Contacts of the helix formed by residues 468 - 481 (chain A) in PDB entry 3PEY
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 468 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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465A PRO* 3.9 18.0 - - + +
466A THR 3.7 1.6 - - - -
467A ASP* 1.3 83.5 - - - +
469A TRP* 1.3 60.4 + - - +
470A ASP* 3.8 7.6 + - - +
471A GLU* 3.0 42.5 + - - +
472A VAL* 3.1 16.2 + - - +
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Residues in contact with TRP 469 (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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309A MET* 3.7 31.9 - - + -
320A VAL* 3.6 29.4 - - + -
323A GLU* 3.3 42.7 - - + +
324A LEU* 3.7 21.1 - - + -
327A LEU* 3.8 31.8 - - + +
466A THR* 3.3 34.8 + - - -
467A ASP* 4.5 3.1 - - - +
468A ASP* 1.3 73.8 + - - +
470A ASP* 1.3 62.6 + - - +
472A VAL* 3.3 9.6 + - + +
473A GLU* 2.8 29.6 + - - +
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Residues in contact with ASP 470 (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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468A ASP* 3.3 7.7 + - - +
469A TRP* 1.3 79.0 - - - +
471A GLU* 1.3 57.3 + - - +
473A GLU* 3.4 18.0 + - - +
474A LYS* 3.0 47.7 + - - +
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Residues in contact with GLU 471 (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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465A PRO* 4.1 16.6 - - + -
468A ASP* 3.0 32.4 + - + +
470A ASP* 1.3 77.5 - - - +
472A VAL* 1.3 65.5 + - - +
474A LYS* 3.2 21.8 + - - +
475A ILE* 3.1 45.0 + - + +
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Residues in contact with VAL 472 (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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307A LEU* 5.6 1.6 - - + -
309A MET* 4.0 22.9 - - + -
324A LEU* 4.5 4.7 - - + -
327A LEU* 3.6 17.3 - - + -
437A ILE* 5.0 2.5 - - + -
464A VAL* 4.4 7.2 - - + -
465A PRO* 3.3 37.7 - - + +
468A ASP 3.1 12.2 + - - +
469A TRP* 3.3 15.7 + - + +
471A GLU* 1.3 75.2 - - - +
473A GLU* 1.3 63.7 + - - +
475A ILE* 3.1 9.6 + - + +
476A VAL* 3.0 33.9 + - + +
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Residues in contact with GLU 473 (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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327A LEU* 3.6 21.9 - - + +
469A TRP 2.8 17.3 + - - +
470A ASP* 3.6 20.3 - - - +
471A GLU 3.2 0.2 - - - -
472A VAL* 1.3 77.1 - - - +
474A LYS* 1.3 57.9 + - + +
476A VAL* 3.4 4.1 + - - +
477A LYS* 2.9 69.4 + - + +
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Residues in contact with LYS 474 (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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470A ASP* 3.0 33.2 + - - +
471A GLU* 3.2 27.5 + - - +
473A GLU* 1.3 75.9 - - + +
475A ILE* 1.3 63.5 + - + +
477A LYS* 4.0 4.9 - - - +
478A LYS* 3.0 25.5 + - - +
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Residues in contact with ILE 475 (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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305A LYS* 5.1 6.3 - - - -
307A LEU* 4.1 31.2 - - + -
462A THR* 6.0 2.7 - - + -
464A VAL* 3.6 27.8 - - + -
465A PRO* 4.9 2.0 - - + -
471A GLU* 3.1 41.5 + - + +
472A VAL* 3.1 8.7 + - - +
474A LYS* 1.3 75.9 - - + +
476A VAL* 1.3 65.7 + - + +
478A LYS* 3.3 9.1 + - - +
479A VAL* 3.1 29.5 + - + +
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Residues in contact with VAL 476 (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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307A LEU* 4.9 6.5 - - + -
327A LEU* 4.8 12.3 - - + +
330A ILE* 4.9 6.1 - - + -
401A MET* 4.1 30.7 - - + -
435A VAL* 4.4 21.3 - - + -
437A ILE* 4.9 1.3 - - + -
472A VAL* 3.0 34.8 + - + +
473A GLU* 3.9 5.6 - - - +
475A ILE* 1.3 76.3 - - - +
477A LYS* 1.3 65.2 + - + +
479A VAL* 3.2 2.9 + - - +
480A LEU* 3.1 45.0 + - + +
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Residues in contact with LYS 477 (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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329A THR* 5.1 8.3 - - - -
330A ILE* 4.0 27.0 - - + +
473A GLU* 2.9 54.5 + - + +
474A LYS* 4.1 4.7 - - - +
476A VAL* 1.3 77.1 - - + +
478A LYS* 1.3 62.7 + - - +
480A LEU 3.8 0.7 - - - +
481A LYS* 3.0 25.8 + - - +
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Residues in contact with LYS 478 (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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433A LYS* 4.9 4.7 + - - -
474A LYS 3.0 18.1 + - - +
475A ILE* 3.5 7.9 - - - +
477A LYS* 1.3 78.7 - - - +
479A VAL* 1.3 64.1 + - + +
481A LYS* 3.5 20.5 - - + +
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Residues in contact with VAL 479 (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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303A ALA 4.8 1.8 - - - +
305A LYS* 3.8 33.7 - - + -
433A LYS* 3.0 43.6 + - + +
434A GLY 3.5 28.5 - - - +
435A VAL* 3.7 15.0 - - + -
475A ILE* 3.1 21.3 + - + +
476A VAL 3.6 5.4 - - - +
478A LYS* 1.3 78.8 - - + +
480A LEU* 1.3 62.7 + - + +
481A LYS 3.3 0.7 + - - -
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Residues in contact with LEU 480 (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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330A ILE* 3.9 34.5 - - + +
400A SER* 3.8 48.0 - - - +
401A MET* 5.8 2.0 - - + -
433A LYS* 3.9 20.0 - - - +
434A GLY* 4.0 7.6 - - - -
435A VAL* 4.2 7.4 - - + -
476A VAL* 3.1 36.5 + - + +
477A LYS 3.8 1.1 - - - +
479A VAL* 1.3 76.3 - - - +
481A LYS* 1.3 64.3 + - - +
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Residues in contact with LYS 481 (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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433A LYS* 4.6 14.4 - - - +
477A LYS 3.0 16.8 + - - +
478A LYS* 3.5 16.4 - - + +
479A VAL 3.2 5.3 - - - -
480A LEU* 1.3 80.9 - - - +
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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