Contacts of the helix formed by residues 487 - 499 (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 THR 487 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401A ARG* 4.7 16.6 - - - +
404A ILE* 4.0 3.8 - - - -
485A ARG 5.0 1.1 - - - +
486A LEU* 1.3 77.7 - - - +
488A ALA* 1.3 64.5 + - - +
490A ARG* 3.1 21.0 + - - +
491A ILE* 3.0 22.5 + - - +
1505A FLC 3.2 17.2 + - - +
1506A FLC 3.4 45.4 + - + +
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Residues in contact with ALA 488 (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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313A ALA* 4.3 4.5 - - - +
316A LEU* 4.0 8.7 - - + -
317A ALA* 3.6 32.3 - - - +
320A HIS* 3.9 18.0 + - - +
404A ILE* 3.5 17.5 - - + +
407A PHE* 5.7 1.3 - - - -
487A THR* 1.3 73.8 - - - +
489A LEU* 1.3 58.1 + - - +
491A ILE* 3.2 9.5 + - - +
492A LYS* 2.9 28.8 + - - +
1506A FLC 3.2 5.6 + - - +
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Residues in contact with LEU 489 (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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317A ALA* 3.9 7.0 - - + +
321A ILE* 4.1 21.1 - - + -
488A ALA* 1.3 74.3 - - - +
490A ARG* 1.3 61.5 + - - +
492A LYS* 3.4 13.5 + - + +
493A LYS* 3.0 46.2 + - + +
1500A FLC 3.8 32.5 - - + +
1505A FLC 3.4 42.8 - - + +
1506A FLC 2.8 33.4 + - - +
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Residues in contact with ARG 490 (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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486A LEU* 4.1 29.1 - - + +
487A THR* 3.1 29.8 + - - +
489A LEU* 1.3 76.1 - - - +
491A ILE* 1.3 58.3 + - - +
493A LYS* 3.4 8.2 + - - +
494A THR* 2.9 44.3 + - - +
1505A FLC 3.1 41.2 + - - +
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Residues in contact with ILE 491 (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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313A ALA* 4.1 0.7 - - + -
404A ILE* 4.2 16.6 - - + -
407A PHE* 3.7 32.8 - - + -
411A LEU* 5.6 3.6 - - + -
473A LEU* 4.4 15.0 - - + -
477A CYS* 3.8 28.5 - - - -
486A LEU* 4.0 19.5 - - + +
487A THR 3.0 19.6 + - - +
488A ALA* 3.5 5.6 - - - +
490A ARG* 1.3 74.5 - - - +
492A LYS* 1.3 59.7 + - - +
494A THR* 3.3 5.6 + - - -
495A LEU* 2.8 51.3 + - + +
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Residues in contact with LYS 492 (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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259A HIS* 5.7 0.6 + - - -
310A LEU* 3.6 20.1 - - + +
313A ALA* 4.0 17.0 - - + +
314A SER* 3.5 37.8 + - - +
317A ALA* 4.7 4.5 - - + +
488A ALA 2.9 17.2 + - - +
489A LEU* 3.5 15.0 - - + +
491A ILE* 1.3 76.2 - - - +
493A LYS* 1.3 59.9 + - + +
495A LEU* 3.2 1.3 + - - -
496A THR* 2.8 36.3 + - - +
1500A FLC 2.8 46.7 + - - +
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Residues in contact with LYS 493 (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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489A LEU* 3.0 45.3 + - + +
490A ARG* 3.9 9.0 - - - +
492A LYS* 1.3 77.0 - - + +
494A THR* 1.3 63.2 + - - +
496A THR* 3.3 16.1 + - - -
497A LYS* 3.3 20.6 + - + +
1500A FLC 5.0 6.1 + - - -
1505A FLC 3.7 31.6 + - - +
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Residues in contact with THR 494 (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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469A SER 6.0 0.2 - - - +
473A LEU* 3.8 31.4 - - + +
486A LEU* 5.4 0.9 - - - +
490A ARG* 2.9 31.5 + - - +
491A ILE 3.6 3.6 - - - -
493A LYS* 1.3 77.2 - - - +
495A LEU* 1.3 62.8 + - - +
497A LYS* 3.1 17.7 + - - +
498A ILE* 3.2 21.8 + - + +
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Residues in contact with LEU 495 (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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306A LEU* 4.5 8.4 - - + +
309A VAL* 3.7 41.3 - - + +
310A LEU* 3.9 18.0 - - + +
313A ALA* 4.1 4.0 - - + -
407A PHE* 4.8 1.8 - - + -
411A LEU* 5.3 2.7 - - + -
470A LEU* 3.5 32.5 - - + -
473A LEU* 3.5 15.3 - - + -
491A ILE* 2.8 41.8 + - + +
492A LYS 3.7 3.6 - - - +
494A THR* 1.3 73.3 - - - +
496A THR* 1.3 60.9 + - - +
498A ILE* 3.5 10.4 + - + +
499A ASP* 3.3 23.7 + - - +
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Residues in contact with THR 496 (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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310A LEU* 3.4 23.3 - - + +
492A LYS* 2.8 29.2 + - - +
493A LYS* 3.5 10.6 - - - -
494A THR 3.2 0.2 - - - -
495A LEU* 1.3 78.5 - - - +
497A LYS* 1.3 61.0 + - + +
499A ASP* 3.7 16.1 - - - +
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Residues in contact with LYS 497 (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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493A LYS* 3.3 14.5 + - + +
494A THR* 3.1 12.2 + - + +
496A THR* 1.3 77.5 - - + +
498A ILE* 1.3 61.3 + - + +
499A ASP 3.3 3.2 - - - -
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Residues in contact with ILE 498 (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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306A LEU* 4.0 23.2 - - + +
466A THR* 4.1 26.2 + - + +
469A SER* 3.6 29.2 - - - +
470A LEU* 4.4 6.7 - - + -
473A LEU* 4.4 4.0 - - + -
494A THR* 3.2 28.3 + - + +
495A LEU* 3.5 27.1 + - + +
497A LYS* 1.3 75.2 - - - +
499A ASP* 1.3 63.7 + - - +
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Residues in contact with ASP 499 (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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306A LEU* 3.9 26.0 - - + -
310A LEU* 4.9 10.8 - - + -
495A LEU 3.3 15.8 + - - +
496A THR* 3.7 14.9 - - - +
497A LYS 3.3 3.8 - - - +
498A ILE* 1.3 82.9 - - - +
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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