Contacts of the helix formed by residues 576 - 589 (chain A) in PDB entry 2PDA
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 PHE 576 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569A LYS* 4.2 26.2 - - + +
574A LEU 3.4 4.0 + - - -
575A PRO* 1.3 68.9 - - - +
577A GLU* 1.3 82.4 + - + +
579A ALA* 3.4 6.2 + - - +
580A VAL* 3.1 50.5 + - + +
610A VAL* 4.1 23.6 - - + -
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Residues in contact with GLU 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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575A PRO* 3.0 3.8 + - + +
576A PHE* 1.3 95.2 - - + +
578A LYS* 1.3 57.6 + - - +
580A VAL* 4.1 1.8 - - - +
581A ASP* 2.9 27.0 + - - +
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Residues in contact with LYS 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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444A ASN* 3.3 30.8 + - - +
445A THR* 4.9 2.2 - - - -
574A LEU* 4.2 12.3 - - + -
575A PRO* 2.9 23.2 + - + +
577A GLU* 1.3 75.9 - - - +
579A ALA* 1.3 58.9 + - - +
581A ASP* 3.1 11.3 + - - +
582A LEU* 2.6 74.8 + - + +
585A LYS* 5.7 1.6 - - - +
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Residues in contact with ALA 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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568A PHE* 3.3 44.3 - - + +
569A LYS* 5.0 0.9 - - - -
574A LEU* 3.9 23.9 - - + +
575A PRO 3.1 10.9 + - - +
576A PHE* 3.5 12.3 - - - +
578A LYS* 1.3 81.0 - - - +
580A VAL* 1.3 65.8 + - + +
582A LEU* 3.7 0.3 - - - +
583A LEU* 3.0 21.3 + - - +
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Residues in contact with VAL 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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568A PHE* 5.6 1.3 - - + -
569A LYS* 5.0 7.0 - - + +
576A PHE* 3.1 45.8 + - + +
577A GLU* 4.6 1.6 - - - +
579A ALA* 1.3 76.8 - - + +
581A ASP* 1.3 63.1 + - - +
583A LEU* 4.0 7.4 - - - +
584A LYS* 3.5 32.7 + - - +
606A VAL* 4.2 21.8 - - + -
607A ASP* 5.6 1.6 - - - +
610A VAL* 4.4 16.4 - - + -
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Residues in contact with ASP 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 GLU 2.9 21.9 + - - +
578A LYS* 3.0 15.7 + - - +
579A ALA 3.0 0.2 - - - -
580A VAL* 1.3 74.1 - - - +
582A LEU* 1.3 76.9 + - - +
584A LYS* 2.8 19.3 + - - +
585A LYS* 3.2 47.1 + - - +
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Residues in contact with LEU 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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440A ILE* 3.8 27.2 - - + +
444A ASN* 3.7 31.2 - - + +
445A THR* 4.6 2.0 - - + -
568A PHE* 4.6 2.7 - - + -
574A LEU* 3.5 26.9 - - + -
578A LYS* 2.6 53.1 + - + +
579A ALA 3.7 2.9 - - - +
581A ASP* 1.3 86.7 - - - +
583A LEU* 1.3 62.4 + - - +
585A LYS* 3.5 17.6 + - + +
586A SER* 3.4 19.6 + - - -
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Residues in contact with LEU 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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440A ILE* 4.8 3.6 - - + -
561A MET* 3.2 37.9 - - + -
564A GLN* 4.2 9.4 - - + +
565A THR* 4.0 16.4 - - + -
568A PHE* 3.8 36.3 - - + -
579A ALA 3.0 15.8 + - - +
580A VAL* 4.0 7.6 - - - +
581A ASP 2.9 1.2 + - - -
582A LEU* 1.3 77.8 - - - +
584A LYS* 1.3 60.8 + - - +
586A SER* 2.6 31.1 + - - +
587A ILE* 3.1 8.6 - - + +
606A VAL* 3.9 21.3 - - + -
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Residues in contact with LYS 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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580A VAL* 3.5 26.3 + - - +
581A ASP* 2.8 12.9 + - - +
583A LEU* 1.3 72.0 - - - +
585A LYS* 1.3 67.0 + - + +
587A ILE* 2.9 25.2 + - + +
588A HIS* 3.4 15.6 + - + +
603A THR* 4.4 25.6 - - + +
606A VAL* 4.5 20.4 - - + -
607A ASP* 3.0 31.1 + - - -
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Residues in contact with LYS 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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444A ASN* 5.7 1.6 + - - -
578A LYS* 5.7 1.4 - - - +
581A ASP* 3.2 46.8 + - - +
582A LEU* 3.8 18.4 - - + +
583A LEU 3.3 0.4 - - - -
584A LYS* 1.3 77.6 - - + +
586A SER* 1.3 60.2 + - - +
588A HIS* 3.4 7.6 + - - +
589A LYS* 3.4 18.8 + - - +
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Residues in contact with SER 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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436A GLN* 4.1 10.5 + - - -
440A ILE* 3.3 35.8 - - - +
582A LEU 3.4 3.9 + - - -
583A LEU* 2.6 25.8 + - - +
585A LYS* 1.3 75.8 - - - +
587A ILE* 1.3 66.5 + - - +
588A HIS 3.0 3.0 + - - -
589A LYS* 4.3 15.7 - - - +
590A ALA* 3.1 28.1 + - - +
591A TYR* 5.3 0.4 - - - -
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Residues in contact with ILE 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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561A MET* 3.3 45.1 - - + -
583A LEU* 3.1 17.7 - - + +
584A LYS* 2.9 16.1 + - + +
586A SER* 1.3 79.3 + - - +
588A HIS* 1.3 54.7 + - - +
590A ALA 2.6 17.3 - - - +
591A TYR* 3.0 28.2 - - + +
599A VAL* 3.9 16.3 - - + +
602A ASN* 3.7 24.9 - - + -
603A THR* 4.1 12.3 - - - +
606A VAL* 4.0 13.9 - - + -
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Residues in contact with HIS 588 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584A LYS* 3.4 16.2 + - + -
585A LYS* 3.8 8.4 - - - +
586A SER 3.0 0.8 - - - -
587A ILE* 1.3 76.7 - - - +
589A LYS* 1.3 59.4 + - - +
590A ALA 2.7 15.1 - - - +
591A TYR* 2.9 12.2 - - - +
592A GLY* 4.1 4.9 + - - -
596A GLU* 3.9 16.8 + - - -
599A VAL* 3.3 33.7 - - + +
603A THR* 4.4 11.7 - - - -
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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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436A GLN* 5.3 12.1 + - - +
439A LYS* 5.8 7.5 - - - +
440A ILE* 6.1 2.8 - - - +
443A ASP* 5.5 4.8 + - - -
585A LYS 3.4 11.2 + - - +
586A SER* 3.3 15.6 + - - +
588A HIS* 1.3 73.9 - - - +
590A ALA* 1.3 66.7 + - - +
591A TYR 2.9 13.3 - - - +
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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