Contacts of the helix formed by residues 570 - 589 (chain A) in PDB entry 5HG1
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 570 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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566A VAL 4.6 0.2 - - - +
569A GLY* 1.3 76.3 - - - -
571A GLY* 1.3 64.2 + - - +
572A ASP* 3.8 9.0 + - - +
573A GLU* 3.1 39.1 + - - +
574A LEU* 3.1 20.8 + - - +
625A ALA* 4.3 1.3 - - - -
626A SER* 3.4 19.1 - - - +
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Residues in contact with GLY 571 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570A THR* 1.3 70.6 - - - +
572A ASP* 1.3 65.8 + - - +
574A LEU* 3.7 5.8 - - - -
575A PHE* 3.0 30.8 + - - +
625A ALA* 4.4 1.1 - - - -
626A SER 2.9 23.9 + - - +
627A GLY 5.1 1.3 - - - -
628A CYS* 3.5 22.0 - - - -
636A LEU* 6.4 2.7 - - - -
643A ARG* 5.1 0.2 + - - -
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Residues in contact with ASP 572 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570A THR* 3.2 9.8 + - - +
571A GLY* 1.3 77.6 - - - +
573A GLU* 1.3 53.2 - - + +
576A ASP* 2.8 47.0 + - - +
636A LEU* 5.9 2.6 - - - +
639A GLU* 5.5 1.4 - - - +
643A ARG* 3.8 29.2 + - - +
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Residues in contact with GLU 573 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565A GLU 4.7 3.3 - - - +
566A VAL* 3.9 15.2 - - + +
569A GLY* 3.5 10.8 - - - -
570A THR* 3.1 41.2 + - - +
572A ASP* 1.3 77.7 - - + +
574A LEU* 1.3 57.0 + - - +
576A ASP* 3.8 7.3 - - - +
577A HIS* 3.0 29.3 + - - +
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Residues in contact with LEU 574 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533A LEU* 5.4 0.9 - - + -
562A ILE* 4.2 17.3 - - + -
566A VAL* 3.8 29.6 - - + +
570A THR 3.1 12.3 + - - +
571A GLY* 3.8 8.3 - - - +
572A ASP 3.2 0.2 - - - -
573A GLU* 1.3 77.5 - - - +
575A PHE* 1.4 71.5 + - + +
577A HIS* 3.4 3.0 + - + +
578A ILE* 3.0 42.0 + - + +
619A TRP* 3.7 37.2 - - + -
623A PHE* 4.2 18.8 - - + -
625A ALA* 4.2 9.9 - - + -
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Residues in contact with PHE 575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533A LEU* 5.7 0.4 - - + -
571A GLY 3.0 19.1 + - - +
572A ASP 4.6 0.2 - - - +
574A LEU* 1.4 94.3 - - + +
576A ASP* 1.3 66.6 + - - +
577A HIS 3.2 0.4 - - - -
578A ILE* 3.8 15.7 - - + +
579A VAL* 3.0 28.1 + - - +
600A PHE* 5.0 5.6 - + - -
602A PHE* 5.2 2.9 - + - -
619A TRP* 4.8 9.4 - + - -
628A CYS* 4.1 16.4 - - - -
633A VAL* 4.1 22.9 - - + -
636A LEU* 3.9 24.0 - - + +
637A LEU* 3.6 41.1 - - + -
640A ALA* 3.5 20.2 - - + -
643A ARG* 4.8 1.6 - - - +
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Residues in contact with ASP 576 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572A ASP* 2.8 31.8 + - - +
573A GLU* 3.8 6.8 + - - +
575A PHE* 1.3 75.5 - - - +
577A HIS* 1.3 55.9 + - - +
579A VAL* 3.1 8.9 - - - +
580A GLN* 2.8 30.1 + - - +
640A ALA* 4.0 8.2 - - - +
643A ARG* 3.1 34.4 + - - +
644A ARG* 4.8 1.0 + - - -
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Residues in contact with HIS 577 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560A TYR* 5.2 0.2 - - + -
561A ALA 3.2 25.3 + - - -
562A ILE* 4.4 11.0 - - + +
563A PRO* 3.7 16.3 - - + +
566A VAL* 4.0 29.2 - - + -
573A GLU 3.0 20.0 + - - +
574A LEU* 3.5 5.6 - - + +
575A PHE 3.2 0.2 - - - -
576A ASP* 1.3 76.4 - - - +
578A ILE* 1.3 65.6 + - + +
580A GLN* 3.2 17.9 + - + +
581A CYS* 3.0 43.1 + - - -
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Residues in contact with ILE 578 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531A LEU* 4.1 22.7 - - + -
533A LEU* 3.9 31.6 - - + -
538A PHE* 4.0 29.9 - - + -
562A ILE* 5.0 3.1 - - + -
574A LEU* 3.0 35.8 + - + +
575A PHE* 3.8 22.9 - - + +
576A ASP 3.4 0.2 - - - -
577A HIS* 1.3 78.8 - - + +
579A VAL* 1.3 58.0 + - - +
581A CYS* 3.1 5.9 + - - +
582A ILE* 3.0 25.1 + - + +
600A PHE* 5.8 2.5 - - + -
637A LEU* 4.1 13.2 - - + -
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Residues in contact with VAL 579 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575A PHE 3.0 24.0 + - - +
576A ASP* 3.1 14.6 - - - +
578A ILE* 1.3 73.7 - - - +
580A GLN* 1.3 61.4 + - - +
582A ILE* 3.2 13.0 + - + +
583A ALA* 3.0 27.7 + - - +
637A LEU* 3.8 19.3 - - + -
640A ALA* 3.5 25.1 - - + +
641A ILE* 3.6 31.0 - - + -
644A ARG* 4.4 13.9 + - + +
647A PHE* 4.3 8.7 - - + -
