Contacts of the helix formed by residues 661 - 668 (chain A) in PDB entry 3NKO
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 ASN 661 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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563A ASP 5.2 0.7 - - - +
564A LEU* 3.1 32.5 - - + +
566A CYS* 4.8 0.7 - - - -
659A SER 5.2 2.0 + - - +
660A GLN* 1.3 78.6 - - - +
662A CYS* 1.3 61.2 + - - +
663A LEU* 3.2 12.5 + - - +
664A ALA* 2.9 47.3 + - - +
665A TYR* 3.8 11.3 - - - -
697A MET* 5.6 0.7 - - - -
755A SER* 4.9 6.1 - - - -
757A ILE* 4.1 5.7 - - - +
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Residues in contact with CYS 662 (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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564A LEU 2.9 6.1 + - - -
565A GLY 3.7 16.2 - - - +
566A CYS* 2.0 46.9 - - - -
648A VAL* 3.3 29.2 - - - -
661A ASN* 1.3 71.0 - - - +
663A LEU* 1.3 59.5 + - - +
665A TYR* 3.0 13.7 + - + +
666A LYS* 2.8 29.1 + - - +
673A TYR* 5.9 2.7 - - + -
697A MET* 4.6 7.9 - - - -
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Residues in contact with LEU 663 (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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564A LEU 3.2 12.2 + - - +
565A GLY* 4.3 11.5 - - - -
661A ASN* 3.2 9.6 + - - +
662A CYS* 1.3 78.0 - - - +
664A ALA* 1.3 57.5 - - - +
666A LYS* 3.3 8.8 + - + +
667A ASN* 2.8 53.3 + - - +
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Residues in contact with ALA 664 (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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661A ASN* 2.9 24.7 + - - +
662A CYS 3.2 0.2 - - - -
663A LEU* 1.3 77.1 - - - +
665A TYR* 1.3 58.3 + - - +
667A ASN* 3.3 4.2 + - - +
668A ASP* 2.9 30.8 + - - +
752A VAL* 4.0 12.3 - - + +
753A GLU 3.8 20.3 - - - +
754A GLY 5.4 0.9 - - - -
755A SER* 3.9 20.0 - - - -
757A ILE* 4.3 4.9 - - + -
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Residues in contact with TYR 665 (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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660A GLN* 2.7 29.6 + - + -
661A ASN 3.8 15.9 - - - -
662A CYS* 3.0 11.0 + - + +
664A ALA* 1.3 72.9 - - + +
666A LYS* 1.3 68.9 + - - +
667A ASN 2.7 3.1 + - - -
668A ASP* 3.0 12.0 + - - +
671A MET* 3.9 10.5 - - + +
672A SER* 3.1 33.9 - - - -
673A TYR* 3.9 20.6 - + + -
697A MET* 4.0 23.1 - - + -
698A VAL 3.9 0.5 - - - -
699A PRO* 3.4 26.5 - - + +
752A VAL* 3.8 24.7 - - + -
757A ILE* 3.9 8.8 - - + +
1005A K 3.1 16.3 - - - -
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Residues in contact with LYS 666 (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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565A GLY 6.0 0.9 - - - +
662A CYS 2.8 17.7 + - - +
663A LEU* 3.6 15.5 - - + +
665A TYR* 1.3 71.9 - - - +
667A ASN* 1.3 67.0 + - - +
668A ASP 4.6 1.6 - - - +
669A LYS* 5.9 0.2 - - - -
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Residues in contact with ASN 667 (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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663A LEU* 2.8 43.4 + - - +
664A ALA* 3.8 5.4 - - - +
665A TYR 2.7 4.2 + - - -
666A LYS* 1.3 81.2 + - - +
668A ASP* 1.3 60.6 + - - +
669A LYS* 3.3 5.4 + - - +
753A GLU* 3.9 17.0 - - + +
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Residues in contact with ASP 668 (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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664A ALA 2.9 16.2 + - - +
665A TYR 3.0 4.1 + - - +
666A LYS 4.6 1.1 - - - +
667A ASN* 1.3 74.6 - - - +
669A LYS* 1.3 59.6 + - - +
670A GLN* 2.8 34.0 + - - +
671A MET* 2.9 29.2 + - - +
751A TYR 4.8 0.5 - - - +
752A VAL* 3.7 9.7 - - + +
753A GLU* 2.9 43.8 + - + +
1005A K 3.0 22.3 - - - -
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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