Contacts of the helix formed by residues 529 - 539 (chain A) in PDB entry 2PUY
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 529 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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356A ZN 2.4 32.8 - - - -
503A CYS* 3.4 14.5 - - + -
506A CYS* 3.9 7.4 - - - -
508A ARG* 4.1 0.4 - - - -
510A TYR* 3.3 27.4 - - + -
527A TRP* 3.6 14.6 - - + -
528A ILE* 1.3 75.9 - - - +
530A PRO* 1.3 74.5 - - + +
531A ARG* 3.4 9.6 - - - -
532A CYS* 3.1 15.7 + - - +
533A GLN* 3.0 20.7 + - - +
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Residues in contact with PRO 530 (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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510A TYR* 3.6 22.9 - - + +
515A LEU* 4.3 13.5 - - + -
516A ASP 6.2 1.1 - - - +
527A TRP* 3.9 12.8 - - + -
528A ILE 4.6 0.2 - - - +
529A CYS* 1.3 90.0 - - + +
531A ARG* 1.3 84.1 + - - +
533A GLN* 3.4 16.8 + - + +
534A ASP* 3.0 22.3 + - - +
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Residues in contact with ARG 531 (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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492A SER* 5.3 0.9 - - - -
506A CYS* 5.7 0.4 - - - -
508A ARG* 3.4 44.2 - - - +
510A TYR* 3.2 16.3 + - + +
529A CYS* 3.2 2.4 - - - -
530A PRO* 1.3 104.4 + - - +
532A CYS* 1.3 67.2 + - - +
534A ASP* 3.2 27.2 + - - +
535A GLN* 3.0 21.8 + - - +
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Residues in contact with CYS 532 (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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356A ZN 2.3 34.8 - - - -
505A THR* 3.1 19.5 - - - +
506A CYS* 3.5 16.4 - - - -
528A ILE* 3.4 21.5 - - + -
529A CYS* 3.1 5.3 + - - +
531A ARG* 1.3 79.1 - - - +
533A GLN* 1.3 61.6 + - - +
535A GLN* 3.1 10.5 + - - +
536A MET* 3.0 29.3 + - + +
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Residues in contact with GLN 533 (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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527A TRP* 5.6 2.0 - - - +
528A ILE* 3.0 30.6 + - + +
529A CYS 3.0 16.0 + - - +
530A PRO* 3.6 16.6 - - - +
532A CYS* 1.3 77.6 - - - +
534A ASP* 1.3 56.5 + - - +
536A MET* 3.1 12.3 + - + +
537A LEU* 2.8 30.1 + - - +
528B ILE* 4.0 16.8 - - + +
533B GLN* 2.8 41.7 + - - +
536B MET* 4.0 12.2 - - + +
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Residues in contact with ASP 534 (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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530A PRO 3.0 14.7 + - - +
531A ARG* 3.4 35.1 + - - +
532A CYS 3.2 0.2 - - - -
533A GLN* 1.3 76.2 - - - +
535A GLN* 1.3 58.7 + - - +
537A LEU* 3.2 14.3 + - - +
538A LYS* 2.8 68.5 + - - +
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Residues in contact with GLN 535 (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 ARG 3.0 12.6 + - - +
532A CYS* 3.3 13.5 - - - +
534A ASP* 1.3 78.3 - - - +
536A MET* 1.3 64.2 + - + +
538A LYS* 3.3 17.5 + - - +
539A LYS* 3.3 26.0 + - + +
540B GLU* 5.9 1.6 - - - +
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Residues in contact with MET 536 (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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528A ILE* 3.9 23.1 - - + -
532A CYS* 3.0 18.1 + - + +
533A GLN* 3.1 12.1 + - + +
535A GLN* 1.3 79.5 - - + +
537A LEU* 1.3 60.5 + - - +
539A LYS* 3.1 13.7 - - - +
540A GLU* 3.3 6.1 + - - +
533B GLN* 5.5 0.7 - - - +
536B MET* 3.7 27.4 - - + +
537B LEU* 3.6 24.7 - - + -
539B LYS* 2.4 41.3 + - - +
540B GLU* 3.4 33.4 - - + +
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Residues in contact with LEU 537 (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 GLN 2.8 16.1 + - - +
534A ASP* 3.2 15.0 + - - +
536A MET* 1.3 74.4 - - - +
538A LYS* 1.3 61.7 + - + +
540A GLU* 2.9 36.7 + - + +
541A GLU* 3.2 8.3 + - - +
505B THR* 4.2 21.1 - - + -
526B MET* 4.0 31.2 - - + -
528B ILE* 4.8 6.3 - - + -
536B MET* 4.3 13.2 - - - -
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Residues in contact with LYS 538 (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 ASP* 2.8 50.4 + - - +
535A GLN* 3.5 19.8 + - - +
537A LEU* 1.3 76.5 - - + +
539A LYS* 1.3 60.5 + - - +
540A GLU 3.2 0.5 + - - -
541A GLU* 3.5 14.0 + - - +
542A ALA* 3.7 9.9 + - - +
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Residues in contact with LYS 539 (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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535A GLN* 3.3 13.3 + - + +
536A MET* 3.1 17.5 - - - +
538A LYS* 1.3 76.9 - - - +
540A GLU* 1.3 55.5 + - - +
541A GLU 3.4 0.2 - - - -
542A ALA* 3.7 8.7 - - + +
543A ILE* 2.7 37.6 + - + +
539B LYS* 3.1 39.5 + - - +
540B GLU* 2.5 42.7 + - - +
543B ILE* 4.1 11.1 - - - +
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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