Contacts of the helix formed by residues 464 - 476 (chain A) in PDB entry 4C02
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 464 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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418A MET* 3.7 5.9 - - - +
420A SER* 3.9 33.1 - - - +
460A ARG 4.6 0.9 - - - +
461A TRP 3.1 7.5 + - - +
462A PHE 3.3 1.0 - - - -
463A SER* 1.3 80.3 - - - +
465A PRO* 1.3 73.0 - - - +
466A THR* 3.0 13.5 + - - -
467A LEU* 2.8 34.1 + - + +
468A THR* 2.8 30.8 + - - -
1511A EDO 3.7 23.4 + - - -
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Residues in contact with PRO 465 (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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463A SER 4.2 4.7 - - - +
464A ASP* 1.3 93.3 - - - +
466A THR* 1.3 59.1 + - - +
468A THR* 3.6 6.9 + - - -
469A SER* 3.1 27.5 + - - -
1511A EDO 6.3 1.8 - - - -
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Residues in contact with THR 466 (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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302A THR* 3.8 13.7 - - + +
306A LEU* 3.8 38.4 - - + +
418A MET* 4.2 22.0 - - - -
464A ASP* 3.0 9.6 + - - -
465A PRO* 1.3 80.0 - - - +
467A LEU* 1.3 57.6 + - - +
469A SER* 3.2 4.3 + - - -
470A LEU* 2.9 32.2 + - + +
498A ILE* 4.1 16.0 + - + +
1511A EDO 4.5 3.8 + - - -
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Residues in contact with LEU 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A ALA* 3.6 41.7 - - + +
418A MET* 3.9 28.0 - - + +
420A SER* 3.8 10.1 - - - +
460A ARG* 3.6 28.0 - - - +
461A TRP* 3.7 39.5 - - + +
464A ASP* 2.8 23.0 + - + +
466A THR* 1.3 69.4 - - - +
468A THR* 1.3 60.6 + - - +
470A LEU* 3.8 7.5 - - + +
471A ALA* 2.8 31.9 + - - +
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Residues in contact with THR 468 (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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461A TRP 3.0 12.1 + - - -
462A PHE* 3.4 31.0 + - + +
464A ASP 2.8 23.5 + - - -
465A PRO* 3.7 7.1 - - - +
467A LEU* 1.3 77.7 - - - +
469A SER* 1.3 64.3 + - - +
471A ALA* 3.2 7.5 + - - +
472A LYS* 3.2 21.6 + - + +
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Residues in contact with SER 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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465A PRO 3.1 16.5 + - - -
466A THR 3.2 7.8 + - - -
468A THR* 1.3 78.4 - - - +
470A LEU* 1.3 60.9 + - - +
472A LYS* 3.4 10.7 + - - +
473A LEU* 3.1 23.7 + - - +
494A THR* 6.0 0.2 - - - +
498A ILE* 3.6 31.5 - - - +
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Residues in contact with LEU 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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305A CYS* 3.9 28.3 - - - -
306A LEU* 4.3 9.6 - - + -
309A VAL* 4.5 1.6 - - + -
411A LEU* 4.0 18.8 - - + +
415A ALA* 4.3 14.4 - - + -
466A THR* 2.9 30.8 + - + +
467A LEU* 3.8 10.5 - - + +
469A SER* 1.3 73.5 - - - +
471A ALA* 1.3 60.8 + - - +
473A LEU* 3.2 7.5 + - + +
474A MET* 2.9 46.9 + - + +
495A LEU* 3.5 32.8 - - + -
498A ILE* 4.4 4.3 - - + -
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Residues in contact with ALA 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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457A ILE* 4.0 19.7 - - + -
461A TRP* 3.9 16.6 - - + -
462A PHE* 4.6 9.4 - - + -
467A LEU 2.8 17.2 + - - +
468A THR* 3.6 6.7 - - - +
470A LEU* 1.3 76.4 - - - +
472A LYS* 1.3 64.1 + - - +
474A MET* 3.4 13.3 - - - +
475A LYS* 3.1 33.6 + - + +
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Residues in contact with LYS 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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468A THR* 3.2 10.2 + - + +
469A SER* 3.5 12.3 - - - +
470A LEU 3.2 0.2 - - - -
471A ALA* 1.3 80.2 - - - +
473A LEU* 1.3 60.9 + - + +
475A LYS* 3.3 10.1 + - - +
476A GLU* 3.2 51.9 + - + +
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Residues in contact with LEU 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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411A LEU* 4.1 9.6 - - + -
469A SER 3.1 10.2 + - - +
470A LEU* 3.4 15.9 - - + +
472A LYS* 1.3 75.5 - - - +
474A MET* 1.3 66.3 + - - +
476A GLU* 3.0 20.9 + - - +
477A CYS* 3.3 14.7 + - - -
486A LEU* 3.8 25.3 - - + +
491A ILE* 4.4 18.6 - - + -
494A THR* 3.8 32.1 - - + +
495A LEU* 3.5 38.8 - - + -
498A ILE* 4.4 4.7 - - + -
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Residues in contact with MET 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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408A GLY* 3.8 14.4 - - - +
411A LEU* 3.8 31.3 - - + +
412A TRP* 3.7 30.5 - - - -
415A ALA* 3.8 6.3 - - + -
457A ILE* 4.1 6.3 - - - -
461A TRP* 3.4 38.6 - - + -
470A LEU* 2.9 24.1 + - + +
471A ALA* 3.4 7.4 - - - +
473A LEU* 1.3 75.3 - - - +
475A LYS* 1.3 64.9 + - - +
477A CYS* 2.9 18.3 + - - +
478A TRP* 3.3 35.6 + - + -
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Residues in contact with LYS 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A ILE* 3.8 19.7 - - + +
462A PHE* 4.4 16.8 - - - -
471A ALA* 3.1 21.4 + - - +
472A LYS* 3.7 8.5 - - - +
474A MET* 1.3 81.2 - - - +
476A GLU* 1.3 59.7 + - + +
478A TRP* 3.2 26.5 + - + +
479A TYR* 3.8 17.6 + - + -
1512A EDO 3.5 44.5 + - - +
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Residues in contact with GLU 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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472A LYS* 3.2 42.6 + - + +
473A LEU* 3.0 18.3 + - - +
475A LYS* 1.3 77.9 - - + +
477A CYS* 1.3 56.7 + - - +
478A TRP 3.5 0.4 - - - -
479A TYR* 3.6 33.2 + - + +
485A ARG* 3.2 9.0 - - - -
486A LEU* 3.2 58.8 + - + +
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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