Contacts of the helix formed by residues 571 - 586 (chain A) in PDB entry 2IO0
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 GLN 571 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A ASP* 6.2 1.6 - - - +
365A LEU* 3.4 37.3 - - + +
566A THR* 5.1 2.4 + - - -
567A PHE* 2.9 18.5 - - - +
568A THR* 2.3 47.7 + - - +
569A GLN 3.2 1.2 - - - -
570A HIS* 1.3 79.7 - - + +
572A MET* 1.3 57.3 + - - +
573A PRO* 3.6 1.1 - - - -
574A LEU* 3.5 4.0 + - - +
575A PHE* 2.9 49.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 572 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A ASN* 6.1 0.7 - - - +
547A ASP* 4.1 26.2 - - - +
550A MET* 3.4 28.7 - - + +
551A PHE* 3.7 43.3 - - + +
554A LYS* 4.4 4.3 - - + -
567A PHE* 4.0 21.8 - - + -
568A THR 4.3 3.8 - - - +
569A GLN* 3.1 24.5 + - - +
571A GLN* 1.3 77.6 - - - +
573A PRO* 1.3 68.5 - - + +
575A PHE* 3.1 20.7 + - + +
576A ARG* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 573 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A ASN* 4.1 27.3 - - - +
569A GLN 4.0 2.5 - - - +
570A HIS* 3.2 17.7 - - - +
572A MET* 1.3 94.7 - - + +
574A LEU* 1.3 60.1 + - - +
576A ARG* 3.4 16.3 + - + +
577A LYS* 3.4 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 574 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A LEU* 2.9 46.2 - - + -
366A LEU 3.8 13.7 - - - +
367A GLU* 5.6 0.7 - - - -
368A LEU* 4.4 14.1 - - + +
570A HIS 5.7 0.4 - - - +
571A GLN* 3.5 5.3 + - - +
572A MET 3.2 0.8 - - - -
573A PRO* 1.3 77.0 - - - +
575A PHE* 1.3 65.9 + - - +
577A LYS* 3.0 36.4 + - - +
578A LYS* 2.9 46.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 575 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A ASP* 4.2 16.6 - - - -
365A LEU* 3.3 29.4 - - + -
550A MET* 4.2 17.0 - - + +
554A LYS* 4.0 41.3 - - + -
558A TYR* 4.5 8.3 - - - -
567A PHE* 3.8 31.6 - + + -
571A GLN* 2.9 41.4 + - + +
572A MET* 3.1 15.5 + - + +
574A LEU* 1.3 76.9 - - - +
576A ARG* 1.3 55.6 + - - +
578A LYS* 3.5 13.8 + - + +
579A MET* 2.9 30.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
404A THR 3.5 12.1 + - - -
405A LEU* 3.1 31.1 + - + +
406A LYS 3.2 18.1 + - - -
407A ASN* 3.8 26.3 - - - +
408A TYR 4.3 2.9 - - - +
409A HIS 3.1 25.2 + - - -
411A LEU* 3.7 7.1 - - - +
546A SER* 3.2 13.1 + - - -
547A ASP* 2.8 31.9 + - - +
550A MET* 3.7 29.6 - - + +
572A MET 2.9 20.5 + - - +
573A PRO* 3.5 9.9 - - - +
574A LEU 3.0 0.2 - - - -
575A PHE* 1.3 73.3 - - - +
577A LYS* 1.3 67.6 + - + +
579A MET* 3.2 4.1 + - - +
580A VAL* 3.1 27.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
368A LEU* 3.8 16.1 - - + +
373A GLU* 3.8 16.4 + - + +
376A ILE* 3.3 29.3 - - + +
380A LEU* 5.6 4.9 - - + -
573A PRO* 3.4 11.6 + - - +
574A LEU* 3.0 41.5 + - - +
576A ARG* 1.3 76.8 - - + +
578A LYS* 1.3 67.6 + - - +
580A VAL* 3.1 17.9 + - - -
581A TRP 3.2 8.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 578 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A ASP 3.8 17.3 - - - +
365A LEU* 4.1 0.4 - - - +
366A LEU* 2.7 70.5 + - + +
368A LEU* 4.6 9.0 - - + +
376A ILE* 5.0 1.3 - - - -
554A LYS* 5.9 2.7 - - - +
574A LEU* 2.9 24.7 + - + +
575A PHE* 3.5 19.5 - - + +
577A LYS* 1.3 77.3 - - - +
579A MET* 1.3 59.0 + - - +
581A TRP* 3.2 8.7 + - - +
582A GLU* 2.8 43.7 + - - +
