Contacts of the helix formed by residues 573 - 593 (chain A) in PDB entry 3BZI
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 CYS 573 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A SER* 3.8 0.7 - - - -
395A VAL* 4.0 4.9 - - + +
397A GLN* 2.6 37.4 + - - +
552A TYR* 5.1 4.9 - - - -
572A CYS* 1.3 80.9 - - - +
574A LYS* 1.3 62.6 - - - +
575A GLU* 3.2 25.8 - - - +
576A LEU* 3.4 20.9 + - - -
577A ALA* 3.0 25.1 + - - +
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Residues in contact with LYS 574 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A SER* 3.8 21.0 - - - +
573A CYS* 1.3 72.3 - - - +
575A GLU* 1.3 79.3 + - - +
577A ALA* 3.9 0.3 - - - +
578A SER* 2.9 38.7 + - - -
581A ARG* 5.0 4.3 + - - +
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Residues in contact with GLU 575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552A TYR* 3.9 17.7 - - + +
555A GLU* 4.7 13.7 - - - +
573A CYS* 3.2 26.7 - - - +
574A LYS* 1.3 101.8 + - - +
576A LEU* 1.3 63.8 + - - +
578A SER* 3.7 1.1 - - - -
579A ARG* 3.0 44.3 + - - +
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Residues in contact with LEU 576 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A GLN* 3.9 19.7 - - - +
541A LEU* 3.9 17.7 - - + -
550A VAL* 4.7 5.2 - - + -
552A TYR* 3.8 34.1 - - + -
562A TYR* 4.0 20.9 - - + -
567A LEU* 4.2 11.7 - - + -
572A CYS* 4.0 19.7 - - + -
573A CYS* 3.4 18.7 + - - +
574A LYS 3.4 0.2 - - - -
575A GLU* 1.3 79.9 - - - +
577A ALA* 1.3 59.2 + - - +
579A ARG* 3.3 7.2 + - - +
580A LEU* 2.8 46.8 + - + +
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Residues in contact with ALA 577 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A ASN* 4.5 1.7 - - - +
389A PRO* 4.3 12.3 - - + -
390A SER* 3.6 22.2 - - - +
572A CYS* 3.7 15.3 - - - -
573A CYS 3.0 19.1 + - - +
574A LYS 3.9 2.7 - - - +
575A GLU 3.3 0.2 - - - -
576A LEU* 1.3 76.7 - - - +
578A SER* 1.3 56.8 + - - +
580A LEU* 3.3 9.1 + - - +
581A ARG* 3.1 38.8 + - - +
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Residues in contact with SER 578 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574A LYS* 2.9 27.0 + - - -
575A GLU* 3.7 4.5 - - - -
577A ALA* 1.3 74.5 - - - +
579A ARG* 1.3 66.6 + - - +
581A ARG* 3.1 34.2 + - - +
582A TYR* 3.0 26.6 + - - +
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Residues in contact with ARG 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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534A PHE* 3.5 27.3 - - + -
537A ASP* 2.4 31.7 + - - -
539A THR* 3.1 24.6 + - - +
541A LEU* 3.5 30.5 - - + +
552A TYR* 3.9 21.4 + - + -
555A GLU* 4.1 7.1 + - - -
575A GLU* 3.0 53.1 + - - +
576A LEU* 3.5 6.1 - - - +
578A SER* 1.3 82.5 + - - +
580A LEU* 1.3 56.9 + - - +
582A TYR* 3.3 7.2 + - - +
583A ALA 2.8 24.6 + - - -
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Residues in contact with LEU 580 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A LEU* 4.0 21.4 - - + +
384A VAL* 4.3 20.0 - - + -
385A ASN* 3.1 24.0 + - - +
389A PRO* 5.5 1.3 - - + -
541A LEU* 4.4 8.3 - - + -
543A LEU* 4.3 2.2 - - + -
550A VAL* 4.0 27.4 - - + -
564A LEU* 4.2 6.7 - - + -
567A LEU* 4.2 24.0 - - + -
572A CYS* 4.8 4.7 - - - -
576A LEU* 2.8 34.8 + - + +
577A ALA* 3.3 8.9 + - - +
579A ARG* 1.3 69.9 - - - +
581A ARG* 1.3 65.2 + - - +
583A ALA* 3.7 3.4 - - - +
584A ARG* 3.1 17.2 + - - +
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Residues in contact with ARG 581 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A ASN* 3.6 25.1 - - + +
390A SER* 4.8 4.8 + - - -
391A GLU* 5.7 2.8 + - - -
574A LYS* 5.0 4.2 + - - +
577A ALA* 3.1 24.8 + - - +
578A SER* 3.1 46.3 + - - +
580A LEU* 1.3 72.6 - - - +
582A TYR* 1.3 67.5 + - - +
584A ARG* 3.2 4.9 + - - +
585A THR* 3.2 24.4 + - - -
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Residues in contact with TYR 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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517A THR* 2.5 37.8 + - - +
518A ARG* 5.4 0.7 - - - +
519A SER* 3.5 20.2 - - - -
520A ALA* 4.0 11.0 - - + -
532A ILE* 4.4 3.1 - - + -
534A PHE* 3.3 33.2 - + + -
578A SER 3.0 13.1 + - - +
579A ARG* 3.5 11.9 - - - +
580A LEU 3.3 0.2 - - - -
581A ARG* 1.3 76.7 - - - +
583A ALA* 1.3 62.9 + - - +
585A THR* 3.1 12.5 + - + -
586A MET* 3.0 55.2 + - + +
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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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381A LEU* 3.9 7.2 - - + -
