Contacts of the helix formed by residues 576 - 591 (chain A) in PDB entry 5H65
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 ASP 576 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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497A THR* 5.0 11.2 + - + +
572A GLU* 3.6 16.0 - - + +
573A VAL 3.2 9.8 + - - +
574A LEU 3.6 0.8 - - - -
575A MET* 1.3 79.7 - - - +
577A ASP* 1.3 63.2 + - - +
578A ASP* 3.1 22.7 + - - +
579A LEU* 3.3 32.2 + - + +
580A GLN* 3.1 23.1 + - - +
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Residues in contact with ASP 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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576A ASP* 1.3 73.7 + - - +
578A ASP* 1.3 61.8 + - - +
580A GLN* 3.4 6.2 + - - +
581A LYS* 2.8 52.8 + - - +
291B THR* 3.6 20.9 - - + +
292B HIS* 2.8 41.7 + - - +
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Residues in contact with ASP 578 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576A ASP* 3.1 10.3 + - - +
577A ASP* 1.3 81.7 - - - +
579A LEU* 1.3 63.5 + - + +
581A LYS* 3.2 13.8 + - - +
582A SER* 3.0 32.1 + - - -
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Residues in contact with LEU 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 GLN 5.9 0.4 - - - +
568A ILE* 3.8 33.6 - - + +
569A PRO* 4.3 9.0 - - + -
572A GLU* 3.7 39.3 - - + +
573A VAL* 3.9 9.6 - - + +
576A ASP* 3.3 29.8 + - + +
578A ASP* 1.3 80.7 - - + +
580A GLN* 1.3 60.9 + - - +
582A SER* 3.5 9.3 + - - +
583A VAL* 3.2 27.7 + - - +
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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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573A VAL* 3.0 32.0 + - + +
574A LEU* 3.3 15.4 + - - +
576A ASP 3.1 14.3 + - - +
577A ASP* 3.5 6.4 - - - +
578A ASP 3.2 0.2 - - - -
579A LEU* 1.3 73.7 - - - +
581A LYS* 1.3 59.7 + - - +
583A VAL* 3.2 4.0 + - - +
584A ASP* 3.0 32.2 + - - +
291B THR* 2.9 33.0 + - - -
292B HIS* 3.5 15.4 + - + -
293B TRP* 3.1 56.1 + - + +
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Residues in contact with LYS 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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577A ASP* 2.8 41.7 + - - +
578A ASP* 3.2 16.1 + - - +
580A GLN* 1.3 74.6 - - - +
582A SER* 1.3 57.2 + - - +
584A ASP* 3.3 9.0 + - - +
585A MET* 2.9 39.3 + - + +
292B HIS* 3.7 17.5 + - + +
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Residues in contact with SER 582 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568A ILE* 3.5 24.5 - - - -
578A ASP 3.0 14.3 + - - -
579A LEU* 3.6 8.7 - - - +
580A GLN 3.3 0.2 - - - -
581A LYS* 1.3 75.5 - - - +
583A VAL* 1.3 56.3 + - - +
585A MET* 3.2 6.3 + - - +
586A ILE* 2.9 36.6 + - - +
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Residues in contact with VAL 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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374A LEU* 4.3 9.4 - - + -
542A PHE* 4.1 23.8 - - + -
544A MET* 4.5 14.8 - - + -
566A PHE* 4.5 11.7 - - + -
568A ILE* 3.5 18.6 - - + -
573A VAL* 4.3 7.0 - - + -
579A LEU 3.2 15.6 + - - +
580A GLN 3.7 6.3 - - - +
582A SER* 1.3 75.8 - - - +
584A ASP* 1.3 63.8 + - - +
586A ILE* 3.4 5.1 + - - +
587A MET* 3.1 32.7 + - + +
293B TRP* 3.8 21.5 - - + -
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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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374A LEU* 3.4 22.0 - - - +
