Contacts of the helix formed by residues 569 - 576 (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 569 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A LYS* 4.6 8.5 + - - +
109A ASN* 4.2 18.8 - - - +
220A ASP* 5.8 1.2 + - - -
226A LYS* 5.9 1.0 - - - +
547O GLU* 3.3 20.0 + - - +
567O ARG* 4.3 26.0 - - - +
568O CYS* 1.3 82.4 - - - +
570O GLU* 1.3 67.6 + - - +
571O THR* 3.0 19.4 + - + +
572O HIS* 3.3 40.7 + - + +
573O SER 3.8 1.2 + - - -
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Residues in contact with GLU 570 (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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512O ARG* 4.4 15.6 + - - +
568O CYS* 3.5 6.8 - - + +
569O LYS* 1.3 77.3 + - - +
571O THR* 1.3 78.8 + - + +
572O HIS 3.3 0.2 - - - -
573O SER* 3.7 10.8 - - - -
574O TYR* 2.8 62.3 + - + +
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Residues in contact with THR 571 (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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109A ASN* 2.9 40.3 + - - +
569O LYS* 3.9 10.3 + - + +
570O GLU* 1.3 89.3 - - + +
572O HIS* 1.3 74.3 + - - +
574O TYR* 3.8 6.5 - - - +
575O ASN* 2.8 30.4 + - - +
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Residues in contact with HIS 572 (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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108A LYS 3.9 22.5 + - - -
109A ASN* 4.4 10.0 + - - -
226A LYS* 4.3 30.4 - - + +
229A ASN* 5.5 2.2 - - + -
230A LEU* 4.1 24.0 - - + +
233A GLN* 6.1 2.0 - - - -
544O ASN* 4.3 21.8 - - - +
545O SER 5.3 2.2 - - - +
547O GLU* 4.8 4.2 + - + +
568O CYS 5.5 0.2 - - - +
569O LYS* 3.6 32.1 - - + +
570O GLU 3.3 0.2 - - - -
571O THR* 1.3 90.3 + - - +
573O SER* 1.3 56.4 + - - +
575O ASN* 2.6 30.0 + - - +
576O PHE* 3.1 18.9 + - + -
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Residues in contact with SER 573 (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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492O TYR* 4.1 16.3 + - - -
545O SER* 3.1 33.9 + - - +
568O CYS 5.1 2.0 - - - -
569O LYS 3.8 2.3 + - - -
570O GLU* 3.2 16.9 + - - -
572O HIS* 1.3 77.3 - - - +
574O TYR* 1.3 66.1 + - - +
576O PHE* 3.4 19.2 - - - -
577O MET* 3.1 21.0 - - - +
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Residues in contact with TYR 574 (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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489O SER* 3.6 22.0 + - - -
492O TYR* 3.3 49.3 - + + +
512O ARG* 4.1 17.9 + - - -
570O GLU* 2.8 51.1 + - + +
571O THR* 3.8 4.9 - - - +
573O SER* 1.3 74.4 - - - +
575O ASN* 1.3 66.0 + - - +
577O MET* 3.1 18.4 - - - +
578O ARG* 4.0 2.4 + - - +
651O PHE* 3.5 25.7 - + + +
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Residues in contact with ASN 575 (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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109A ASN 5.2 5.1 + - - -
110A CYS* 5.0 4.4 + - - +
233A GLN* 2.6 43.8 + - - +
571O THR 2.8 20.0 + - - +
572O HIS* 2.6 17.6 + - - +
574O TYR* 1.3 71.1 - - - +
576O PHE* 1.3 51.5 + - - +
578O ARG* 2.5 76.5 + - - +
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Residues in contact with PHE 576 (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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229A ASN* 4.3 19.7 - - - +
232A LYS* 6.2 2.0 - - + -
233A GLN* 4.9 9.4 - - - +
543O TYR* 2.8 33.9 - - + -
544O ASN* 3.4 24.7 - - + +
545O SER* 3.5 11.2 - - - -
572O HIS* 3.1 19.5 - - - -
573O SER* 3.4 29.6 - - - -
575O ASN* 1.3 73.8 - - - +
577O MET* 1.3 70.4 + - - +
578O ARG* 2.9 7.2 - - - +
579O GLN* 2.8 37.4 + - - +
312P PHE* 4.9 7.4 - + - -
315P TRP* 5.0 13.2 - + + -
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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