532A ILE* 3.7 20.6 - - + +
541A LEU* 3.9 7.2 - - + -
543A LEU* 3.8 28.7 - - + -
579A ARG 2.8 19.7 + - - +
580A LEU* 3.7 8.1 - - - +
581A ARG 3.3 0.2 - - - -
582A TYR* 1.3 70.5 - - - +
584A ARG* 1.3 66.3 + - - +
586A MET* 3.0 2.8 + - - +
587A VAL* 2.9 26.7 + - - +
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Residues in contact with ARG 584 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A LEU* 3.2 30.8 - - + +
381A LEU* 3.8 20.8 - - + +
382A HIS* 2.7 55.0 + - - +
385A ASN* 3.5 28.8 - - - +
580A LEU 3.1 7.0 + - - +
581A ARG* 3.2 6.0 + - - +
583A ALA* 1.3 74.7 - - - +
585A THR* 1.3 66.1 + - - +
587A VAL* 3.2 3.9 + - - +
588A ASP* 3.0 36.5 + - - +
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Residues in contact with THR 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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581A ARG 3.2 11.0 + - - -
582A TYR* 3.1 13.4 + - + -
584A ARG* 1.3 81.1 - - - +
586A MET* 1.3 76.8 + - + +
588A ASP* 3.4 12.4 + - + +
589A LYS* 3.1 24.3 + - + +
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Residues in contact with MET 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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515A PHE* 3.8 13.2 - - + -
517A THR* 3.8 10.1 - - + -
522A ILE* 3.7 39.9 - - + -
530A VAL* 5.9 0.2 - - + -
532A ILE* 3.8 16.4 - - + -
582A TYR* 3.0 49.2 + - + +
583A ALA 3.0 7.6 + - - +
585A THR* 1.3 92.4 - - + +
587A VAL* 1.3 58.8 + - + +
589A LYS* 3.2 21.4 + - + +
590A LEU* 2.9 31.0 + - + +
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Residues in contact with VAL 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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374A LEU* 3.7 32.1 - - + +
377A MET* 3.6 26.9 - - + -
378A LEU* 3.8 22.7 - - + +
381A LEU* 3.8 12.1 - - + -
530A VAL* 4.6 15.0 - - + -
532A ILE* 5.8 0.2 - - + -
543A LEU* 5.1 1.3 - - + -
583A ALA* 2.9 20.7 + - - +
584A ARG* 3.7 4.5 - - - +
586A MET* 1.3 73.2 - - + +
588A ASP* 1.3 61.5 + - - +
590A LEU* 3.1 8.4 + - - +
591A LEU* 2.9 32.2 + - + +
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Residues in contact with ASP 588 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A LEU* 3.3 25.5 - - - +
584A ARG* 3.0 36.4 + - - +
585A THR* 3.4 14.4 - - + +
587A VAL* 1.3 77.1 - - - +
589A LYS* 1.3 61.4 + - + +
591A LEU* 3.4 5.6 + - - +
592A SER* 3.1 23.9 + - - -
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Residues in contact with LYS 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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515A PHE* 3.7 40.4 - - + -
517A THR* 4.9 5.0 - - + +
585A THR* 3.1 18.1 + - + +
586A MET* 3.2 25.3 + - + +
588A ASP* 1.3 74.9 - - + +
590A LEU* 1.3 63.0 + - - +
592A SER* 3.0 22.2 + - - -
593A SER* 3.6 8.5 + - - -
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Residues in contact with LEU 590 (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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374A LEU* 3.9 22.9 - - + +
513A THR* 3.8 29.8 - - + +
515A PHE* 3.6 25.1 - - + -
522A ILE* 3.9 19.3 - - + -
524A HIS* 4.2 13.9 - - + +
530A VAL* 3.8 31.6 - - + -
586A MET 2.9 17.3 + - - +
587A VAL* 3.1 12.0 + - - +
589A LYS* 1.3 78.2 - - - +
591A LEU* 1.3 62.5 + - - +
592A SER 3.6 0.2 + - - -
593A SER* 3.8 17.1 + - - +
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Residues in contact with LEU 591 (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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371A ASP* 4.4 11.4 - - + +
374A LEU* 3.8 42.2 - - + +
375A SER* 4.1 17.3 - - - +
378A LEU* 3.5 34.3 - - + -
587A VAL* 2.9 20.7 + - + +
588A ASP* 3.8 6.3 - - - +
589A LYS 3.4 0.2 - - - -
590A LEU* 1.3 72.5 - - - +
592A SER* 1.3 69.2 + - - +
593A SER 4.0 2.9 - - - -
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Residues in contact with SER 592 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A ASP 3.1 14.2 + - - -
589A LYS* 3.0 15.6 + - - -
591A LEU* 1.3 75.6 - - - +
593A SER* 1.3 79.5 + - - +
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Residues in contact with SER 593 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589A LYS 3.6 6.8 + - - -
590A LEU* 3.9 15.8 - - - +
591A LEU 4.0 5.4 - - - -
592A SER* 1.3 93.6 + - - +
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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
------------------------------------------------------------
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