Contacts of the helix formed by residues 482 - 489 (chain O) in PDB entry 6CNB
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 482 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350O GLU* 3.3 22.6 + - + +
354O GLU* 4.2 9.9 + - + +
470O GLU* 3.8 32.4 + - - +
479O PRO* 5.1 2.9 - - + -
480O TYR 3.0 4.0 - - - -
481O SER* 1.3 76.7 - - - +
483O LEU* 1.3 58.0 + - - +
485O PRO* 3.2 3.3 - - - +
486O VAL* 2.9 51.5 + - + +
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Residues in contact with LEU 483 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312O TYR* 5.8 0.2 - - - +
466O PRO 4.7 1.6 - - - +
467O PHE* 3.6 17.9 - - + -
468O LEU* 3.2 46.2 - - + +
478O VAL* 3.6 2.0 - - + -
479O PRO* 3.0 36.0 - - + +
480O TYR* 2.5 29.8 + - + +
482O LYS* 1.3 70.7 - - - +
484O MET* 1.3 60.0 + - - +
486O VAL* 2.9 14.4 + - + -
487O LEU* 2.5 50.1 + - + +
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Residues in contact with MET 484 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289O LYS* 4.8 5.4 - - - +
296O LEU* 4.4 16.8 - - + -
316O LEU* 5.3 7.4 - - + -
319O THR* 6.1 2.9 - - + -
323O SER* 3.7 26.9 - - - +
325O LYS* 3.4 36.6 - - + +
353O GLU* 6.1 0.9 - - + -
480O TYR* 2.4 65.4 + - + +
481O SER* 5.2 0.4 - - - -
483O LEU* 1.3 69.6 - - - +
485O PRO* 1.3 67.7 - - + +
487O LEU* 3.4 9.1 - - - +
488O LYS* 3.1 34.8 + - - +
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Residues in contact with PRO 485 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328O ASP* 5.6 4.7 - - - +
346O GLN* 4.9 7.0 - - - +
349O ALA* 4.5 13.7 - - + +
350O GLU* 4.8 11.4 - - - +
480O TYR 3.1 9.0 - - - +
481O SER* 3.1 30.1 - - - +
482O LYS 3.2 4.7 - - - +
484O MET* 1.3 89.5 - - + +
486O VAL* 1.3 62.3 + - + +
487O LEU 3.1 1.2 + - - -
488O LYS* 3.5 12.5 + - + +
489O SER* 3.9 13.3 + - - -
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Residues in contact with VAL 486 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350O GLU* 4.8 8.7 - - - +
466O PRO 5.1 5.2 - - - +
482O LYS* 2.9 46.0 + - + +
483O LEU* 2.9 25.4 + - + +
485O PRO* 1.3 73.1 - - + +
487O LEU* 1.3 58.3 + - - +
489O SER* 4.6 10.3 + - - -
490O SER* 4.8 3.3 + - - -
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Residues in contact with LEU 487 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296O LEU* 3.5 44.9 - - + -
299O LEU* 5.3 6.3 - - + -
312O TYR* 5.1 3.6 - - - +
466O PRO* 4.1 7.2 - - + +
467O PHE* 3.7 31.6 - - + -
480O TYR* 6.3 0.2 - - + -
483O LEU* 2.5 38.5 + - + +
484O MET* 3.4 11.7 - - - +
486O VAL* 1.3 71.2 - - - +
488O LYS* 1.3 69.0 + - + +
489O SER 3.1 2.2 - - - -
490O SER* 2.6 40.9 + - - +
491O VAL* 3.8 3.6 - - + +
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Residues in contact with LYS 488 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292O ARG* 3.1 41.1 - - - +
296O LEU* 4.6 11.3 - - - +
325O LYS* 3.3 26.9 - - - +
484O MET* 3.1 23.7 + - - +
485O PRO* 3.5 7.8 + - + +
487O LEU* 1.3 76.9 - - + +
489O SER* 1.3 62.9 + - - +
490O SER 3.0 1.7 + - - -
491O VAL* 3.0 29.2 + - + +
492O TYR 4.7 0.7 + - - -
650O VAL* 5.8 0.7 - - - +
654O ALA* 3.8 35.2 - - + -
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Residues in contact with SER 489 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485O PRO 3.9 12.0 + - - -
486O VAL* 4.7 8.0 - - - -
487O LEU 2.9 1.8 + - - -
488O LYS* 1.3 77.5 - - - +
490O SER* 1.3 59.2 + - - +
492O TYR 4.9 0.4 + - - -
574O TYR* 3.6 22.2 + - - -
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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