Contacts of the helix formed by residues 580 - 592 (chain A) in PDB entry 1HS6
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 SER 580 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A ILE* 3.7 35.0 - - - -
555A LEU* 5.9 0.7 - - - -
574A LEU* 2.7 34.3 + - - +
577A PHE* 2.9 21.0 + - - +
579A LYS* 1.3 74.5 - - - +
581A HIS* 1.3 59.4 + - - +
582A ASP 3.4 2.2 - - - -
583A GLN* 3.2 10.0 + - - +
584A ALA* 2.8 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 581 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574A LEU 3.6 7.9 - - - -
575A ALA* 2.9 32.7 - - + +
577A PHE 2.9 14.6 + - - +
578A ASP* 3.6 12.1 + - - +
579A LYS 3.5 1.8 - - - -
580A SER* 1.3 75.8 - - - +
582A ASP* 1.3 83.9 + - - +
584A ALA* 3.0 11.4 + - - +
585A VAL* 3.1 33.0 + - + +
607A LEU 6.0 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 582 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578A ASP 4.9 2.1 + - - -
579A LYS 5.3 0.8 + - - +
580A SER 3.4 0.4 - - - -
581A HIS* 1.3 100.3 + - - +
583A GLN* 1.3 64.3 + - - +
585A VAL* 3.4 4.5 + - - +
586A ARG* 3.0 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 583 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A ILE* 3.9 12.6 - - - +
555A LEU* 3.5 31.3 - - + +
579A LYS 5.5 1.6 + - - +
580A SER* 3.2 11.9 + - - +
581A HIS 3.2 0.4 - - - -
582A ASP* 1.3 82.6 - - - +
584A ALA* 1.3 58.8 + - - +
586A ARG* 3.5 32.8 - - - +
587A THR* 2.5 39.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 584 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A LEU* 4.1 13.0 - - - +
571A PHE* 3.5 22.1 - - + -
574A LEU* 3.9 23.3 - - + -
575A ALA* 4.1 17.0 - - + +
580A SER 2.8 18.0 + - - +
581A HIS 3.0 8.5 + - - +
583A GLN* 1.3 74.2 - - - +
585A VAL* 1.3 63.9 + - + +
587A THR* 3.3 0.3 + - - -
588A TYR* 3.1 19.2 + - - +
607A LEU* 4.7 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 585 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575A ALA* 5.3 1.3 - - + -
581A HIS* 3.1 37.5 + - + +
582A ASP* 3.8 5.2 - - - +
584A ALA* 1.3 80.8 - - + +
586A ARG* 1.3 66.0 + - - +
588A TYR* 3.3 4.0 + - - +
589A GLN* 3.0 36.1 + - + +
607A LEU* 4.4 31.2 - - + +
609A VAL* 4.7 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 586 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582A ASP* 3.0 23.7 + - - +
583A GLN* 3.5 48.6 - - - +
585A VAL* 1.3 81.0 - - - +
587A THR* 1.3 63.5 + - - +
589A GLN* 3.3 8.4 + - + +
590A GLU* 3.0 47.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 587 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A LEU* 3.7 23.4 - - + +
559A THR* 3.6 30.3 - - + +
571A PHE* 4.5 2.7 - - + -
583A GLN* 2.5 30.7 + - - +
584A ALA 3.6 4.5 - - - -
585A VAL 3.3 0.2 - - - -
586A ARG* 1.3 77.0 - - - +
588A TYR* 1.3 63.7 + - - +
590A GLU* 3.2 10.1 + - - +
591A HIS* 2.8 40.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 588 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571A PHE* 4.0 8.0 - + + -
584A ALA 3.1 10.8 + - - +
585A VAL 3.5 7.4 - - - +
587A THR* 1.3 80.5 - - - +
589A GLN* 1.3 58.4 + - - +
591A HIS 2.7 2.9 + - - -
592A LYS* 2.5 71.5 + - + +
595A MET* 3.6 21.8 - - + -
600A ALA* 2.8 26.6 + - - +
603A VAL* 3.4 30.1 - - + -
604A GLY* 3.3 14.4 - - - -
607A LEU* 3.8 11.4 - - + -
609A VAL* 3.5 39.0 - - + -
610A ASP* 4.5 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 589 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585A VAL* 3.0 25.8 + - + +
586A ARG* 3.5 11.0 - - - +
588A TYR* 1.3 90.7 - - + +
590A GLU* 1.3 62.1 + - + +
592A LYS* 2.7 50.1 + - - +
593A ALA* 4.9 1.2 + - - +
609A VAL* 3.9 20.6 - - - +
610A ASP* 4.8 3.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 590 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A ARG* 3.0 44.1 + - + +
587A THR* 3.6 12.8 + - - +
589A GLN* 1.3 79.1 - - + +
591A HIS* 1.3 72.3 + - + +
593A ALA* 5.1 3.0 + - - +
594A SER* 5.3 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 591 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559A THR* 3.8 32.4 + - + -
587A THR* 2.8 37.5 + - + +
588A TYR 2.7 1.8 + - - -
590A GLU* 1.3 91.6 - - + +
592A LYS* 1.3 66.3 + - - +
593A ALA 3.3 2.2 - - - -
594A SER* 3.0 33.4 + - - -
595A MET* 3.0 32.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 592 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A TYR* 2.5 50.5 + - + +
589A GLN* 2.7 43.1 + - - +
590A GLU 3.5 0.4 - - - -
591A HIS* 1.3 73.6 - - - +
593A ALA* 1.3 63.8 + - + +
595A MET* 3.1 25.8 + - - +
600A ALA* 4.2 11.0 - - + +
610A ASP* 3.6 24.3 + - - +
----------------------------------------------------------
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