Contacts of the helix formed by residues 463 - 473 (chain B) in PDB entry 4I5L
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 LEU 463 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444B LEU* 3.6 27.7 - - + +
461B CYS* 3.2 13.9 - - - +
462B LYS* 1.3 76.7 - - - +
464B ALA* 1.3 65.5 + - - +
465B ASN* 3.1 11.2 - - - +
466B VAL* 3.0 32.9 + - + +
467B PHE 3.1 9.5 + - - -
91C TYR* 4.3 21.8 - - + -
135C ARG* 3.4 57.9 - - - +
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Residues in contact with ALA 464 (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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387B LYS 4.0 1.6 - - - +
388B LYS* 5.3 1.9 - - - +
393B ILE* 3.8 21.8 - - + -
458B LEU* 3.5 28.5 - - + +
461B CYS* 3.7 5.8 - - - -
462B LYS* 3.6 2.7 - - - -
463B LEU* 1.3 77.2 - - - +
465B ASN* 1.3 57.0 + - - +
467B PHE* 3.2 9.1 + - - +
468B PHE* 2.8 52.4 + - + -
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Residues in contact with ASN 465 (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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387B LYS* 3.8 33.1 + - + +
388B LYS* 3.8 32.7 - - + +
463B LEU* 3.5 19.8 - - - +
464B ALA* 1.3 72.5 - - - +
466B VAL* 1.3 77.5 + - - +
468B PHE* 3.3 1.2 + - - +
469B ASP* 2.9 43.1 + - - +
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Residues in contact with VAL 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440B GLN* 5.7 1.3 - - - +
441B MET* 5.1 2.7 - - + -
444B LEU* 3.8 20.4 - - + -
463B LEU* 3.0 24.1 + - + +
465B ASN* 1.3 92.8 - - - +
467B PHE* 1.3 58.3 + - - +
469B ASP* 4.0 5.7 - - - +
470B THR* 2.7 40.5 + - - +
477B TYR* 6.3 0.9 - - + -
91C TYR* 4.8 5.8 - - + +
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Residues in contact with PHE 467 (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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400B MET* 4.0 17.3 - - + -
408B LEU* 3.8 23.1 - - + -
413B LEU* 3.8 16.2 - - + -
441B MET* 3.8 28.5 - - + -
444B LEU* 3.9 9.7 - - + +
445B VAL* 3.5 19.1 - - + -
453B ILE* 3.8 25.8 - - + -
458B LEU* 4.1 12.1 - - + -
463B LEU 3.1 11.0 + - - +
464B ALA* 3.2 11.6 + - - +
466B VAL* 1.3 79.2 - - - +
468B PHE* 1.3 77.6 + + - +
470B THR* 3.4 5.0 + - - -
471B PHE* 3.2 45.8 + + - -
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Residues in contact with PHE 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B LYS* 3.9 22.0 - - + -
393B ILE* 3.8 37.0 - - + -
396B TRP* 3.7 34.8 - + + -
397B PHE* 4.1 2.9 - - - -
400B MET* 3.7 27.6 - - - -
408B LEU* 5.4 0.4 - - + -
458B LEU* 4.2 17.7 - - + -
464B ALA* 2.8 42.5 + - + +
465B ASN 3.9 2.7 - - - +
467B PHE* 1.3 82.1 - + - +
469B ASP* 1.3 66.4 + - - +
471B PHE* 3.0 11.6 + - - -
472B PHE* 3.0 37.0 + + + -
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Residues in contact with ASP 469 (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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387B LYS* 2.8 32.9 + - - +
420B GLN* 3.4 2.8 + - - -
465B ASN* 2.9 28.9 + - - +
466B VAL* 4.1 5.1 + - - +
468B PHE* 1.3 74.1 - - - +
470B THR* 1.3 63.0 + - - +
473B ASN* 2.9 39.7 + - - +
476B LYS* 3.4 26.7 - - - +
477B TYR* 3.7 20.9 - - - +
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Residues in contact with THR 470 (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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417B TYR* 4.0 10.9 - - + -
420B GLN* 3.3 20.3 + - - +
437B CYS* 3.8 29.4 - - - -
441B MET* 4.0 21.8 - - + +
466B VAL* 2.7 28.4 + - - +
467B PHE 3.5 6.3 - - - -
468B PHE 3.2 0.2 - - - -
469B ASP* 1.3 76.9 - - - +
471B PHE* 1.3 61.0 + - + +
477B TYR* 3.8 33.4 - - + +
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Residues in contact with PHE 471 (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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348B SER* 4.8 0.9 + - - -
400B MET* 3.7 22.7 - - + -
413B LEU* 3.5 50.3 - - + -
416B PHE* 3.5 21.0 - - + +
417B TYR* 4.0 26.2 - + + -
420B GLN* 3.1 17.1 - - - +
434B PHE* 4.4 6.1 - + - -
437B CYS* 4.3 7.6 - - - -
438B LEU* 5.7 2.5 - - + -
441B MET* 3.8 24.2 - - + -
467B PHE* 3.2 54.7 - + - -
468B PHE 3.0 6.8 + - - +
470B THR* 1.3 80.8 - - - +
472B PHE* 1.3 61.1 + - + +
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Residues in contact with PHE 472 (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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346B ALA 3.7 0.3 - - - +
347B LEU* 3.4 15.9 - - + -
348B SER* 2.8 34.3 + - - +
351B MET* 3.4 48.2 - - + -
387B LYS* 4.0 18.8 - - - -
396B TRP* 3.6 39.7 - + + -
400B MET* 4.0 11.0 - - + -
416B PHE* 4.7 3.8 - + + -
420B GLN* 3.6 10.1 - - - -
423B ARG* 3.8 0.3 + - - -
468B PHE* 3.0 53.1 + + + -
469B ASP 3.4 0.2 + - - -
471B PHE* 1.3 83.0 - - + +
473B ASN* 1.3 61.0 + - - +
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Residues in contact with ASN 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B ALA* 3.4 13.5 - - - +
347B LEU* 3.0 18.3 - - + +
384B GLU* 2.9 29.3 + - - -
387B LYS* 3.9 1.3 - - - +
420B GLN* 3.5 2.2 - - - +
469B ASP* 2.9 40.0 + - - +
472B PHE* 1.3 81.4 - - + +
474B ILE* 1.3 61.6 + - - +
475B GLU* 3.2 11.8 + - - +
476B LYS* 3.0 34.1 + - - +
477B TYR* 3.2 14.9 + - - +
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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