580A GLN 3.0 13.8 + - - +
581A LYS* 3.4 10.5 - - - +
583A VAL* 1.3 76.8 - - - +
585A MET* 1.3 70.7 + - + +
587A MET* 3.5 1.7 + - - +
588A ASP* 2.9 30.1 + - - +
292B HIS* 2.7 32.2 + - - -
293B TRP* 3.0 19.6 + - - -
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Residues in contact with MET 585 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581A LYS* 2.9 25.3 + - + +
582A SER* 3.8 5.4 - - - +
584A ASP* 1.3 87.9 - - + +
586A ILE* 1.3 61.8 + - + +
588A ASP* 3.7 16.5 - - + +
589A MET* 2.8 30.0 + - - +
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Residues in contact with ILE 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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566A PHE* 3.9 37.0 - - + +
568A ILE* 4.2 6.5 - - + -
582A SER* 2.9 28.1 + - - +
583A VAL 3.9 3.4 - - - +
585A MET* 1.3 75.9 - - + +
587A MET* 1.3 77.9 + - + +
589A MET* 3.2 7.0 + - - +
590A PHE* 3.1 32.4 + - + -
629A VAL* 3.7 27.4 - - + -
630A ALA* 5.5 2.7 - - + -
633A VAL* 4.8 17.5 - - + -
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Residues in contact with MET 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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366A LEU* 4.9 8.7 - - + +
369A TYR* 4.0 26.5 - - + +
374A LEU* 3.9 22.9 - - + -
544A MET* 3.9 24.9 - - - +
546A PHE* 4.4 13.5 - - + -
565A PHE* 4.4 9.6 - - + -
566A PHE* 3.5 24.2 - - + -
583A VAL* 3.1 23.9 + - + +
584A ASP 3.9 2.2 - - - +
586A ILE* 1.3 85.9 - - + +
588A ASP* 1.3 57.6 + - - +
590A PHE* 4.3 8.2 - - + +
591A CYS* 2.9 35.2 + - - +
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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
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369A TYR* 5.2 0.8 + - - -
584A ASP 2.9 19.1 + - - +
585A MET* 3.7 20.9 - - + +
587A MET* 1.3 76.9 - - - +
589A MET* 1.3 61.1 + - - +
591A CYS 4.5 4.7 - - - -
592A PRO* 3.2 29.1 - - - +
593A PRO* 3.7 22.7 - - - +
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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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585A MET 2.8 17.9 + - - +
586A ILE* 3.2 7.8 + - - +
588A ASP* 1.3 79.7 - - - +
590A PHE* 1.3 73.3 + - + +
592A PRO* 3.7 5.7 - - - +
601A PRO* 3.2 37.9 - - + +
633A VAL* 3.6 40.4 - - + -
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Residues in contact with PHE 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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366A LEU* 3.9 28.9 + - + +
565A PHE* 5.7 1.1 - + - -
586A ILE* 3.1 33.9 + - + +
587A MET* 4.3 8.1 - - + +
589A MET* 1.3 90.4 - - + +
591A CYS* 1.3 59.3 + - - +
592A PRO* 3.6 1.1 - - - -
600A TYR* 3.5 26.9 - - - +
601A PRO* 4.0 21.7 - - + +
602A TRP 3.6 22.4 - - - -
603A LEU* 3.9 25.6 - - + -
629A VAL* 3.5 44.6 - - + -
633A VAL* 5.8 4.0 - - + -
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Residues in contact with CYS 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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366A LEU* 3.5 17.7 - - + +
367A ARG 3.4 25.6 - - - -
368A SER* 3.8 13.2 - - - -
369A TYR* 3.8 32.5 + - + -
587A MET 2.9 14.1 + - - +
588A ASP* 4.5 0.9 - - - -
590A PHE* 1.3 80.3 - - - +
592A PRO* 1.4 65.0 - - - +
593A PRO* 3.5 6.2 - - - +
600A TYR* 4.1 10.1 - - - -
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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