Contacts of the helix formed by residues 572 - 584 (chain A) in PDB entry 1B3U
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 VAL 572 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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570A GLN 3.7 5.3 + - - +
571A ASP* 1.3 75.8 + - - +
573A ASP* 1.3 65.3 + - - +
575A LYS* 2.9 44.7 - - - +
576A TYR* 3.2 11.6 + - + +
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Residues in contact with ASP 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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537A PHE* 4.1 28.0 - - + -
571A ASP* 2.8 17.6 + - - +
572A VAL* 1.3 80.4 - - - +
574A VAL* 1.3 64.3 + - - +
576A TYR* 3.1 5.6 + - - +
577A PHE* 2.9 40.2 + - + -
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Residues in contact with VAL 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 ALA 3.7 23.3 - - - +
536A ARG* 4.0 16.2 - - + +
537A PHE* 3.7 16.8 - - + +
540A ALA* 4.9 1.9 - - + +
566A LEU* 3.8 24.7 - - + +
569A ASP* 3.6 33.2 - - + +
571A ASP* 3.4 24.6 + - + +
573A ASP* 1.3 75.5 - - - +
575A LYS* 1.3 62.5 + - - +
577A PHE* 4.0 0.7 - - - +
578A ALA* 3.1 26.3 + - - +
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Residues in contact with LYS 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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566A LEU 3.7 11.4 + - - +
567A THR* 3.9 21.8 - - - +
569A ASP 4.3 10.8 - - - +
570A GLN 5.8 1.1 - - - +
571A ASP 3.2 9.7 + - - +
572A VAL* 2.9 54.3 - - - +
574A VAL* 1.3 78.3 - - - +
576A TYR* 1.3 62.6 + - - +
578A ALA* 3.7 1.4 - - - +
579A GLN* 3.2 23.9 + - - +
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Residues in contact with TYR 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 VAL* 3.5 10.8 - - + +
573A ASP* 3.1 11.1 + - - +
575A LYS* 1.3 85.1 - - + +
577A PHE* 1.3 100.9 + + - +
578A ALA 3.2 0.3 + - - -
579A GLN* 3.3 4.1 + - - +
580A GLU* 3.0 47.2 + - + +
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Residues in contact with PHE 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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537A PHE* 3.9 40.2 - + + +
540A ALA* 3.8 9.3 - - + +
541A LYS* 3.7 39.0 - - + -
544A GLN* 4.7 2.0 - - - +
573A ASP* 2.9 38.4 + - + +
574A VAL 4.5 0.7 - - - +
576A TYR* 1.3 101.7 - + - +
578A ALA* 1.3 59.8 + - - +
580A GLU* 3.8 18.4 - - - +
581A ALA* 3.1 23.9 + - - +
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Residues in contact with ALA 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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540A ALA* 3.9 10.3 - - + +
563A LEU* 3.8 8.5 - - + +
566A LEU* 3.7 28.7 - - + -
567A THR* 3.8 16.2 - - + -
574A VAL 3.1 20.0 + - - +
575A LYS 3.7 4.7 - - - +
576A TYR 3.1 0.2 - - - -
577A PHE* 1.3 77.3 - - - +
579A GLN* 1.3 62.8 + - - +
581A ALA* 3.3 4.7 + - - +
582A LEU* 3.1 24.8 + - - +
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Residues in contact with GLN 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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567A THR* 4.1 13.0 - - + +
575A LYS 3.2 13.5 + - - +
576A TYR* 3.9 3.8 - - - +
578A ALA* 1.3 76.6 - - - +
580A GLU* 1.3 66.6 + - - +
582A LEU* 3.3 21.9 + - - +
583A THR* 3.0 29.6 + - - +
588A ALA* 5.4 4.7 - - - +
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Residues in contact with GLU 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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544A GLN* 4.0 18.3 + - - +
576A TYR* 3.0 44.9 + - + +
577A PHE* 3.9 25.1 - - - +
578A ALA 3.3 0.2 - - - -
579A GLN* 1.3 73.1 - - - +
581A ALA* 1.3 61.1 + - - +
583A THR* 3.0 7.3 + - - +
584A VAL* 2.8 41.5 + - + +
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Residues in contact with ALA 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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540A ALA 3.8 18.2 - - - +
544A GLN* 3.2 27.2 + - + +
563A LEU* 3.8 19.5 - - + -
577A PHE 3.1 19.8 + - - +
578A ALA 3.5 4.7 - - - +
579A GLN 3.3 0.2 - - - -
580A GLU* 1.3 76.5 - - - +
582A LEU* 1.3 61.7 + - - +
584A VAL* 3.8 0.3 - - - +
585A LEU* 2.9 31.7 + - - +
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Residues in contact with LEU 582 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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560A LYS* 4.5 9.6 - - + +
563A LEU* 3.6 28.9 - - + +
564A GLU* 4.2 17.9 - - + -
567A THR* 3.8 28.0 - - + -
578A ALA 3.1 10.4 + - - +
579A GLN* 3.5 23.3 - - - +
581A ALA* 1.3 81.5 - - - +
583A THR* 1.3 59.4 + - - +
585A LEU 3.5 0.2 + - - -
586A SER 3.4 1.2 + - - -
587A LEU* 2.9 60.4 + - + +
588A ALA* 3.3 5.9 + - - +
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Residues in contact with THR 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 GLN* 3.0 25.9 + - - +
580A GLU* 3.0 12.3 + - - -
582A LEU* 1.3 76.4 - - - +
584A VAL* 1.3 62.2 + - + +
586A SER* 2.9 22.2 + - - -
588A ALA* 4.3 16.6 - - + +
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Residues in contact with VAL 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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544A GLN* 3.9 39.5 - - + +
548A PRO* 6.5 0.2 - - + -
580A GLU* 2.8 33.0 + - + +
581A ALA 4.0 1.1 - - - +
583A THR* 1.3 77.2 - - + +
585A LEU* 1.3 63.5 + - + +
586A SER* 3.3 3.5 + - - -
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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
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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