Contacts of the helix formed by residues 487 - 501 (chain C) in PDB entry 1O23
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 LEU 487 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405C LEU* 4.1 15.0 - - + -
413C ALA* 3.6 30.7 - - + +
414C ILE* 5.1 2.7 - - + -
440C THR* 4.4 10.3 - - + -
454C LEU* 3.9 27.8 - - + -
455C PHE* 5.5 0.2 - - + -
484C ASP 4.0 14.1 - - - +
485C ASP 3.5 13.7 + - - +
486C GLU* 1.3 73.8 - - - +
488C ASP* 1.3 66.4 + - - +
489C ASP 3.2 3.4 - - - -
490C ASP* 3.1 20.5 + - + +
491C ILE* 2.9 38.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 488 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413C ALA 5.2 2.1 - - - +
486C GLU* 3.5 3.6 - - + +
487C LEU* 1.3 77.3 - - - +
489C ASP* 1.3 57.6 + - - +
491C ILE* 3.5 15.5 + - - +
492C ALA* 2.9 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 489 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477C ILE* 4.6 17.8 - - + +
481C LYS* 3.6 30.5 - - - +
482C LEU* 4.3 3.0 - - - +
484C ASP* 4.8 1.0 - - - +
486C GLU* 3.0 5.8 - - - +
488C ASP* 1.3 73.2 - - - +
490C ASP* 1.3 69.8 + - - +
491C ILE 3.2 0.2 - - - -
492C ALA* 3.9 6.5 - - - +
493C CYS* 3.0 24.9 + - - +
806C CA 2.3 31.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 490 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440C THR* 5.5 0.7 - - - +
452C TYR 5.3 0.3 - - - +
454C LEU* 4.6 11.7 + - + +
455C PHE* 3.8 23.8 + - + +
457C ILE* 3.8 4.9 - - + +
481C LYS 3.6 0.7 - - - +
482C LEU* 3.5 41.2 - - + +
484C ASP 5.0 1.0 - - - +
486C GLU 3.4 3.8 - - - +
487C LEU* 3.1 22.6 + - + +
489C ASP* 1.3 76.7 - - - +
491C ILE* 1.3 58.0 + - - +
493C CYS* 3.2 3.5 + - - +
494C ALA* 2.8 30.0 + - - +
806C CA 2.4 29.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 491 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413C ALA 3.6 24.0 - - - +
414C ILE* 3.7 29.2 - - + -
416C ASP* 4.9 10.8 - - + +
417C ILE* 4.0 26.9 - - + +
455C PHE* 4.2 7.9 - - + -
487C LEU* 2.9 28.8 + - + +
488C ASP* 3.6 14.4 - - - +
490C ASP* 1.3 77.3 - - - +
492C ALA* 1.3 63.3 + - - +
494C ALA* 3.1 7.5 + - - +
495C LYS* 2.9 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 492 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488C ASP 2.9 17.2 + - - +
489C ASP* 3.4 7.2 + - - +
491C ILE* 1.3 77.3 - - - +
493C CYS* 1.3 62.1 + - - +
495C LYS* 3.4 14.0 + - - +
496C LYS* 3.3 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 493 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457C ILE* 3.5 37.7 - - + -
462C TRP* 4.2 2.5 - - - -
475C CYS* 2.0 52.7 - - + -
477C ILE* 4.4 9.9 - - + -
489C ASP 3.0 18.4 + - - +
490C ASP 3.6 3.6 - - - +
492C ALA* 1.3 75.4 - - - +
494C ALA* 1.3 66.5 + - - +
496C LYS* 2.9 14.6 + - - +
497C ILE* 3.1 16.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 494 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417C ILE* 4.2 9.2 - - + -
455C PHE* 3.6 36.3 - - + -
457C ILE* 4.1 1.1 - - - +
490C ASP 2.8 18.3 + - - +
491C ILE 3.5 4.7 - - - +
493C CYS* 1.3 76.0 - - - +
495C LYS* 1.3 57.3 + - - +
497C ILE* 3.2 8.6 + - - +
498C LEU* 2.8 33.4 + - - +
506C TRP* 3.8 15.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 495 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416C ASP* 2.4 44.4 + - - -
417C ILE* 4.1 14.8 - - + +
420C TYR* 3.6 43.5 + - + +
491C ILE* 2.9 27.5 + - - +
492C ALA* 3.5 13.9 - - - +
493C CYS 3.1 0.2 - - - -
494C ALA* 1.3 77.6 - - - +
496C LYS* 1.3 56.3 + - - +
498C LEU* 3.2 10.2 + - - +
499C ALA* 2.9 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 496 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462C TRP* 5.0 0.2 - - + -
474C ILE* 3.2 34.9 + - + +
475C CYS* 3.9 28.7 + - - -
492C ALA 3.3 11.4 + - - +
493C CYS* 2.9 10.1 + - - +
495C LYS* 1.3 76.0 - - - +
497C ILE* 1.3 66.7 + - - +
499C ALA* 3.2 5.0 + - - +
500C ILE* 2.9 40.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 497 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457C ILE* 4.0 28.9 - - + -
462C TRP* 3.4 49.4 - - + -
493C CYS* 3.1 14.9 + - - +
494C ALA* 3.5 5.8 - - - +
496C LYS* 1.3 75.7 - - - +
498C LEU* 1.3 58.6 + - - +
501C LYS* 2.7 27.9 + - + -
502C GLY 2.7 6.9 + - - +
505C TYR* 3.5 45.5 - - + -
506C TRP* 3.8 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 498 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417C ILE* 4.2 12.1 - - + -
420C TYR* 3.7 37.9 - - + +
421C GLN* 3.6 24.7 + - + -
423C ILE* 4.6 2.2 - - + -
428C TRP* 3.8 20.9 - - + +
494C ALA 2.8 14.8 + - - +
495C LYS* 3.4 9.6 - - - +
497C ILE* 1.3 78.0 - - - +
499C ALA* 1.3 59.4 + - - +
502C GLY* 2.9 24.2 + - - +
503C ILE* 3.2 43.7 - - + +
506C TRP* 4.0 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 499 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420C TYR* 3.9 16.8 - - + +
421C GLN* 4.3 12.2 + - - +
495C LYS 2.9 16.3 + - - +
496C LYS* 3.2 6.0 + - - +
498C LEU* 1.3 77.6 - - - +
500C ILE* 1.3 63.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 500 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462C TRP* 4.1 17.9 - - + -
474C ILE* 4.0 33.2 - - + -
496C LYS* 2.9 24.0 + - + +
499C ALA* 1.3 82.4 - - + +
501C LYS* 1.3 64.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 501 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462C TRP* 4.4 20.9 - - + +
497C ILE* 2.7 17.2 + - + +
500C ILE* 1.3 76.2 - - + +
502C GLY* 1.3 63.8 + - - +
504C ASP* 4.8 11.0 + - - +
505C TYR* 4.1 36.3 - - + +
----------------------------------------------------------
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