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Residues in contact with GLN 580 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576A ASP 2.8 17.6 + - - +
577A HIS* 3.2 19.5 + - - +
579A VAL* 1.3 77.1 - - - +
581A CYS* 1.3 57.7 + - - +
583A ALA* 3.6 1.6 + - + +
584A ASP* 3.1 26.5 + - + +
644A ARG* 3.0 31.2 - - - +
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Residues in contact with CYS 581 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538A PHE* 3.8 16.8 - - + -
540A VAL* 4.3 2.2 - - + -
560A TYR* 3.3 53.6 + - + -
577A HIS* 3.0 45.0 + - - -
578A ILE 3.4 7.4 - - - +
580A GLN* 1.3 75.9 - - - +
582A ILE* 1.3 66.6 + - - +
583A ALA 3.1 1.8 - - - -
584A ASP* 3.4 0.4 + - - -
585A PHE* 3.0 20.6 + - - +
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Residues in contact with ILE 582 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529A LEU* 4.7 10.5 - - + -
531A LEU* 4.0 37.5 - - + -
540A VAL* 4.3 11.4 - - + -
578A ILE* 3.0 19.8 + - + +
579A VAL* 3.2 24.6 + - + +
581A CYS* 1.3 75.1 - - - +
583A ALA* 1.3 55.0 + - - +
585A PHE* 3.4 2.3 + - - +
586A LEU* 2.7 54.4 + - + +
598A LEU* 4.2 15.5 - - + -
637A LEU* 4.7 4.7 - - + -
641A ILE* 5.1 3.4 - - + -
647A PHE* 3.8 23.3 - - + -
649A LEU* 5.2 0.4 - - + -
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Residues in contact with ALA 583 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579A VAL 3.0 16.3 + - - +
580A GLN* 3.9 5.6 - - + +
581A CYS 3.1 0.2 - - - -
582A ILE* 1.3 74.1 - - - +
584A ASP* 1.3 66.2 + - - +
585A PHE 3.0 1.3 + - - -
586A LEU* 3.2 6.0 + - - +
587A GLU* 3.0 26.1 + - - +
644A ARG* 4.4 10.5 - - - +
646A GLU* 3.5 27.4 - - - +
647A PHE* 4.0 10.8 - - + -
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Residues in contact with ASP 584 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558A LYS* 3.6 20.1 + - - -
560A TYR* 3.5 21.8 - - + -
580A GLN* 3.1 16.5 + - + +
581A CYS* 3.9 3.8 - - - +
583A ALA* 1.3 78.2 - - - +
585A PHE* 1.3 57.8 + - - +
587A GLU* 4.0 9.4 - - - +
588A TYR* 3.0 25.3 + - - +
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Residues in contact with PHE 585 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529A LEU* 4.1 10.5 - - + -
540A VAL* 3.6 40.2 - - + -
541A LEU 4.1 0.7 - - - -
542A LEU* 3.7 38.4 - - + -
556A HIS 4.1 3.8 - - - -
557A ASN* 3.9 17.0 - - - -
558A LYS* 4.0 12.3 - - + -
560A TYR* 3.0 20.1 + - - +
581A CYS 3.0 14.3 + - - +
582A ILE 3.6 3.4 - - - +
584A ASP* 1.3 73.7 - - - +
586A LEU* 1.3 71.3 + - + +
587A GLU 3.1 1.6 - - - -
588A TYR* 3.0 12.5 + + - +
589A MET* 2.9 51.7 + - + +
591A MET* 5.8 0.4 - - + -
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Residues in contact with LEU 586 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529A LEU* 4.1 28.7 - - + -
582A ILE* 2.7 47.7 + - + +
583A ALA* 3.7 5.4 - - - +
585A PHE* 1.3 80.8 - - + +
587A GLU* 1.3 58.3 + - - +
589A MET 3.3 0.5 + - - -
590A GLY 3.2 2.4 + - - -
591A MET* 2.6 48.5 + - + +
592A LYS 3.2 29.2 - - - +
594A VAL* 4.5 12.3 - - + +
596A LEU* 5.0 2.5 - - + -
647A PHE* 4.1 32.3 - - + -
649A LEU* 5.7 0.4 - - + -
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Residues in contact with GLU 587 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583A ALA 3.0 16.4 + - - +
584A ASP* 4.0 10.0 - - - +
586A LEU* 1.3 73.8 - - - +
588A TYR* 1.3 57.9 + - - +
589A MET 3.0 1.8 - - - -
590A GLY* 2.8 23.7 + - - +
592A LYS* 4.4 10.5 - - - +
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Residues in contact with TYR 588 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556A HIS* 6.1 0.4 - - + -
557A ASN 4.6 16.2 + - - -
558A LYS* 4.6 27.4 - - + -
584A ASP* 3.0 23.5 + - - +
585A PHE* 3.0 16.1 + + - +
587A GLU* 1.3 75.1 - - - +
589A MET* 1.3 82.0 + - + +
590A GLY 3.3 0.8 + - - -
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Residues in contact with MET 589 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542A LEU* 4.5 16.8 - - + -
544A ARG* 5.5 6.5 - - - +
556A HIS* 3.6 50.0 - - + +
585A PHE* 2.9 40.3 + - + +
586A LEU* 3.7 0.4 - - - +
587A GLU 3.0 0.4 - - - -
588A TYR* 1.3 93.8 - - + +
590A GLY* 1.3 60.1 + - - +
591A MET* 3.0 30.4 + - + +
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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
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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) + - + + + + + -
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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