Contacts of the helix formed by residues 604 - 619 (chain A) in PDB entry 1SNX
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 ALA 604 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A GLU* 3.5 12.3 - - - +
538A LYS* 4.2 11.9 - - - +
541A VAL* 5.0 1.8 - - - -
603A PRO* 1.3 76.0 - - - +
605A PHE* 1.3 58.0 + - - +
606A SER* 3.5 17.0 - - - +
607A ARG* 2.6 35.3 + - + +
608A LEU* 2.9 12.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 605 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A CYS* 3.9 14.5 - - - -
470A MET* 3.5 38.6 - - + -
471A ALA* 3.4 17.4 - - + +
474A GLU* 2.4 41.3 + - + +
483A LEU* 4.4 2.2 - - + -
537A SER* 3.4 25.6 - - - -
540A ASP* 4.3 9.2 - - + -
541A VAL* 3.5 27.3 - - + +
544A PHE* 3.7 32.5 - + + -
604A ALA* 1.3 70.3 - - - +
606A SER* 1.3 59.9 + - - +
608A LEU* 3.3 18.2 + - + +
609A LEU* 3.1 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 606 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A ALA* 4.1 9.2 - - - +
474A GLU* 2.6 19.7 + - - -
604A ALA* 2.8 10.3 + - - +
605A PHE* 1.3 74.8 - - - +
607A ARG* 1.3 82.1 + - - -
609A LEU* 3.6 9.1 - - - +
610A ARG* 2.8 40.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 607 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A PRO* 4.8 8.1 - - + -
604A ALA* 2.6 25.1 + - - +
606A SER* 1.3 91.2 + - - +
608A LEU* 1.3 58.4 + - - +
610A ARG* 2.8 24.6 + - + +
611A GLN* 2.8 44.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 608 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A CYS* 3.8 9.9 - - - -
541A VAL* 4.5 13.5 - - + -
544A PHE* 4.2 16.4 - - + -
590A ILE* 3.7 29.8 - - + -
594A CYS* 4.7 7.0 - - - -
603A PRO* 3.9 22.2 - - + +
604A ALA 2.9 11.5 + - - +
605A PHE* 3.4 46.0 - - + +
607A ARG* 1.3 77.3 - - - +
609A LEU* 1.3 52.2 + - - +
611A GLN* 2.9 11.2 + - - +
612A LEU* 2.6 41.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 609 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A LEU* 3.3 28.8 - - + +
467A CYS* 3.5 8.9 - - + -
468A GLU* 3.3 48.2 - - + +
471A ALA* 4.2 15.3 - - + -
605A PHE 3.1 6.0 + - - +
606A SER* 3.6 12.1 - - - +
607A ARG 3.1 0.2 + - - -
608A LEU* 1.3 78.1 - - - +
610A ARG* 1.3 67.5 + - - +
613A ALA* 2.9 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 610 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606A SER* 2.8 51.2 + - - +
607A ARG* 2.8 24.8 + - + +
609A LEU* 1.3 81.0 - - - +
611A GLN* 1.3 64.7 + - + +
613A ALA* 3.2 8.8 - - - +
614A GLU* 3.0 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 611 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590A ILE* 4.0 30.0 - - + +
593A HIS* 4.6 13.7 + - - -
603A PRO* 4.5 11.2 - - - +
607A ARG* 2.8 35.4 + - + +
608A LEU* 2.9 17.9 + - + +
610A ARG* 1.3 77.6 - - + +
612A LEU* 1.3 57.9 + - + +
614A GLU* 3.0 36.1 + - - +
615A ILE* 3.3 12.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 612 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A LEU* 3.9 22.8 - - + +
463A CYS* 4.1 12.6 - - + -
464A LEU* 3.1 50.7 - - + +
467A CYS* 4.2 13.5 - - + -
544A PHE* 4.5 9.6 - - + -
548A MET* 4.6 10.5 - - + -
590A ILE* 3.3 33.9 - - + -
608A LEU* 2.6 19.6 + - + +
611A GLN* 1.3 69.9 - - + +
613A ALA* 1.3 59.4 + - - +
615A ILE* 4.0 6.1 - - + +
616A ALA* 3.0 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 613 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A LEU* 4.0 11.9 - - + +
609A LEU 2.9 19.2 + - - +
610A ARG* 3.2 10.5 - - - +
612A LEU* 1.3 76.0 - - - +
614A GLU* 1.3 71.0 + - - +
616A ALA* 3.4 5.2 + - - +
617A GLU* 2.8 26.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 614 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610A ARG* 3.0 16.8 + - - +
611A GLN* 3.0 18.3 + - - +
613A ALA* 1.3 75.9 - - - +
615A ILE* 1.3 57.1 + - + +
617A GLU* 2.6 47.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 615 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A LEU* 3.7 16.2 - - + +
584A SER* 5.6 1.3 - - - -
586A HIS* 2.9 49.8 - - + +
587A VAL* 4.3 13.5 - - + +
589A GLN* 4.8 3.4 - - - +
590A ILE* 3.6 22.7 - - + -
611A GLN* 3.3 14.0 + - + +
612A LEU* 3.7 3.1 + - - +
614A GLU* 1.3 77.2 - - + +
616A ALA* 1.3 57.3 + - - +
617A GLU* 2.8 11.8 + - - -
618A SER* 3.8 8.8 + - - -
619A GLY* 4.0 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 616 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A GLU* 4.9 18.4 - - - +
460A LEU* 3.2 22.8 - - + +
461A GLY* 6.4 0.2 - - - -
464A LEU* 4.7 8.3 - - + -
612A LEU 3.0 21.0 + - - +
613A ALA* 3.7 8.1 - - - +
614A GLU 3.0 0.4 + - - -
615A ILE* 1.3 74.9 - - - +
617A GLU* 1.3 60.4 + - + +
618A SER 3.7 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 617 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613A ALA* 2.8 29.8 - - - +
614A GLU* 2.6 22.4 + - - +
615A ILE* 2.8 1.7 - - - -
616A ALA* 1.3 81.0 - - + +
618A SER* 1.3 67.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 618 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A GLU* 5.1 12.6 + - - +
615A ILE* 4.3 2.5 - - - -
616A ALA 3.7 4.4 + - - -
617A GLU* 1.3 79.3 - - - +
619A GLY* 1.3 61.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 619 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584A SER* 4.9 16.3 + - - -
585A THR* 5.3 1.6 + - - -
586A HIS* 4.6 16.9 - - - -
615A ILE* 4.0 25.2 + - - +
618A SER* 1.3 84.8 + - - +
----------------------------------------------------------
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