Contacts of the helix formed by residues 578 - 592 (chain A) in PDB entry 3FA2
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 578 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576A GLY 4.0 0.2 + - - -
577A LEU* 1.3 78.8 - - - +
579A SER* 1.3 66.2 + - - +
580A GLU* 3.4 10.3 + - - +
581A GLN* 2.7 37.9 + - - +
582A GLN* 3.2 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 579 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578A SER* 1.3 74.9 + - - +
580A GLU* 1.3 60.9 + - - +
582A GLN* 3.5 6.3 + - - +
583A LYS* 3.1 44.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 580 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578A SER* 3.4 8.2 + - - +
579A SER* 1.3 76.3 - - - +
581A GLN* 1.3 55.9 + - + +
583A LYS* 3.0 26.3 + - - +
584A MET* 2.7 47.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 581 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577A LEU* 3.2 26.2 - - + +
578A SER* 2.7 43.7 + - - +
580A GLU* 1.3 79.6 - - + +
582A GLN* 1.3 57.7 + - - +
584A MET* 4.1 2.7 - - - -
585A LEU* 2.9 28.4 + - - +
610A PRO* 3.8 18.7 + - - +
633A PHE* 3.4 52.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 582 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574A GLY* 4.3 14.1 + - - +
577A LEU* 4.1 22.8 + - - +
578A SER 3.2 18.9 + - - +
579A SER* 3.6 7.6 - - - +
580A GLU 3.1 0.6 - - - -
581A GLN* 1.3 75.2 - - - +
583A LYS* 1.3 64.3 + - - +
585A LEU* 3.4 15.9 + - - +
586A SER* 3.2 22.9 + - - -
596A LYS* 2.9 32.8 - - - +
597A TYR 5.8 0.4 - - - -
598A THR* 6.1 3.1 - - + +
----------------------------------------------------------
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 SER* 3.1 29.8 + - - +
580A GLU* 3.0 28.5 + - - +
582A GLN* 1.3 72.4 - - - +
584A MET* 1.3 65.1 - - + +
586A SER* 2.7 23.3 + - - -
587A GLU* 3.0 14.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 584 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580A GLU* 2.7 30.3 + - + +
581A GLN* 3.5 9.6 - - - +
583A LYS* 1.3 73.3 - - - +
585A LEU* 1.3 59.8 + - - +
587A GLU* 3.3 15.9 + - - +
588A LEU* 3.2 17.3 + - - +
633A PHE* 3.5 33.0 - - + -
636A VAL* 4.3 2.0 - - - -
637A LYS* 4.3 17.5 - - + -
640A LEU* 3.7 33.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 585 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572A LEU* 4.4 17.2 - - + +
573A ILE* 3.9 11.0 - - - +
574A GLY* 3.7 27.1 - - - +
577A LEU* 4.1 3.6 - - + -
581A GLN 2.9 18.7 + - - +
582A GLN* 3.5 24.2 - - - +
583A LYS 3.2 0.4 - - - -
584A MET* 1.3 73.4 - - - +
586A SER* 1.3 64.8 + - - +
588A LEU* 3.3 14.5 + - + +
589A ALA* 3.3 11.6 + - - +
596A LYS* 3.9 12.3 - - + +
608A VAL* 3.7 17.5 - - + -
633A PHE* 4.8 1.6 - - + -
636A VAL* 3.3 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 586 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582A GLN 3.2 11.0 + - - -
583A LYS* 2.7 23.4 + - - -
585A LEU* 1.3 78.0 - - - +
587A GLU* 1.3 61.4 + - - +
589A ALA* 3.2 15.8 + - - +
590A VAL* 3.5 18.2 + - - +
596A LYS* 3.9 27.1 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
583A LYS* 3.0 11.8 + - - +
584A MET* 3.4 22.6 + - - +
586A SER* 1.3 78.0 + - - +
588A LEU* 1.3 59.2 + - - +
590A VAL* 3.5 9.5 - - + +
591A ILE* 3.2 38.1 + - + +
640A LEU* 4.9 12.4 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
572A LEU* 3.9 11.2 - - + -
584A MET 3.2 7.2 + - - +
585A LEU* 3.4 9.9 - - + +
586A SER 3.2 0.2 - - - -
587A GLU* 1.3 77.4 - - - +
589A ALA* 1.3 54.8 + - - +
591A ILE* 3.1 8.1 + - + +
592A LEU* 2.6 72.4 + - + +
635A TRP* 3.8 27.1 - - + -
636A VAL* 4.2 15.0 - - + -
639A CYS* 3.1 36.1 - - + +
640A LEU* 3.2 24.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 589 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572A LEU* 4.4 11.6 - - + +
585A LEU 3.3 6.2 + - - +
586A SER 3.2 10.0 + - - +
588A LEU* 1.3 79.6 - - - +
590A VAL* 1.3 53.1 + - + +
592A LEU* 3.5 2.2 - - - -
593A LYS 2.7 29.1 + - - -
594A ALA* 2.7 31.4 + - - +
595A LYS 4.2 3.1 - - - +
596A LYS* 4.0 28.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 590 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A SER 3.5 10.9 + - - +
587A GLU* 3.5 18.8 - - + +
589A ALA* 1.3 78.0 - - + +
591A ILE* 1.3 68.3 + - + +
593A LYS* 3.2 18.6 + - - +
594A ALA 4.8 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 591 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A GLU* 3.2 37.0 - - + +
588A LEU* 3.1 12.7 + - + +
590A VAL* 1.3 88.2 - - + +
592A LEU* 1.3 69.1 + - + +
593A LYS* 3.2 2.3 + - - +
640A LEU* 5.3 10.8 - - + -
643A LYS* 4.4 48.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 592 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570A LEU* 4.6 12.8 - - + -
572A LEU* 4.9 4.5 - - + -
588A LEU* 2.6 56.0 + - + +
589A ALA* 4.1 3.4 - - - +
591A ILE* 1.3 78.3 - - + +
593A LYS* 1.3 71.3 + - - +
594A ALA* 4.4 7.1 - - + +
635A TRP* 4.6 3.8 - - + -
639A CYS* 4.7 0.9 - - - -
643A LYS 4.9 1.3 - - - +
644A VAL* 3.5 11.2 - - - +
645A CYS* 3.3 50.7 - - + +
----------------------------------------------------------
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