Contacts of the helix formed by residues 462 - 473 (chain B) in PDB entry 4OE5
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 LYS 462 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459B PRO* 2.7 29.0 + - + +
461B ASP* 1.3 97.8 - - - +
463B TYR* 1.3 58.8 + - - +
464B LYS 3.4 2.2 - - - -
465B GLU* 3.4 15.2 + - + +
466B THR* 2.7 36.1 + - - +
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Residues in contact with TYR 463 (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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322B PHE* 3.9 5.2 - + + -
324B HIS* 4.4 22.4 - + + -
458B TYR* 3.6 32.3 - - + +
459B PRO 3.8 0.4 + - - -
460B ASP 3.8 12.5 + - - +
461B ASP 3.6 3.7 + - - -
462B LYS* 1.3 73.9 - - - +
464B LYS* 1.3 70.6 + - + +
466B THR* 3.0 2.6 + - - -
467B LEU* 2.8 44.4 + - + +
489B VAL* 4.0 28.1 - - + +
492B GLU* 2.5 39.3 + - - -
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Residues in contact with LYS 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B TYR* 1.3 94.0 - - + +
465B GLU* 1.3 63.8 + - - +
467B LEU* 3.2 17.6 + - - +
468B GLN* 3.3 13.5 + - - +
492B GLU* 4.0 17.9 - - - +
496B VAL* 5.4 0.9 - - - +
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Residues in contact with GLU 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462B LYS* 3.4 21.7 + - + +
463B TYR 3.3 0.2 - - - -
464B LYS* 1.3 77.9 - - - +
466B THR* 1.3 57.3 + - - +
468B GLN* 3.3 8.9 + - - +
469B LEU* 3.0 25.6 + - - +
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Residues in contact with THR 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B PHE* 3.8 17.3 - - + -
355B TYR* 4.0 18.8 - - + -
456B TYR* 4.8 1.7 - - + -
458B TYR* 3.4 40.6 - - + +
459B PRO* 5.2 0.3 - - - +
462B LYS* 2.7 24.0 + - - +
463B TYR 3.0 5.6 + - - -
465B GLU* 1.3 74.0 - - - +
467B LEU* 1.3 67.3 + - - +
469B LEU* 3.0 16.5 + - + +
470B VAL* 2.8 22.2 + - - +
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Residues in contact with LEU 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B PHE* 3.6 34.2 - - + -
463B TYR* 2.8 40.4 + - + +
464B LYS* 3.4 10.3 - - - +
466B THR* 1.3 76.1 - - - +
468B GLN* 1.3 62.3 + - - +
470B VAL* 3.1 15.4 + - - +
471B ASP 3.3 8.5 + - - -
489B VAL* 5.1 1.3 - - + +
492B GLU* 4.4 9.9 - - + -
493B ALA* 3.7 41.1 - - + +
496B VAL* 3.9 15.7 - - + +
497B LEU* 3.6 25.1 - - + +
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Residues in contact with GLN 468 (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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464B LYS 3.3 8.4 + - - +
465B GLU* 3.5 12.1 - - - +
466B THR 3.2 0.4 - - - -
467B LEU* 1.3 78.4 - - - +
469B LEU* 1.3 56.4 + - - +
471B ASP* 3.3 5.9 + - + +
472B SER* 2.9 30.4 + - - -
496B VAL* 3.9 18.5 - - + +
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Residues in contact with LEU 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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355B TYR* 5.2 4.3 - - + -
439B PRO* 3.5 35.0 - - + +
440B GLN* 3.9 14.8 - - - +
456B TYR* 4.4 14.6 - - + +
465B GLU 3.0 13.0 + - - +
466B THR* 3.2 21.8 - - + +
468B GLN* 1.3 74.7 - - - +
470B VAL* 1.3 62.3 + - - +
472B SER* 3.3 9.3 + - - +
473B THR* 2.8 49.1 + - + +
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Residues in contact with VAL 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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320B PHE* 3.7 40.6 - - + -
322B PHE* 4.0 16.8 - - + -
353B ARG* 3.3 10.9 + - - +
355B TYR* 3.7 36.8 - - + -
466B THR 2.8 20.5 + - - +
467B LEU* 3.1 8.5 + - - +
469B LEU* 1.3 73.7 - - - +
471B ASP* 1.3 56.4 + - - +
473B THR* 4.0 4.0 - - - -
474B THR* 2.6 30.5 + - - +
497B LEU* 3.8 13.2 - - + -
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Residues in contact with ASP 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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201A GLU* 5.0 9.0 - - - +
467B LEU 3.3 7.1 + - - +
468B GLN* 3.6 10.3 - - + +
469B LEU 3.2 0.4 - - - -
470B VAL* 1.3 81.6 - - - +
472B SER* 1.3 60.6 + - - +
474B THR* 3.0 30.1 + - - +
496B VAL* 4.0 21.7 - - + +
497B LEU* 4.2 1.5 - - + +
499B ASN* 4.1 7.4 + - - +
500B ALA* 3.4 31.8 + - + +
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Residues in contact with SER 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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440B GLN* 5.1 1.6 + - - -
468B GLN 2.9 17.0 + - - -
469B LEU* 3.3 22.2 + - - +
471B ASP* 1.3 79.8 - - - +
473B THR* 1.3 62.6 + - - +
474B THR 3.3 3.2 + - - +
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Residues in contact with THR 473 (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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318B LYS* 5.8 1.6 - - - +
353B ARG* 3.4 23.4 + - - -
355B TYR* 3.8 7.4 + - - -
439B PRO 4.3 9.6 + - - +
440B GLN* 3.5 37.2 - - - +
444B MET* 5.0 1.0 + - - +
445B LYS* 4.0 33.5 - - + +
469B LEU* 2.8 31.7 + - + +
470B VAL 3.8 0.7 - - - -
472B SER* 1.3 80.6 - - - +
474B THR* 1.3 59.1 + - - +
475B SER* 3.7 3.2 + - - -
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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