Contacts of the helix formed by residues 576 - 587 (chain A) in PDB entry 1R1H
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 576 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563A PHE* 3.9 21.5 - - - -
572A LEU 3.0 15.3 + - - -
574A TYR 3.1 0.8 - - - -
575A GLY* 1.3 77.1 - - - +
577A ILE* 1.3 65.4 + - - -
578A GLY 3.2 0.2 - - - -
579A MET* 3.1 8.0 + - - +
580A VAL* 3.0 22.5 + - - +
688A ASN* 4.2 4.7 - - - -
692A VAL* 4.9 7.6 - - - -
2001A BIR 5.0 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 577 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A VAL* 5.3 3.4 - - + -
442A LEU* 3.8 26.0 - - + -
554A PHE* 4.8 5.2 - - + -
558A ILE* 4.1 23.1 - - + +
559A LEU* 3.7 30.5 - - + -
563A PHE* 3.1 22.4 + - + +
564A PHE* 3.9 16.4 - - + -
573A ASN 3.0 12.9 + - - +
576A GLY* 1.3 69.4 - - - -
578A GLY* 1.3 64.8 + - - +
580A VAL* 3.0 18.9 + - + -
581A ILE* 2.8 43.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 578 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A LEU* 5.6 2.0 - - - -
446A ILE* 3.8 22.9 - - - +
573A ASN 2.9 12.7 + - - -
574A TYR* 3.1 17.5 - - - -
577A ILE* 1.3 79.2 - - - +
579A MET* 1.3 61.2 + - - +
581A ILE* 3.2 5.3 + - - +
582A GLY* 3.1 18.7 + - - -
657A ALA* 3.6 10.3 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
574A TYR 2.9 7.7 + - - +
575A GLY* 3.6 15.7 - - - +
576A GLY 3.1 9.6 + - - +
578A GLY* 1.3 74.8 - - - +
580A VAL* 1.3 58.5 + - - +
582A GLY* 3.4 1.4 + - - -
583A HIS* 2.9 26.3 + - - +
649A ALA 4.7 0.7 - - - +
650A ASP* 2.9 41.3 - - + +
653A GLY* 3.4 4.5 - - - -
654A LEU* 3.0 32.8 - - + -
657A ALA* 3.7 10.8 - - + -
689A PHE* 3.5 33.2 - - + -
2001A BIR 3.8 30.1 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
543A ALA* 3.8 29.2 - - + -
554A PHE* 4.1 6.1 - - + -
558A ILE* 4.5 4.3 - - + -
563A PHE* 3.5 31.0 - - + -
576A GLY 3.0 19.7 + - - +
577A ILE* 3.0 16.8 + - + +
579A MET* 1.3 75.8 - - - +
581A ILE* 1.3 62.7 + - - +
583A HIS* 3.2 8.5 + - - +
584A GLU* 3.0 27.9 + - - +
2001A BIR 3.8 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 581 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A VAL* 4.8 3.8 - - + +
442A LEU* 4.1 15.5 - - + -
443A ILE* 3.7 32.8 - - + -
446A ILE* 3.7 29.8 - - + -
554A PHE* 3.6 30.0 - - + -
577A ILE* 2.8 38.5 + - + +
578A GLY* 3.6 5.6 - - - +
580A VAL* 1.3 72.9 - - - +
582A GLY* 1.3 57.3 + - - +
584A GLU* 3.3 3.8 + - - +
585A ILE* 3.0 46.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 582 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A ILE* 3.8 13.2 - - - +
578A GLY 3.1 9.7 + - - -
579A MET 3.9 0.4 - - - -
581A ILE* 1.3 76.1 - - - +
583A HIS* 1.3 57.1 + - - +
585A ILE* 3.7 2.2 - - - +
586A THR* 2.6 38.1 + - - -
653A GLY* 3.6 8.5 - - - -
656A GLN* 3.1 24.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 583 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579A MET* 2.9 16.6 + - + +
580A VAL 3.3 10.1 - - - +
582A GLY* 1.3 76.5 - - - +
584A GLU* 1.3 79.0 + - - +
586A THR 3.3 0.3 + - - -
587A HIS* 3.0 22.3 + + - -
646A GLU* 3.0 12.3 - - - -
649A ALA* 3.3 39.2 - - + +
650A ASP* 2.8 30.1 + - - -
653A GLY* 3.6 2.0 - - - -
717A ARG* 3.3 10.8 - - - -
1001A ZN 2.0 38.2 - - - -
2001A BIR 3.4 16.5 + + + +
----------------------------------------------------------
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
----------------------------------------------------------
543A ALA* 3.7 6.0 - - + +
544A PHE 3.1 30.3 - - - +
545A TYR* 3.3 13.5 + - - -
552A ILE* 3.7 19.1 - - + -
554A PHE* 3.7 19.7 - - + -
580A VAL 3.0 17.3 + - - +
581A ILE 3.8 4.0 - - - +
583A HIS* 1.3 90.1 - - - +
585A ILE* 1.3 67.1 + - - +
587A HIS* 3.1 21.4 + - - +
2001A BIR 2.4 45.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 585 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A ILE* 4.8 1.6 - - + +
446A ILE* 3.8 15.9 - - + -
447A ARG* 4.1 23.6 - - + +
450A PHE* 4.3 30.1 - - + -
472A ALA* 6.0 0.9 - - + -
475A ILE* 4.2 24.3 - - + +
545A TYR* 4.9 0.4 - - - -
552A ILE* 3.9 25.5 - - + +
581A ILE* 3.0 37.5 + - + +
582A GLY* 3.7 5.2 - - - +
584A GLU* 1.3 75.3 - - - +
586A THR* 1.3 58.0 + - - +
588A GLY* 2.9 20.1 + - - -
589A PHE* 3.4 13.5 - - + -
656A GLN* 5.3 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 586 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A PHE* 4.7 2.3 - - - -
582A GLY 2.6 26.7 + - - -
583A HIS 3.7 4.3 - - - -
584A GLU 3.2 0.2 - - - -
585A ILE* 1.3 73.5 - - - +
587A HIS* 1.3 57.8 + - - +
589A PHE* 2.9 23.2 + - - -
590A ASP* 3.1 9.9 + - - +
648A ILE* 3.7 22.9 - - + +
649A ALA* 3.8 12.3 - - - -
652A GLY* 4.4 2.2 - - - -
653A GLY 3.9 1.9 + - - -
656A GLN* 3.1 23.2 + - - -
749A TRP* 3.6 33.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 587 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A TYR* 3.6 22.9 - + + -
583A HIS* 3.0 27.2 + + - -
584A GLU* 3.1 16.9 + - - +
585A ILE 3.1 0.2 - - - -
586A THR* 1.3 72.9 - - - +
588A GLY* 1.3 56.2 + - - +
589A PHE 2.9 9.6 + - - -
590A ASP* 2.8 36.1 + - - +
593A GLY* 3.5 16.1 + - - -
645A GLY 4.2 4.0 - - - -
646A GLU* 3.3 18.4 + - - -
649A ALA* 4.1 8.6 - - + +
1001A ZN 2.1 36.7 - - - -
2001A BIR 3.6 13.3 + - + +
----------------------------------------------------------
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