Contacts of the helix formed by residues 575 - 590 (chain A) in PDB entry 2ADS
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 TYR 575 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A ILE 5.0 2.7 - - - -
505A ARG* 3.9 24.5 - - + +
570A ARG* 4.3 7.9 - - - -
573A ARG* 4.1 45.5 - - + +
574A LEU* 1.4 74.9 - - - +
576A ARG* 1.3 66.4 + - - +
577A ASP* 3.3 7.0 - - + +
578A GLU* 2.9 42.3 + - + -
579A VAL* 3.0 12.9 + - - +
13G C 4.6 10.4 + - + -
14G C 5.0 9.2 - - - -
10M G 4.5 9.5 + - - -
11M G 4.1 30.8 + - - -
12M G 5.1 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 576 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575A TYR* 1.3 74.5 - - - +
577A ASP* 1.3 67.2 + - - +
579A VAL* 3.6 6.7 + - - +
580A ALA* 3.4 20.4 + - - +
14G C 5.5 0.4 - - - -
15G C 3.5 44.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 577 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A ARG* 4.8 7.7 + - - +
541A GLU* 3.3 29.1 - - + +
544A THR* 4.1 18.3 - - - +
575A TYR* 3.3 4.4 - - + +
576A ARG* 1.3 81.1 + - - +
578A GLU* 1.3 58.8 + - + +
580A ALA* 3.5 4.8 + - - +
581A ALA* 3.0 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 578 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A ILE* 3.2 29.8 - - + +
505A ARG* 3.1 36.8 + - - +
544A THR* 4.1 9.0 - - - +
570A ARG* 2.9 36.0 + - - -
574A LEU* 3.7 10.8 - - + -
575A TYR* 2.9 29.1 + - + +
577A ASP* 1.3 73.2 - - - +
579A VAL* 1.3 67.2 + - - +
581A ALA* 3.2 1.4 + - - +
582A PHE* 3.0 36.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 579 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574A LEU* 3.6 32.7 - - + +
575A TYR 3.0 16.4 + - - +
576A ARG* 3.9 5.8 - - - +
578A GLU* 1.3 76.7 - - - +
580A ALA* 1.3 65.4 + - - +
582A PHE* 3.6 5.3 + - - +
583A LYS* 3.3 52.8 + - + +
595A LEU* 4.7 4.6 - - + +
597A GLU* 5.3 0.9 - - - +
646A VAL* 4.5 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 580 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576A ARG 3.4 10.1 + - - +
577A ASP* 3.8 8.3 - - - +
578A GLU 3.3 0.4 - - - -
579A VAL* 1.3 80.5 - - - +
581A ALA* 1.3 64.9 + - - +
583A LYS* 3.2 8.7 + - - +
584A LYS* 3.1 41.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 581 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A THR* 3.3 20.4 - - + -
545A GLU* 3.2 27.4 - - - +
548A ILE* 3.6 6.3 - - + -
577A ASP 3.0 18.0 + - - +
578A GLU 3.2 2.4 + - - +
580A ALA* 1.3 76.2 - - - +
582A PHE* 1.3 63.1 + - - +
584A LYS* 3.1 18.9 + - - +
585A TYR* 3.1 22.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 582 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A ILE* 3.4 37.7 - - + -
503A ILE* 4.0 13.7 - - + -
548A ILE* 3.5 41.1 - - + -
552A PHE* 4.2 10.0 - + - -
568A VAL* 4.4 12.6 - - + -
570A ARG* 4.8 2.0 - - - -
574A LEU* 3.5 28.7 - - + -
578A GLU* 3.0 34.5 + - + +
579A VAL* 4.0 4.3 - - - +
581A ALA* 1.3 75.7 - - - +
583A LYS* 1.3 56.4 + - - +
585A TYR* 3.3 4.5 + - - +
586A GLY 2.8 24.1 + - - -
593A LEU* 3.1 12.8 - - + +
595A LEU* 4.0 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 583 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579A VAL* 3.3 36.2 - - + +
580A ALA* 3.2 10.0 + - - +
581A ALA 3.2 0.4 - - - -
582A PHE* 1.3 75.1 - - - +
584A LYS* 1.3 62.7 + - + +
586A GLY* 3.1 2.3 + - - -
587A GLU* 3.1 33.7 + - - +
593A LEU* 4.5 4.9 - - + -
595A LEU* 3.9 23.3 - - + -
646A VAL* 4.4 10.0 + - - +
647A TYR* 4.6 16.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 584 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A GLU* 5.2 10.3 + - - +
580A ALA* 3.1 29.6 + - - +
581A ALA* 3.1 12.0 + - - +
583A LYS* 1.3 75.3 - - + +
585A TYR* 1.3 65.1 + - + +
587A GLU* 3.0 14.2 + - - +
588A LEU* 3.0 34.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 585 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A GLU* 2.8 65.7 + - - +
548A ILE* 3.4 25.4 - - + -
549A GLY* 4.2 12.3 - - - -
552A PHE* 3.6 24.1 - + + -
581A ALA* 3.1 24.4 + - + -
582A PHE 3.8 3.1 - - - +
584A LYS* 1.3 78.7 - - + +
586A GLY* 1.3 62.0 + - - +
588A LEU* 4.2 18.4 - - + -
589A TYR* 3.0 48.3 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 586 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552A PHE* 3.7 1.5 - - - -
582A PHE 2.8 12.9 + - - -
583A LYS 3.5 6.1 - - - -
584A LYS 3.1 0.6 - - - -
585A TYR* 1.3 77.6 - - - +
587A GLU* 1.3 56.0 + - - +
590A GLY* 2.9 7.6 + - - -
591A TYR 2.8 29.0 + - - +
593A LEU* 3.4 31.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 587 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562A LYS* 5.4 2.9 + - - -
583A LYS* 3.4 21.7 - - - +
584A LYS* 3.0 12.4 + - - +
586A GLY* 1.3 76.6 - - - +
588A LEU* 1.3 68.8 + - + +
590A GLY* 3.3 11.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 588 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562A LYS* 5.0 7.4 + - - +
584A LYS* 3.0 26.1 + - + +
585A TYR* 3.8 22.7 - - + +
587A GLU* 1.3 80.0 - - + +
589A TYR* 1.3 69.4 + - + +
590A GLY* 4.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 589 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549A GLY* 3.8 5.8 + - - -
552A PHE* 3.4 39.0 - + + -
553A SER* 3.5 23.6 + - - -
556A GLU* 3.5 27.8 - - - +
562A LYS* 3.2 33.0 + - - +
585A TYR* 3.0 33.8 + + + +
588A LEU* 1.3 86.7 - - + +
590A GLY* 1.3 58.9 + - - +
591A TYR* 3.4 37.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 590 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562A LYS* 4.3 12.9 - - - +
563A GLY* 3.5 20.8 + - - -
586A GLY 2.9 13.7 + - - -
587A GLU* 3.5 9.6 - - - -
588A LEU 3.2 1.2 - - - -
589A TYR* 1.3 79.8 - - - +
591A TYR* 1.3 66.2 + - - +
592A SER 4.0 0.3 + - - -
----------------------------------------------------------
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