Contacts of the helix formed by residues 566 - 581 (chain A) in PDB entry 5DO7
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 THR 566 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A GLY* 4.5 13.2 - - - +
544A VAL* 4.8 2.7 - - + -
545A GLY* 3.7 6.6 - - - -
562A ILE* 4.1 17.3 - - + +
563A SER* 2.4 29.9 + - - +
565A PHE* 1.3 83.2 - - + +
567A PHE* 1.3 64.0 + - - +
568A GLN* 3.2 24.7 - - - +
569A LYS 3.6 12.0 + - - -
570A TYR* 3.1 19.8 - - - -
630A PHE* 3.6 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 567 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A VAL* 4.6 2.9 - - + -
431A PRO* 4.1 26.5 - - + -
509A PRO* 4.5 13.9 - - + -
512A ILE* 3.6 50.0 - - + -
516A LEU* 6.1 3.8 - - + -
538A SER* 4.9 4.5 - - - -
566A THR* 1.3 71.4 - - - +
568A GLN* 1.3 116.7 + - + +
570A TYR* 2.8 14.6 + - - +
571A CYS* 2.8 13.4 + - + +
627A LEU* 3.9 9.6 - - + +
630A PHE* 3.3 38.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 568 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A VAL* 4.1 11.0 - - + -
431A PRO* 5.1 0.2 - - - +
537A LEU 4.2 0.4 + - - -
538A SER* 3.4 25.1 + - - +
541A GLY* 3.2 35.0 - - - +
542A VAL* 3.5 26.7 - - + +
545A GLY 3.2 7.4 - - - +
546A SER* 5.4 0.4 - - - -
566A THR* 3.2 24.6 - - - +
567A PHE* 1.3 124.2 - - + +
569A LYS* 1.3 66.1 + - - +
571A CYS* 2.9 1.8 + - - +
572A SER* 2.8 25.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 569 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A GLY 2.3 27.2 + - - +
546A SER* 4.5 1.1 - - - +
552A ILE* 3.5 28.5 - - + +
563A SER* 3.8 3.4 - - - +
564A TYR* 3.6 52.5 + - - +
566A THR* 3.6 11.9 + - - +
567A PHE 3.4 0.2 - - - -
568A GLN* 1.3 73.1 - - - +
570A TYR* 1.3 73.8 + - + +
571A CYS 3.1 0.2 + - - -
572A SER* 3.1 0.5 + - - -
573A GLU* 2.8 78.5 + - - +
619A ARG* 4.3 4.4 - - - +
644C ILE* 4.8 7.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 570 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564A TYR* 2.5 54.3 + - - +
566A THR 3.1 21.3 - - - -
567A PHE* 2.8 11.6 + - - +
569A LYS* 1.3 91.9 - - + +
571A CYS* 1.3 58.0 - - - +
573A GLU* 4.5 2.7 - - - -
574A ILE* 3.1 27.4 - - - +
619A ARG* 5.5 0.9 - - - -
623A ASN* 3.7 28.1 - - - +
626A ILE* 3.2 53.6 - - + -
627A LEU* 3.9 10.6 - - - +
630A PHE* 4.8 2.5 - + - -
637C LEU* 4.5 10.0 - - + +
640C VAL* 4.1 11.1 - - + +
644C ILE* 4.6 7.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 571 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A VAL* 3.7 24.5 - - + -
505A ALA* 3.6 24.2 - - - -
506A LEU* 4.6 0.7 - - - -
509A PRO* 4.1 11.7 - - + -
567A PHE* 2.8 10.8 + - + +
568A GLN* 2.9 10.7 + - - +
570A TYR* 1.3 77.6 - - - +
572A SER* 1.3 67.8 + - - +
574A ILE* 2.8 15.6 + - - +
575A LEU* 3.0 21.5 + - - +
627A LEU* 3.6 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 572 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A VAL* 3.6 17.4 - - - +
546A SER* 3.0 38.2 - - - -
547A GLY 5.0 1.1 - - - -
548A PHE* 3.1 20.2 - - - -
568A GLN 2.8 15.7 + - - -
569A LYS 3.8 2.0 - - - -
571A CYS* 1.3 72.5 - - - +
573A GLU* 1.3 59.1 + - - +
574A ILE 2.8 6.9 + - - -
575A LEU* 2.8 8.3 + - - +
576A VAL* 2.8 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 573 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A GLY 5.3 0.2 - - - +
547A GLY 5.0 6.5 + - - +
552A ILE* 4.1 12.0 - - - +
569A LYS* 2.8 60.9 + - - +
570A TYR* 5.1 1.0 - - - -
572A SER* 1.3 71.8 - - - +
574A ILE* 1.3 55.8 + - - +
576A VAL* 4.5 1.3 - - - -
577A VAL* 3.4 23.2 - - - +
613A CYS* 3.3 38.4 - - + +
