Contacts of the helix formed by residues 589 - 598 (chain A) in PDB entry 1RS0
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 589 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A THR 4.1 7.2 - - - +
588A THR* 1.3 82.3 - - - +
590A CYS* 1.3 66.3 + - - +
591A GLN* 3.7 9.7 + - - +
592A GLN* 2.7 41.1 + - - +
593A GLN* 2.9 22.3 + - - +
739A LEU* 3.9 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 590 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574A CYS* 2.0 57.6 - - + -
589A THR* 1.3 71.6 - - - +
591A GLN* 1.3 65.0 + - - +
593A GLN* 3.1 6.0 + - - +
594A LYS* 2.9 23.9 + - - +
721A PHE* 4.6 4.0 - - - -
724A LEU* 3.5 15.7 - - - -
739A LEU* 3.7 16.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 591 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589A THR* 3.7 8.9 + - - +
590A CYS* 1.3 81.3 - - - +
592A GLN* 1.3 57.8 + - + +
594A LYS* 2.8 47.6 + - - +
595A GLU* 2.9 59.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 592 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584A LEU* 5.9 1.8 - - + -
587A THR 3.7 5.0 - - - +
588A THR* 3.2 21.1 - - + -
589A THR* 2.7 46.4 + - - +
591A GLN* 1.3 74.5 - - + +
593A GLN* 1.3 66.5 + - - +
595A GLU* 3.2 18.0 + - - +
596A GLU* 3.0 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 593 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A PRO* 3.7 1.0 - - - +
574A CYS* 2.6 32.4 + - - +
575A THR 3.1 16.4 + - - +
578A THR* 3.3 26.4 - - + +
579A THR* 2.9 27.1 + - - +
582A LEU* 4.5 9.0 - - + -
584A LEU* 5.6 0.9 - - - -
588A THR* 4.2 10.3 - - + -
589A THR 2.9 11.0 + - - +
590A CYS* 3.4 9.0 - - - +
592A GLN* 1.3 76.6 - - - +
594A LYS* 1.3 52.3 + - - +
596A GLU* 3.2 6.0 + - - +
597A LEU* 2.7 47.6 + - + +
721A PHE* 4.4 0.7 - - + -
739A LEU* 3.5 17.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 594 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590A CYS* 2.9 13.0 + - - +
591A GLN* 2.8 48.9 + - - +
592A GLN 3.1 0.2 - - - -
593A GLN* 1.3 75.2 - - - +
595A GLU* 1.3 60.9 + - - +
598A LEU* 2.6 48.0 + - + +
721A PHE* 3.6 32.7 - - + -
722A GLN* 5.7 1.6 - - - +
745A NA 3.1 26.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 595 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591A GLN* 2.9 52.1 + - - +
592A GLN* 3.7 19.0 - - - +
594A LYS* 1.3 77.3 - - + +
596A GLU* 1.3 60.3 + - - +
598A LEU 4.3 4.3 - - - -
599A PRO* 3.7 21.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 596 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582A LEU* 4.2 21.8 - - + -
584A LEU* 4.9 15.5 - - + +
592A GLN 3.0 15.9 + - - +
593A GLN* 3.5 7.4 - - - +
595A GLU* 1.3 80.8 - - - +
597A LEU* 1.3 61.1 + - - +
599A PRO* 4.2 6.1 - - - +
682A LYS* 2.7 51.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 597 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A PRO* 4.9 2.2 - - + -
578A THR* 4.0 14.6 - - + -
582A LEU* 4.0 16.2 - - + -
593A GLN* 2.7 26.6 + - - +
596A GLU* 1.3 74.6 - - - +
598A LEU* 1.3 67.0 - - - +
599A PRO* 3.4 8.1 - - - +
603A ILE* 3.8 11.3 - - - +
680A VAL* 4.1 13.9 - - + +
682A LYS* 3.9 23.7 - - + +
687A ILE* 3.7 43.5 - - + -
689A VAL* 4.3 10.3 - - + -
721A PHE* 3.9 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 598 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594A LYS* 2.6 35.2 + - + +
595A GLU* 4.2 2.2 - - - -
597A LEU* 1.3 80.7 - - - +
599A PRO* 1.3 64.6 - - - +
603A ILE* 3.3 21.8 - - + -
622A ILE* 4.3 19.1 - - + -
624A ASN* 3.7 11.2 + - - +
656A LEU* 4.3 10.3 - - + -
680A VAL* 5.0 0.4 - - + -
689A VAL* 4.4 17.5 - - + -
719A ASN* 3.5 29.2 - - - +
721A PHE* 3.5 30.3 - - + -
----------------------------------------------------------
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