Contacts of the helix formed by residues 486 - 497 (chain A) in PDB entry 4OE5
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 ASP 486 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A HIS* 4.1 5.2 - - + -
326A SER* 3.1 19.0 + - - +
484A SER* 3.1 6.7 + - - +
485A GLN* 1.3 77.4 - - - +
487A LYS* 1.3 66.0 + - - +
488A ASP* 3.1 17.8 + - - +
489A VAL* 2.8 43.9 + - + +
490A VAL* 3.0 20.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 487 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A GLN 3.3 6.9 + - - +
486A ASP* 1.3 71.8 - - - +
488A ASP* 1.3 62.4 + - - +
490A VAL* 3.1 12.2 + - - +
491A GLN* 3.0 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 488 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A ASP* 3.1 13.6 + - - +
487A LYS* 1.3 77.5 - - - +
489A VAL* 1.3 56.6 + - + +
491A GLN* 3.7 5.7 + - - +
492A GLU* 3.1 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 489 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A PHE* 5.4 2.7 - - + -
324A HIS* 3.7 42.6 - - + +
463A TYR* 4.1 28.0 - - + +
467A LEU* 5.4 1.6 - - + -
482A VAL* 5.4 1.1 - - + -
484A SER* 3.6 9.2 - - - +
486A ASP* 2.8 36.4 + - + +
488A ASP* 1.3 73.5 - - + +
490A VAL* 1.3 61.1 + - - +
492A GLU* 3.4 6.1 - - - +
493A ALA* 2.7 35.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 490 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A VAL* 4.8 7.2 - - + -
484A SER* 4.0 26.0 - - - +
486A ASP 3.0 17.1 + - - +
487A LYS* 3.1 13.6 + - - +
489A VAL* 1.3 78.0 - - - +
491A GLN* 1.3 63.3 + - - +
493A ALA* 3.8 5.5 - - - +
494A THR* 2.8 31.5 + - - +
506A ILE* 3.7 46.2 - - + -
507A ASN* 5.2 0.2 - - - +
549B GLU* 5.2 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 491 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A LYS 3.0 15.3 + - - +
488A ASP* 4.0 6.5 - - - +
490A VAL* 1.3 78.6 - - - +
492A GLU* 1.3 65.3 + - - +
494A THR* 3.4 7.0 + - - -
495A LYS* 3.4 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 492 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A TYR* 2.4 37.8 + - - -
464A LYS* 3.5 19.8 - - - +
467A LEU* 4.5 5.7 - - + +
488A ASP 3.1 19.8 + - - +
489A VAL* 3.4 7.7 - - - +
490A VAL 3.2 0.2 - - - -
491A GLN* 1.3 75.7 - - - +
493A ALA* 1.3 63.9 + - - +
495A LYS* 3.1 16.4 + - - +
496A VAL* 3.2 27.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 493 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A PHE* 5.4 0.2 - - + -
467A LEU* 3.9 27.1 - - + +
482A VAL* 3.7 35.2 - - + -
489A VAL* 2.7 23.2 + - + +
490A VAL 3.8 2.9 - - - +
492A GLU* 1.3 72.8 - - - +
494A THR* 1.3 57.2 + - - +
496A VAL* 3.4 1.1 + - - -
497A LEU* 2.9 36.2 + - - +
504A PHE* 4.7 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 494 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A VAL* 2.8 26.3 + - - +
491A GLN* 3.8 7.7 - - - -
492A GLU 3.2 0.2 - - - -
493A ALA* 1.3 79.1 - - - +
495A LYS* 1.3 61.9 + - - +
497A LEU 3.8 0.9 - - - -
498A ARG* 3.1 24.8 + - + +
504A PHE* 3.8 25.0 - - + -
506A ILE* 4.6 4.7 - - - +
545B GLN* 4.9 4.4 + - - +
547B ILE* 3.7 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 495 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A GLN 3.4 9.4 + - - +
492A GLU* 3.1 10.4 + - - +
494A THR* 1.3 77.4 - - - +
496A VAL* 1.3 67.2 + - + +
498A ARG* 3.3 22.0 + - - +
118B LEU* 4.1 33.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 496 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A LYS 5.6 0.2 - - - +
467A LEU* 3.8 45.8 - - + +
468A GLN* 4.0 10.3 - - + +
471A ASP* 3.9 16.6 - - + +
492A GLU* 3.2 26.8 + - + +
493A ALA 3.9 5.2 - - - +
495A LYS* 1.3 79.1 - - + +
497A LEU* 1.3 59.2 + - + +
498A ARG* 3.3 2.6 + - - +
499A ASN 4.8 0.9 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
320A PHE* 3.7 22.7 - - + -
322A PHE* 4.9 1.6 - - + -
467A LEU* 3.6 35.0 - - + +
470A VAL* 3.6 27.8 - - + -
471A ASP* 4.1 5.8 - - + +
482A VAL* 3.8 22.2 - - + -
493A ALA 2.9 20.2 + - - +
494A THR 3.8 2.2 - - - -
496A VAL* 1.3 76.1 - - + +
498A ARG* 1.3 58.2 + - - +
499A ASN 3.1 2.9 - - - -
500A ALA* 2.7 39.1 + - + +
501A ALA 3.7 4.5 + - - -
504A PHE* 3.9 15.4 - - + -
545B GLN* 4.1 4.6 + - - -
----------------------------------------------------------
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