Contacts of the helix formed by residues 459 - 470 (chain A) in PDB entry 5H65
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 459 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A PHE* 4.3 7.0 - - - -
432A ARG* 4.0 13.9 - - - +
457A GLY 5.2 0.2 - - - +
458A GLY* 1.3 74.5 - - - -
460A LEU* 1.3 59.7 + - - +
461A SER* 3.4 9.4 + - - -
462A GLU* 3.0 40.3 + - - +
463A ILE* 2.9 32.9 + - - +
285B CYS* 5.9 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 460 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A GLU* 4.1 28.7 - - + +
397A LEU* 4.1 25.6 - - + -
398A ASP* 4.0 15.3 + - - +
401A PHE* 3.9 35.7 - - + +
459A THR* 1.3 73.0 - - - +
461A SER* 1.3 58.3 + - - +
463A ILE* 3.4 8.2 + - + +
464A CYS* 2.9 52.0 + - - -
491A PRO* 6.1 0.7 - - + -
494A ILE* 5.9 1.1 - - + -
499A HIS* 4.0 15.5 - - + +
575A MET* 5.7 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 461 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A THR* 3.4 8.4 + - - -
460A LEU* 1.3 79.7 - - - +
462A GLU* 1.3 58.4 + - - +
464A CYS* 3.3 7.1 + - - +
465A LYS* 3.0 46.6 + - - +
286B THR 5.6 2.5 + - - -
288B PRO* 3.9 33.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 462 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A ARG* 2.8 41.9 + - - -
434A VAL* 4.6 1.0 - - - +
455A ILE* 5.3 0.2 - - + -
458A GLY* 3.5 6.5 - - - -
459A THR* 3.0 31.7 + - - +
461A SER* 1.3 73.0 - - - +
463A ILE* 1.3 60.5 + - - +
465A LYS* 3.2 3.8 + - - +
466A LEU* 2.8 37.5 + - + +
278B CYS 3.7 21.4 - - - +
279B LEU* 3.6 21.0 - - + +
280B THR* 2.8 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 463 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A PHE* 3.5 39.7 - - + -
455A ILE* 3.9 34.5 - - + -
458A GLY 4.1 4.5 - - - +
459A THR 2.9 21.9 + - - +
460A LEU* 3.6 9.0 - - + +
462A GLU* 1.3 75.5 - - - +
464A CYS* 1.3 59.8 + - - +
466A LEU* 3.4 9.1 + - - +
467A SER* 2.9 27.4 + - - -
473A VAL* 3.9 13.3 - - + +
475A PRO* 4.5 4.7 - - + -
494A ILE* 3.8 33.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 464 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A LEU* 2.9 32.6 + - - +
461A SER* 3.7 6.1 - - - +
463A ILE* 1.3 75.4 - - - +
465A LYS* 1.3 63.5 + - - +
467A SER* 2.7 23.4 + - - +
468A ASN* 3.4 15.8 + - - +
494A ILE* 5.2 0.4 - - - -
499A HIS* 3.8 32.8 - - - -
575A MET* 5.3 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 465 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A SER* 3.0 29.3 + - - +
462A GLU* 3.6 7.4 - - + +
464A CYS* 1.3 74.4 - - + +
466A LEU* 1.3 64.0 + - - +
468A ASN* 3.2 24.4 + - - +
469A LYS* 3.4 9.5 + - - +
277B SER 5.3 1.3 - - - +
278B CYS* 3.6 39.9 + - + +
280B THR* 4.6 12.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 466 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A VAL* 4.9 3.8 - - + -
453A LEU* 3.8 23.3 - - + -
455A ILE* 3.6 32.8 - - + -
462A GLU 2.8 25.0 + - - +
463A ILE* 3.4 7.6 + - - +
465A LYS* 1.3 72.2 - - - +
467A SER* 1.3 59.1 + - - +
469A LYS 3.1 1.4 + - - -
470A PHE* 2.8 36.9 + - + +
473A VAL* 3.9 15.9 - - + -
275B ALA* 3.8 27.8 - - + +
278B CYS* 3.6 24.4 - - + -
279B LEU* 4.2 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 467 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A ILE 2.9 14.1 + - - -
464A CYS* 2.7 25.1 + - - +
466A LEU* 1.3 74.9 - - - +
468A ASN* 1.3 59.3 + - - +
470A PHE 2.9 20.2 - - - +
471A ASN 4.5 0.3 - - - +
472A SER* 5.2 2.5 - - - +
473A VAL* 4.0 7.8 - - - +
494A ILE* 3.7 30.9 - - - +
496A GLY* 3.4 31.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 468 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A CYS 3.5 15.1 + - - +
465A LYS* 3.2 17.5 + - - +
467A SER* 1.3 83.3 + - - +
469A LYS* 1.3 62.7 + - + +
470A PHE 4.2 1.7 - - - +
496A GLY* 5.1 5.7 - - - +
497A THR* 5.9 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 469 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A SER* 3.4 24.6 + - - -
449A ASN* 4.3 2.6 + - - +
465A LYS 3.4 4.2 + - - +
466A LEU 3.1 3.4 + - - +
468A ASN* 1.3 80.4 - - + +
470A PHE* 1.3 73.3 + - + +
274B LEU* 3.9 25.8 - - + +
277B SER* 3.3 26.7 - - - +
278B CYS* 3.6 22.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 470 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A PHE* 4.0 12.8 - + - -
448A SER* 3.2 29.4 - - - -
449A ASN* 4.4 4.3 - - - -
451A CYS* 3.6 12.8 - - + +
453A LEU* 3.6 42.8 - - + -
466A LEU* 2.8 26.5 + - + +
467A SER 2.9 19.9 - - - +
468A ASN 4.2 1.7 - - - +
469A LYS* 1.3 83.1 - - + +
471A ASN* 1.3 63.8 + - - +
472A SER 3.4 4.7 - - - +
271B LEU* 3.4 33.9 - - + -
274B LEU* 3.8 17.5 - - + -
275B ALA* 3.8 18.6 - - - -
----------------------------------------------------------
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