Contacts of the helix formed by residues 573 - 587 (chain A) in PDB entry 6BGH
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 SER 573 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571A PRO* 2.7 28.5 + - - +
572A MET* 1.3 76.1 + - - +
574A TYR* 1.3 68.6 + - - +
575A ASP* 4.2 8.7 - - - -
576A GLU* 2.7 34.0 + - - +
577A LYS* 3.1 12.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 574 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A SER* 1.3 76.9 - - - +
575A ASP* 1.3 59.1 + - - +
577A LYS* 3.4 5.9 + - + +
578A ARG* 2.8 34.2 + - - +
619A GLU* 3.9 32.5 - - + -
1591B ARG* 3.2 45.8 + - + +
1592B SER* 3.9 25.7 - - - -
1593B VAL* 4.1 28.3 - - + +
1595B VAL* 4.3 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 575 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A SER* 3.2 7.2 - - - -
574A TYR* 1.3 76.6 + - - +
576A GLU* 1.3 59.0 + - - +
578A ARG* 3.7 4.6 - - - +
579A GLN* 2.9 29.3 + - - +
1593B VAL* 5.7 6.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 576 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570A LEU* 3.4 42.0 - - + +
571A PRO 3.5 10.0 - - - +
572A MET* 3.0 11.8 - - - +
573A SER* 2.7 46.1 + - - +
575A ASP* 1.3 77.2 - - - +
577A LYS* 1.3 69.1 + - - +
579A GLN* 3.2 24.2 + - - +
580A LEU* 3.5 10.7 - - - +
623A PRO* 4.4 7.6 - - - +
626A LEU* 3.7 21.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 577 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572A MET* 4.1 25.3 - - - +
573A SER 3.1 17.0 + - - +
574A TYR* 3.8 7.1 - - + +
576A GLU* 1.3 96.3 - - - +
578A ARG* 1.3 61.2 + - - +
580A LEU* 3.3 17.8 + - - +
618A PHE* 2.8 23.5 - - + +
619A GLU* 2.8 22.8 + - - +
620A THR 4.4 1.6 - - - -
621A LEU 2.8 26.5 + - - +
622A LYS* 4.9 0.4 - - - +
623A PRO* 4.4 11.2 - - - +
626A LEU* 3.5 23.2 - - + +
1595B VAL* 3.5 21.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 578 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574A TYR 2.8 18.7 + - - +
575A ASP* 3.7 5.6 - - - +
577A LYS* 1.3 75.6 - - - +
579A GLN* 1.3 59.4 + - - +
580A LEU 3.0 2.5 - - - -
581A SER* 2.8 39.9 + - - -
582A LEU* 3.0 23.2 - - + +
1593B VAL* 3.3 32.2 - - - +
1594B LYS* 2.7 44.0 + - - +
1595B VAL* 3.5 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 579 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566A GLU* 5.9 1.2 + - - -
575A ASP 2.9 13.7 + - - +
576A GLU* 3.2 14.2 + - - +
578A ARG* 1.3 75.5 - - - +
580A LEU* 1.3 76.3 + - + +
582A LEU* 3.3 21.1 + - - +
583A ASP* 3.4 17.0 + - - +
630A GLU* 5.4 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 580 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576A GLU 3.5 18.2 - - - +
577A LYS 3.5 8.3 - - - +
578A ARG 3.0 0.8 - - - -
579A GLN* 1.3 94.9 - - - +
581A SER* 1.3 63.9 + - - +
583A ASP* 3.1 21.2 + - - +
584A ILE* 3.0 24.6 + - - +
618A PHE* 3.8 5.8 - - + -
626A LEU* 3.7 28.0 - - + +
629A LEU* 3.6 24.8 - - + +
630A GLU* 3.5 43.3 - - + +
633A VAL* 4.7 0.4 - - + -
1595B VAL* 5.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 581 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577A LYS 3.6 2.2 + - - -
578A ARG* 2.8 29.8 + - - +
580A LEU* 1.3 76.6 - - - +
582A LEU* 1.3 59.6 + - - +
584A ILE* 3.0 12.9 - - - +
585A ASN* 3.0 29.2 + - - +
1594B LYS 4.4 2.1 + - - -
1595B VAL* 3.4 38.6 + - - +
1597B ILE* 3.4 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 582 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578A ARG* 3.0 42.4 - - + +
579A GLN* 3.6 10.3 - - - +
580A LEU 3.2 0.4 - - - -
581A SER* 1.3 81.7 - - - +
583A ASP* 1.3 64.7 + - - +
585A ASN* 3.5 16.7 + - + +
586A ARG* 3.1 29.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 583 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579A GLN* 3.4 15.9 + - - +
580A LEU* 3.1 31.3 + - - +
582A LEU* 1.3 76.1 - - - +
584A ILE* 1.3 66.1 + - - +
586A ARG* 3.0 18.1 + - - +
587A LEU* 3.2 18.2 + - - +
633A VAL* 3.4 38.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 584 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580A LEU 3.0 13.7 + - - +
581A SER* 3.0 24.7 - - - +
583A ASP* 1.3 75.3 - - - +
585A ASN* 1.3 60.5 + - - +
587A LEU* 3.1 24.8 + - + +
592A LEU* 3.8 13.2 - - + -
595A VAL* 3.5 32.1 - - + -
614A ILE* 4.5 4.3 - - + -
616A ILE* 3.6 27.6 - - + -
629A LEU* 4.2 11.8 - - + +
633A VAL* 5.1 0.2 - - - +
1597B ILE* 3.6 14.1 - - + -
1599B LEU* 3.3 27.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 585 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581A SER 3.0 19.5 + - - +
582A LEU* 3.5 22.0 + - + +
584A ILE* 1.3 78.8 - - - +
586A ARG* 1.3 69.8 + - - +
587A LEU 4.0 3.8 - - - +
1597B ILE* 3.9 15.7 - - + +
1599B LEU* 4.4 10.8 - - - +
1600B GLY 5.8 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 586 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582A LEU* 3.1 19.3 + - + +
583A ASP* 3.0 11.4 + - - +
585A ASN* 1.3 85.0 - - - +
587A LEU* 1.3 66.2 + - + +
588A PRO* 3.7 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 587 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A ASP 3.4 16.4 - - - +
584A ILE* 3.1 34.4 + - + +
585A ASN 4.0 1.9 - - - +
586A ARG* 1.3 83.8 - - + +
588A PRO* 1.4 77.0 - - + +
591A LYS* 3.8 12.3 - - + -
592A LEU* 4.9 0.2 - - - +
595A VAL* 4.8 0.4 - - + -
629A LEU* 5.1 0.7 - - + -
632A TYR* 3.4 30.1 - - + -
633A VAL* 4.4 13.0 - - + -
636A CYS* 3.3 35.2 - - + -
637A LEU* 6.5 0.7 - - + -
1599B LEU* 3.8 14.2 - - - +
----------------------------------------------------------
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