589A LEU* 4.1 27.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 579 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A LEU* 3.8 24.5 - - + -
411A LEU* 4.4 0.7 - - - -
415A VAL* 4.3 10.8 - - - -
419A TYR* 3.8 39.7 - - + -
550A MET* 3.1 31.4 - - + -
553A CYS* 3.6 29.2 - - + -
554A LYS* 4.4 6.5 - - + +
575A PHE 2.9 16.5 + - - +
576A ARG* 3.8 4.5 - - - +
577A LYS 3.1 0.6 - - - -
578A LYS* 1.3 75.3 - - - +
580A VAL* 1.3 64.5 + - - +
582A GLU* 3.2 11.1 + - - +
583A ILE* 2.9 37.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 580 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A ILE* 3.4 42.6 - - + +
379A ALA* 4.4 7.0 - - + -
380A LEU* 4.1 14.6 - - + -
402A ILE* 4.0 12.6 - - + +
405A LEU* 3.6 29.1 - - + +
576A ARG 3.1 19.8 + - - +
577A LYS* 3.1 6.2 + - - +
579A MET* 1.3 74.1 - - - +
581A TRP* 1.3 59.3 + - - +
583A ILE* 3.2 2.5 + - - +
584A LEU* 2.9 41.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 581 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A LEU* 5.7 0.4 - - + -
372A MET* 3.7 52.6 - - + +
375A GLU* 4.0 11.9 + - + -
376A ILE* 3.9 18.2 - - + -
577A LYS 3.2 5.3 + - - -
578A LYS* 3.5 8.3 - - - +
580A VAL* 1.3 81.1 - - - +
582A GLU* 1.3 63.5 + - - +
584A LEU* 3.1 6.4 + - - +
585A HIS* 2.8 72.0 + + + -
587A GLN* 3.7 27.1 - - + -
589A LEU* 3.7 37.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 582 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A TYR* 3.8 13.0 + - - -
422A LEU* 3.9 5.4 - - + +
554A LYS* 5.1 7.3 + - - -
578A LYS* 2.8 31.8 + - - +
579A MET* 3.3 21.3 + - + +
581A TRP* 1.3 85.1 - - + +
583A ILE* 1.3 59.5 + - + +
586A GLN* 2.7 27.5 + - - -
587A GLN 3.1 24.3 + - - +
588A LEU* 3.5 28.1 - - + +
589A LEU* 3.1 33.7 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
390A SER* 2.7 30.8 + - - -
397A ILE* 4.2 24.2 - - + -
402A ILE* 4.4 8.1 - - + -
405A LEU* 4.2 15.3 - - + -
415A VAL* 4.3 26.7 - - + +
418A PHE* 3.5 33.6 - - + -
419A TYR* 5.2 3.1 - - + +
422A LEU* 4.5 7.0 - - + -
579A MET* 2.9 39.6 + - + +
580A VAL 3.8 3.6 - - - +
581A TRP 3.1 0.2 - - - -
582A GLU* 1.3 77.0 - - + +
584A LEU* 1.3 63.1 + - - +
586A GLN* 3.3 8.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 584 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A GLU* 3.8 42.2 - - + +
379A ALA* 3.9 15.7 - - + -
389A LEU* 3.8 36.3 - - + +
390A SER* 3.8 10.8 + - - -
402A ILE* 3.9 13.9 - - + -
580A VAL* 2.9 27.9 + - + +
581A TRP* 3.6 6.5 - - - +
583A ILE* 1.3 78.7 - - - +
585A HIS* 1.3 70.1 + - + +
586A GLN* 4.1 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 585 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A GLU* 2.7 40.8 + - - -
581A TRP* 2.8 65.3 + + + +
584A LEU* 1.3 81.7 - - + +
586A GLN* 1.3 75.2 + - - +
587A GLN* 3.0 8.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 586 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A SER* 2.8 28.8 + - - +
391A SER 3.0 31.9 + - - +
392A ALA* 3.6 19.0 - - - +
393A PHE* 6.0 0.2 - - + -
418A PHE* 3.6 6.6 - - + -
422A LEU* 3.7 24.6 - - + +
582A GLU 2.7 17.9 + - - -
583A ILE 3.3 3.1 + - - +
584A LEU 4.1 2.9 + - - +
585A HIS* 1.3 79.4 - - - +
587A GLN* 1.3 57.5 + - - +
----------------------------------------------------------
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