616A ALA* 3.5 6.7 - - + +
619A ARG* 2.3 33.3 + - - +
620A PHE* 4.9 1.2 - - - -
623A ASN* 3.4 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 574 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A TYR 5.4 0.7 - - - +
505A ALA* 4.0 11.7 - - + -
570A TYR 3.1 22.6 + - - +
571A CYS 2.8 7.4 + - - +
572A SER 2.8 0.6 + - - -
573A GLU* 1.3 74.3 - - - +
575A LEU* 1.3 69.5 + - + +
576A VAL 3.2 1.8 - - - -
577A VAL* 2.8 7.3 + - - +
578A ASN* 2.8 26.4 + - + -
620A PHE* 3.8 17.0 - - + -
623A ASN* 3.5 14.6 - - + -
624A PHE* 3.3 63.0 - - + +
627A LEU* 3.8 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 575 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A LEU* 3.5 26.0 - - + +
426A PHE* 5.2 0.9 - - + -
427A VAL* 3.6 30.7 - - + -
502A PHE* 3.6 38.1 - - + +
505A ALA* 3.7 24.2 - - + -
506A LEU* 3.7 21.3 - - + -
571A CYS* 3.0 10.8 + - - +
572A SER* 2.8 12.3 + - - +
574A ILE* 1.3 77.1 - - + +
576A VAL* 1.3 56.0 + - + +
578A ASN* 3.7 5.4 - - - +
579A GLU* 2.8 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 576 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A LEU* 4.9 4.5 - - + -
548A PHE* 3.3 36.3 - - + -
572A SER* 2.8 25.0 + - - +
573A GLU* 4.8 1.1 - - - -
575A LEU* 1.3 71.8 - - - +
577A VAL* 1.3 59.8 + - + +
580A PHE* 2.8 45.2 + - + +
608A PHE* 3.8 29.6 - - + -
609A ILE* 4.2 14.8 - - + -
613A CYS* 4.3 23.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 577 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A GLU 3.4 7.9 - - - +
574A ILE 2.8 12.3 + - - +
576A VAL* 1.3 74.6 - - + +
578A ASN* 1.3 57.7 + - - +
581A TYR* 2.8 52.2 + - + +
609A ILE* 4.1 20.4 - - + -
616A ALA* 3.3 35.4 - - + -
617A THR* 3.6 27.1 - - - +
620A PHE* 3.7 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 578 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A TYR* 4.5 3.8 + - - -
493A HIS* 3.6 18.0 + - - -
498A ARG* 2.5 54.5 + - - +
501A TYR* 3.4 17.4 - - + +
502A PHE* 3.7 16.7 - - - +
574A ILE* 2.8 22.8 + - + +
575A LEU* 3.7 9.6 - - - +
577A VAL* 1.3 73.4 - - - +
579A GLU* 1.3 70.9 + - - +
581A TYR* 4.9 1.7 - - - +
620A PHE* 3.8 20.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 579 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A ARG* 3.3 22.7 + - - +
423A LEU* 5.0 8.2 - - + +
487A TYR* 4.6 1.6 - - - +
492A LEU* 2.8 49.9 - - + +
493A HIS* 2.6 33.6 + - - -
502A PHE* 5.9 0.4 - - + -
575A LEU 2.8 20.1 + - - +
578A ASN* 1.3 82.3 + - - +
580A PHE* 1.3 82.7 + - + +
581A TYR 3.7 0.7 - - - -
583A LEU* 3.5 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 580 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A ILE* 3.9 23.3 - - + -
419A ARG* 4.5 18.4 - - + -
420A VAL* 5.5 1.3 - - + -
423A LEU* 4.4 18.8 - - + -
576A VAL* 2.8 31.4 + - + +
577A VAL 3.7 0.2 - - - -
579A GLU* 1.3 95.7 - - + +
581A TYR* 1.3 52.9 + - - +
582A GLY* 2.4 27.3 + - - -
583A LEU* 3.0 12.3 - - + +
585A PHE* 4.3 9.2 - + - -
605A GLY* 3.5 34.9 - - - +
608A PHE* 3.2 38.8 - + + -
609A ILE* 3.7 10.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 581 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A HIS* 3.9 17.5 + - + +
498A ARG* 3.2 46.4 + - - +
577A VAL* 2.8 40.3 + - + +
578A ASN* 4.9 0.9 - - - +
579A GLU 3.7 1.4 - - - -
580A PHE* 1.3 68.8 - - - +
582A GLY* 1.3 55.8 + - - +
583A LEU* 3.9 0.4 - - - +
606A ILE* 4.0 18.0 - - - +
609A ILE* 4.5 7.6 - - - +
617A THR* 5.4 7.0 + - - -
620A PHE* 5.5 5.8 - + - -
----------------------------------------------------------
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