Contacts of the helix formed by residues 529 - 543 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358B ZN 2.4 34.1 - - - -
503B CYS* 3.3 14.2 - - - -
506B CYS* 3.8 7.2 - - - -
508B ARG* 4.2 0.4 - - - -
510B TYR* 3.3 35.0 - - + -
527B TRP* 3.6 13.3 - - + -
528B ILE* 1.3 72.6 - - - +
530B PRO* 1.3 76.3 - - + +
531B ARG* 3.5 4.9 - - - -
532B CYS* 3.1 14.5 + - - +
533B GLN* 2.9 23.8 + - - +
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Residues in contact with PRO 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510B TYR* 4.0 13.2 - - + -
515B LEU* 4.3 12.1 - - + -
516B ASP* 5.9 5.8 - - - +
527B TRP* 4.1 12.3 - - + -
528B ILE 4.6 0.4 - - - +
529B CYS* 1.3 88.5 - - + +
531B ARG* 1.3 83.3 + - - +
533B GLN* 3.4 9.6 + - + +
534B ASP* 3.0 28.1 + - - +
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Residues in contact with ARG 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492B SER* 4.3 12.3 + - - -
493B VAL* 4.5 12.3 - - - +
508B ARG* 3.5 38.1 - - - +
510B TYR* 3.3 35.5 + - - +
516B ASP* 5.8 2.0 + - - -
529B CYS* 3.2 4.5 - - - -
530B PRO* 1.3 98.8 - - - +
532B CYS* 1.3 57.6 + - - +
534B ASP* 3.3 8.4 + - - +
535B GLN* 2.9 27.2 + - - +
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Residues in contact with CYS 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358B ZN 2.3 35.9 - - - -
505B THR* 3.1 19.3 - - - +
506B CYS* 3.6 16.4 - - - -
508B ARG* 4.7 2.2 - - - +
528B ILE* 3.4 23.3 - - + -
529B CYS* 3.1 3.9 + - - +
531B ARG* 1.3 75.8 - - - +
533B GLN* 1.3 66.0 + - - +
535B GLN* 3.2 8.0 + - - +
536B MET* 3.0 29.3 + - + +
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Residues in contact with GLN 533 (chain B).
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* 5.3 4.2 - - - +
533A GLN* 2.8 46.5 + - - +
536A MET* 5.5 0.9 - - - +
528B ILE* 3.3 27.0 + - + +
529B CYS 2.9 20.6 + - - +
530B PRO* 3.5 11.0 - - + +
532B CYS* 1.3 77.1 - - - +
534B ASP* 1.3 61.1 + - - +
536B MET* 3.4 17.1 + - - +
537B LEU* 3.0 35.7 + - + +
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Residues in contact with ASP 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530B PRO 3.0 17.2 + - - +
531B ARG* 3.5 10.4 - - - +
533B GLN* 1.3 74.9 - - - +
535B GLN* 1.3 60.0 + - - +
537B LEU* 3.1 13.1 + - - +
538B LYS* 2.9 61.5 + - - +
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Residues in contact with GLN 535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540A GLU* 6.1 0.9 - - - +
531B ARG 2.9 14.2 + - - +
532B CYS* 3.2 12.5 + - - +
534B ASP* 1.3 77.2 - - - +
536B MET* 1.3 64.3 + - + +
538B LYS* 3.3 16.9 + - - +
539B LYS* 3.1 28.0 + - + +
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Residues in contact with MET 536 (chain B).
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* 4.0 23.8 - - + +
536A MET* 3.7 31.9 - - + +
537A LEU* 4.3 15.7 - - - -
540A GLU* 5.8 3.8 - - + +
528B ILE* 3.9 29.6 - - + -
532B CYS* 3.0 15.3 + - + +
533B GLN* 3.4 31.6 - - - +
535B GLN* 1.3 78.0 - - + +
537B LEU* 1.3 63.3 + - - +
539B LYS* 2.7 48.3 - - + +
540B GLU 3.3 2.1 + - - -
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Residues in contact with LEU 537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526A MET* 4.2 19.1 - - + -
528A ILE* 2.8 40.2 - - + -
536A MET* 3.6 20.6 - - + -
533B GLN* 3.0 20.8 + - + +
534B ASP* 3.1 15.2 + - - +
536B MET* 1.3 76.7 - - - +
538B LYS* 1.3 62.6 + - + +
540B GLU* 3.1 7.3 + - + +
541B GLU* 3.0 23.8 + - - +
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Residues in contact with LYS 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534B ASP* 2.9 49.6 + - - +
535B GLN* 3.3 15.7 + - - +
537B LEU* 1.3 78.9 - - + +
539B LYS* 1.3 60.5 + - - +
541B GLU* 3.4 7.9 + - - +
542B ALA* 3.2 24.8 + - - +
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Residues in contact with LYS 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536A MET* 2.4 62.5 + - - +
539A LYS* 3.1 31.1 - - - +
540A GLU* 4.7 13.5 + - - +
535B GLN* 3.1 17.9 + - + +
536B MET* 2.7 34.4 - - + +
537B LEU 3.2 0.2 - - - -
538B LYS* 1.3 76.2 - - - +
540B GLU* 1.3 59.7 + - - +
542B ALA* 3.4 5.0 + - - +
543B ILE* 3.0 30.1 + - - +
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Residues in contact with GLU 540 (chain B).
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* 5.9 1.6 - - - +
536A MET* 3.4 36.6 - - - +
539A LYS* 2.5 37.3 + - - +
536B MET 3.7 2.2 - - - +
537B LEU* 3.1 9.6 + - + +
539B LYS* 1.3 80.5 - - - +
541B GLU* 1.3 58.5 + - - +
542B ALA 3.0 10.0 + - - -
543B ILE* 3.1 23.2 + - - +
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Residues in contact with GLU 541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537B LEU 3.0 15.3 + - - +
538B LYS* 3.9 9.0 - - - +
540B GLU* 1.3 76.0 - - - +
542B ALA* 1.3 56.2 + - - +
543B ILE* 4.8 0.7 - - - -
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Residues in contact with ALA 542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538B LYS 3.2 15.5 + - - +
539B LYS* 3.7 4.7 - - - +
540B GLU 3.0 0.8 - - - -
541B GLU* 1.3 77.2 - - - +
543B ILE* 1.3 64.2 + - - +
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Residues in contact with ILE 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539A LYS* 4.1 15.7 - - - +
539B LYS 3.0 17.5 + - - +
540B GLU* 3.1 16.7 + - - +
541B GLU 4.8 0.9 - - - -
542B ALA* 1.3 82.5 - - - +
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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