1.3 63.9 + - - +
480G TYR* 4.0 4.1 - - - +
481G ALA* 3.3 32.2 + - + +
482G LEU* 3.5 21.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 479 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D C 2.6 52.1 + - - -
9D A 3.3 19.0 + - - -
458G LYS* 3.4 51.2 - - - +
459G GLN* 3.5 11.5 + - - +
461G SER 4.6 2.6 + - - -
463G ILE* 5.0 6.6 - - + +
467G LYS* 5.0 10.9 - - - +
478G GLU* 1.3 74.5 - - - +
480G TYR* 1.3 67.7 + - - +
482G LEU* 3.0 12.1 + - + +
483G ILE* 3.0 45.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 480 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441G HIS 4.7 4.0 - - - -
442G CYS* 3.4 35.2 - - + +
443G ASP* 4.6 4.3 + - - +
444G THR* 4.9 4.3 + - - -
455G HIS* 5.1 3.6 - + - -
459G GLN* 3.0 37.3 + - + +
460G HIS* 3.6 25.6 - + + +
478G GLU* 3.5 5.1 - - - +
479G ARG* 1.3 75.5 - - - +
481G ALA* 1.3 67.3 + - + +
483G ILE* 3.3 5.7 + - + +
484G GLN* 3.1 67.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 481 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476G PHE* 3.8 22.3 - - + -
478G GLU* 3.3 25.7 + - + +
479G ARG 3.3 0.6 - - - -
480G TYR* 1.3 82.6 - - + +
482G LEU* 1.3 63.0 + - - +
484G GLN* 4.0 4.2 - - - +
485G HIS* 3.1 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 482 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467G LYS* 4.1 34.3 - - + +
468G LYS 4.3 2.5 - - - +
469G CYS* 4.0 14.1 - - - +
476G PHE* 3.9 32.0 - - + -
478G GLU 3.5 12.9 + - - +
479G ARG* 3.0 15.3 + - + +
481G ALA* 1.3 79.7 - - - +
483G ILE* 1.3 66.5 + - + +
485G HIS* 3.3 2.5 + - - +
486G GLN* 3.1 51.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 483 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D C 4.8 0.4 - - - +
9D A 3.2 26.9 - - - +
459G GLN* 4.0 6.5 - - - +
479G ARG* 3.0 44.2 + - + +
480G TYR* 3.9 4.0 - - + +
482G LEU* 1.3 80.2 - - + +
484G GLN* 1.3 69.8 + - - +
486G GLN* 3.3 11.8 + - + +
487G LYS* 3.0 51.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 484 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480G TYR* 3.1 60.1 + - + +
481G ALA* 4.2 4.7 - - - +
483G ILE* 1.3 90.1 - - - +
485G HIS* 1.3 61.3 + - - +
487G LYS* 3.5 22.2 + - - +
488G SER* 3.3 20.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 485 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469G CYS* 3.4 19.7 - - + -
472G CYS* 3.2 11.0 - - - -
474G ALA* 4.7 4.0 - - + -
476G PHE* 3.4 29.2 - + + -
481G ALA 3.1 19.1 + - - +
482G LEU 3.5 3.6 - - - +
483G ILE 3.2 0.2 - - - -
484G GLN* 1.3 77.6 - - - +
486G GLN* 1.3 58.9 + - + +
488G SER* 2.6 29.2 + - - -
489G HIS* 3.1 19.3 - + - -
502G ZN 2.1 36.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 486 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468G LYS 4.3 1.6 + - - -
469G CYS* 3.8 17.7 - - - +
470G ARG* 3.3 52.5 + - - +
471G TYR* 3.8 18.0 + - + +
482G LEU* 3.1 45.4 + - + +
483G ILE* 3.3 10.8 + - - +
485G HIS* 1.3 72.6 - - - +
487G LYS* 1.3 65.8 + - - +
489G HIS* 3.4 21.3 + - - +
490G LYS* 4.7 6.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 487 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C G 5.6 4.4 + - - +
483G ILE* 3.0 39.6 + - + +
484G GLN* 3.7 27.6 - - - +
485G HIS 3.3 0.2 - - - -
486G GLN* 1.3 76.3 - - + +
488G SER* 1.3 62.3 + - - +
489G HIS 3.3 0.7 + - - -
490G LYS* 3.4 33.8 + - + +
491G ASN 4.8 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 488 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484G GLN 3.3 10.5 + - - -
485G HIS* 2.6 27.7 + - - -
487G LYS* 1.3 75.4 - - - +
489G HIS* 1.3 63.1 + - - +
490G LYS 2.8 12.8 + - - -
491G ASN* 2.8 44.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 489 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469G CYS* 3.8 0.2 - - - -
471G TYR* 3.3 41.0 - + + +
472G CYS* 3.9 8.5 - - + -
485G HIS* 3.0 34.4 + + - -
486G GLN* 3.7 9.9 - - - +
487G LYS 3.2 1.8 - - - -
488G SER* 1.3 83.7 + - - +
490G LYS* 1.3 59.7 + - + +
491G ASN* 3.5 3.7 - - - +
502G ZN 2.0 37.9 - - - -
----------------------------------------------------------
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