Contacts of the helix formed by residues 485 - 493 (chain A) in PDB entry 3L6X
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 ILE 485 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A LYS* 3.5 46.4 - - + +
445A ILE* 4.1 11.9 - - + +
448A LYS* 4.2 15.3 - - + -
453A VAL* 4.3 12.3 - - + -
479A LEU* 3.8 20.4 - - + +
482A HIS* 2.9 22.2 + - + +
484A SER* 1.3 80.3 - - - +
486A LYS* 1.3 64.7 + - - +
487A MET 3.5 1.3 - - - -
488A GLU* 3.2 14.1 - - + +
489A ILE* 3.0 38.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 486 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A SER 3.2 22.2 - - - +
481A SER 4.3 2.2 - - - -
482A HIS 3.5 5.4 + - - +
483A ASP* 3.4 38.8 + - - +
485A ILE* 1.3 76.7 - - - +
487A MET* 1.3 60.3 + - + +
489A ILE* 3.1 5.1 + - - +
490A VAL* 2.8 31.8 + - - +
536A ASN 2.9 14.2 + - - +
537A VAL* 3.8 27.3 - - + +
539A SER* 2.8 25.4 + - - +
540A GLU* 5.2 4.9 + - + +
541A ARG* 4.2 11.2 - - - +
758B ASP* 2.5 31.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 487 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A ASP 4.8 1.6 + - - -
484A SER 5.3 1.4 + - - -
486A LYS* 1.3 73.4 - - - +
488A GLU* 1.3 57.3 + - - +
490A VAL* 4.0 12.3 - - + -
491A ASP* 2.7 62.6 + - - +
537A VAL 5.4 0.4 - - - +
541A ARG* 3.7 37.5 - - - +
543A GLU* 3.4 39.0 - - + +
544A ALA* 4.0 23.3 - - - +
547A LYS* 4.0 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 488 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A LYS* 4.1 40.9 - - + +
451A ASP* 4.7 5.0 - - - +
453A VAL* 3.7 23.4 - - + +
454A PRO* 3.7 18.7 - - - +
484A SER 4.9 1.0 + - - +
485A ILE* 3.2 15.6 - - + +
487A MET* 1.3 76.8 - - - +
489A ILE* 1.3 58.2 + - - +
491A ASP* 4.8 0.9 - - - -
492A HIS* 2.9 62.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 489 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A VAL* 4.3 20.6 - - + -
476A LEU* 3.9 13.9 - - + +
479A LEU* 4.2 4.5 - - + -
480A SER* 3.5 41.5 - - - +
485A ILE* 3.0 29.0 + - + +
486A LYS 3.5 5.4 - - - +
488A GLU* 1.3 74.1 - - - +
490A VAL* 1.3 65.1 + - - +
493A ALA* 2.8 35.5 + - + -
494A LEU 3.2 5.2 + - - -
497A LEU* 4.7 3.6 - - + -
533A CYS* 3.9 16.6 - - - -
534A LEU* 5.5 2.5 - - + -
537A VAL* 3.8 17.0 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
486A LYS 2.8 22.4 + - - +
487A MET* 3.7 13.2 - - + +
489A ILE* 1.3 77.0 - - - +
491A ASP* 1.3 64.1 + - - +
494A LEU* 3.0 27.8 - - - +
495A HIS* 5.5 1.0 - - - -
534A LEU* 6.3 0.7 - - - -
537A VAL* 3.5 28.0 - - + +
544A ALA* 4.0 21.3 - - + -
547A LYS* 3.7 39.6 - - + +
548A LEU* 4.3 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 491 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A MET* 2.7 36.6 + - - +
488A GLU* 4.1 2.7 - - - +
490A VAL* 1.3 75.4 - - - +
492A HIS* 1.3 77.1 + - + +
494A LEU* 5.0 0.4 - - - -
495A HIS* 5.6 6.2 - - - -
543A GLU* 4.7 0.7 - - - +
547A LYS* 2.7 39.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 492 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A VAL* 4.2 11.9 - - + -
454A PRO* 4.6 18.8 - - + +
457A VAL* 3.6 19.8 - - - +
461A ARG* 5.2 3.3 + - - -
488A GLU* 2.9 54.6 + - - +
491A ASP* 1.3 93.4 + - + +
493A ALA* 1.3 59.0 + - - +
494A LEU 3.7 0.7 - - - -
495A HIS 5.4 0.9 - - - -
496A ALA* 5.2 1.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
453A VAL* 4.4 7.0 - - + -
457A VAL* 3.5 24.0 - - + -
476A LEU* 4.7 6.7 - - + -
489A ILE* 2.8 24.4 + - + +
492A HIS* 1.3 74.1 - - - +
494A LEU* 1.3 68.5 + - - +
495A HIS 3.2 2.4 + - - -
496A ALA* 3.2 2.9 + - - +
497A LEU* 2.8 43.7 + - + +
----------------------------------------------------------
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