Contacts of the helix formed by residues 421 - 428 (chain A) in PDB entry 5K9S
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 421 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A VAL* 4.0 17.9 - - + -
386A LEU* 3.8 21.1 - - + -
401A ILE* 3.7 33.4 - - + -
416A LEU* 3.5 41.1 + - + +
417A VAL* 4.0 9.1 + - - -
419A CYS 3.6 0.6 - - - -
420A GLY* 1.3 77.0 - - - +
422A ILE* 1.3 87.2 + - + +
424A PRO* 3.2 6.2 - - + +
425A LEU* 3.1 32.2 + - + +
447A ILE* 4.4 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 422 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A VAL* 4.6 6.5 - - + +
420A GLY* 3.3 2.4 - - - -
421A ILE* 1.3 90.9 - - + +
423A GLU* 1.3 60.0 + - - +
425A LEU* 3.1 8.3 + - + +
426A MET* 2.8 53.9 + - + +
444A ILE* 6.3 1.3 - - + -
447A ILE* 4.4 15.3 - - + -
460A LEU* 4.1 20.9 - - + -
463A MET* 4.1 26.2 - - + +
464A ILE* 4.0 26.0 - - + -
467A CYS* 4.1 16.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 423 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A GLY 4.1 2.3 + - - +
422A ILE* 1.3 78.5 - - - +
424A PRO* 1.3 71.8 - - + +
426A MET* 3.0 3.4 + - - +
427A ASN* 2.9 38.8 + - - +
466A GLU 4.8 1.9 - - - +
467A CYS* 3.7 47.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 424 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A VAL* 4.1 11.0 - - + -
386A LEU* 4.1 18.9 - - + +
387A SER* 3.2 34.1 - - - +
420A GLY 3.1 25.1 - - - +
421A ILE* 3.2 13.5 - - - +
423A GLU* 1.3 89.7 - - + +
425A LEU* 1.3 58.7 + - - +
427A ASN* 3.5 13.6 + - + +
428A LEU* 3.5 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 425 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A LEU* 3.7 25.7 - - + +
398A ALA* 5.1 4.5 - - - +
401A ILE* 4.3 21.8 - - + -
421A ILE* 3.1 28.9 + - + +
422A ILE* 3.1 10.9 + - + +
423A GLU 3.1 0.6 - - - -
424A PRO* 1.3 75.1 - - - +
426A MET* 1.3 77.0 + - + +
428A LEU* 3.2 17.8 + - + +
429A LEU 3.7 3.8 + - - -
440A ILE* 3.8 37.1 - - + +
443A ALA* 4.3 15.3 - - + -
444A ILE* 4.9 5.2 - - + -
447A ILE* 4.8 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 426 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A ILE* 2.8 48.1 + - + +
423A GLU* 3.6 7.0 - - - +
425A LEU* 1.3 80.7 - - + +
427A ASN* 1.3 66.3 + - - +
429A LEU* 3.0 31.2 + - - +
444A ILE* 3.4 40.2 - - + -
464A ILE* 4.1 16.8 - - + -
467A CYS* 4.6 7.2 - - + +
469A GLY* 3.7 38.1 - - - +
472A LYS* 3.4 14.0 - - + +
473A ILE* 4.7 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 427 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A GLU* 2.9 34.9 + - - +
424A PRO* 3.7 13.2 - - + +
425A LEU 3.2 0.4 - - - -
426A MET* 1.3 78.9 - - - +
428A LEU* 1.3 61.4 + - + +
430A SER* 3.4 21.7 + - - -
467A CYS 4.5 7.8 - - - +
472A LYS* 3.9 13.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 428 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A LEU* 3.5 36.3 - - + +
391A PHE* 4.1 21.8 - - + -
394A GLN* 4.0 35.2 - - + +
398A ALA* 4.6 1.8 - - + -
424A PRO 3.5 8.9 + - - +
425A LEU* 3.2 5.9 + - + +
426A MET 3.2 1.0 - - - -
427A ASN* 1.3 75.2 - - + +
429A LEU* 1.3 56.0 + - - +
430A SER 3.0 6.1 - - - -
431A ALA* 3.0 27.8 + - + +
436A ILE* 3.9 20.8 - - + +
437A ILE* 4.9 0.5 - - - +
440A ILE* 3.4 24.6 - - + +
----------------------------------------------------------
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