Contacts of the helix formed by residues 578 - 588 (chain A) in PDB entry 4FWF
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 GLY 578 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A ASP* 3.4 14.1 - - - -
431A THR* 4.7 0.9 - - - -
437A GLN* 4.2 11.0 - - - -
456A ILE* 5.0 1.0 - - - +
575A LEU* 2.8 29.2 + - - +
576A THR 3.1 1.0 - - - -
577A PRO* 1.3 85.4 - - - +
579A TYR* 1.3 60.9 + - - -
580A SER 3.1 6.1 + - - -
581A VAL* 3.6 12.5 + - - +
582A ILE* 4.5 2.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 579 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A VAL* 3.6 24.2 - - + -
423A ASP* 3.3 3.6 + - - -
436A ALA* 3.4 29.8 + - + +
437A GLN* 3.6 27.1 - - - -
438A ILE 2.7 24.1 + - - -
439A VAL* 3.3 19.5 - - + +
447A VAL* 3.8 18.0 - - + +
575A LEU* 3.7 17.7 - - + +
578A GLY* 1.3 69.2 - - - -
580A SER* 1.3 60.5 + - - +
581A VAL 3.3 0.2 - - - -
582A ILE* 3.1 18.1 + - + +
583A ILE* 2.8 29.8 + - + +
805A VAL* 3.5 33.4 - - + +
806A THR* 5.1 1.4 + - - -
904A FAD 3.6 8.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 580 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A VAL* 3.9 5.9 - - - +
422A TRP* 5.7 0.4 - - - -
423A ASP* 2.8 39.1 + - - +
425A LYS* 4.1 12.6 + - - +
577A PRO 4.3 6.9 + - - -
578A GLY 3.1 0.2 - - - -
579A TYR* 1.3 75.0 - - - +
581A VAL* 1.3 62.7 + - - +
583A ILE* 3.7 9.4 - - - +
584A GLU* 2.8 51.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 581 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A LEU* 4.4 7.3 - - + +
456A ILE* 4.5 16.4 - - + -
577A PRO* 3.6 37.9 - - + +
578A GLY 3.6 4.7 + - - +
579A TYR 3.3 0.6 - - - -
580A SER* 1.3 78.8 + - - +
582A ILE* 1.3 57.6 + - - +
584A GLU* 3.8 10.0 - - - +
585A LYS* 2.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 582 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A VAL* 4.0 3.3 - - + +
447A VAL* 4.2 10.3 - - + -
450A MET* 3.7 47.3 - - + -
451A CYS* 4.2 13.5 - - - -
454A LEU* 4.2 20.0 - - + -
456A ILE* 4.6 8.5 - - + -
575A LEU* 4.1 24.7 - - + -
578A GLY 4.9 0.9 - - - +
579A TYR* 3.1 18.7 + - + +
581A VAL* 1.3 73.6 - - - +
583A ILE* 1.3 63.4 + - + +
585A LYS* 3.3 2.5 + - - +
586A LEU* 2.9 40.0 + - + +
805A VAL* 6.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 583 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A GLY 4.7 0.2 - - - -
392A PRO* 4.0 32.3 - - + -
395A LEU* 3.6 30.3 - - + +
417A ILE* 3.8 15.5 - - + -
418A GLY* 3.8 16.8 - - - -
421A VAL* 3.6 22.7 - - + -
579A TYR* 2.8 23.0 + - + +
580A SER* 3.7 9.0 - - - +
582A ILE* 1.3 74.6 - - + +
584A GLU* 1.3 63.4 + - + +
586A LEU* 3.7 12.4 + - + +
587A ALA* 3.1 22.0 + - - +
805A VAL* 5.7 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 584 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A ILE* 4.3 17.0 - - + -
425A LYS* 3.3 25.7 + - - -
580A SER* 2.8 36.1 + - - +
581A VAL* 3.8 6.9 + - - +
583A ILE* 1.3 71.6 - - + +
585A LYS* 1.3 66.5 + - - +
587A ALA* 3.1 4.0 + - - +
588A GLU* 3.0 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 585 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A VAL* 3.6 35.2 - - + +
368A SER* 5.3 8.2 - - - -
399A ARG* 3.9 4.3 + - - -
454A LEU* 3.6 26.0 - - + -
581A VAL 2.9 17.1 + - - +
582A ILE 3.3 3.6 + - - +
584A GLU* 1.3 76.5 - - - +
586A LEU* 1.3 64.4 + - - +
588A GLU* 3.1 56.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 586 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A GLY 4.0 13.5 - - - +
366A VAL* 3.8 13.6 - - + +
392A PRO* 5.1 2.0 - - + +
395A LEU* 4.3 21.8 - - + +
396A ALA* 4.5 3.1 - - - +
399A ARG* 2.6 63.2 + - + +
450A MET* 4.6 0.7 - - + -
582A ILE* 2.9 36.1 + - + +
583A ILE* 3.8 20.9 - - + +
585A LYS* 1.3 71.1 - - - +
587A ALA* 1.3 54.4 + - - +
590A LEU* 3.4 8.4 - - - +
809A TYR* 4.2 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 587 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A LEU* 4.2 6.5 - - + +
399A ARG* 3.9 0.7 - - - -
417A ILE* 3.5 22.2 - - + -
583A ILE 3.1 14.7 + - - +
584A GLU 3.1 6.1 + - - +
586A LEU* 1.3 78.5 - - - +
588A GLU* 1.3 66.1 + - - +
589A GLY 3.0 4.0 + - - -
590A LEU* 3.0 26.7 + - - +
592A ILE* 3.9 18.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 588 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A SER* 4.8 12.5 + - - -
399A ARG* 2.6 25.4 + - - +
402A HIS* 5.8 0.3 - - - -
584A GLU 3.0 9.0 + - - +
585A LYS* 3.1 53.0 + - - +
586A LEU 3.2 0.2 - - - -
587A ALA* 1.3 74.0 - - - +
589A GLY* 1.3 62.5 + - - +
----------------------------------------------------------
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