Contacts of the strand formed by residues 68 - 73 (chain K) in PDB entry 6D6U
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 ALA 68 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48K ILE* 4.4 18.8 - - + -
60K TYR* 3.5 26.0 - - + -
64K PHE* 3.5 14.4 + - + +
66K GLY* 3.6 6.4 + - - -
67K LYS* 1.3 82.3 + - - +
69K THR* 1.3 66.6 + - - +
81K LEU* 4.3 15.9 - - + -
82K GLN 4.1 4.5 - - - -
83K LEU* 4.4 10.5 - - + -
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Residues in contact with THR 69 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60K TYR* 3.3 6.3 - - - +
66K GLY 5.7 0.7 + - - -
68K ALA* 1.3 78.6 + - - +
70K ILE* 1.3 64.9 + - - +
71K THR* 4.1 20.1 + - + -
80K TYR 4.0 0.5 - - - +
81K LEU* 3.6 2.9 - - - +
82K GLN* 3.0 47.8 + - + +
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Residues in contact with ILE 70 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36K TRP* 3.6 38.8 - - + +
48K ILE* 5.0 2.2 - - + -
49K GLY* 3.8 21.8 - - - +
50K ARG 4.0 8.3 - - - +
51K ILE* 3.5 37.3 - - + +
58K THR* 3.8 13.1 - - + +
59K LYS 4.9 0.2 - - - +
60K TYR* 2.7 33.5 + - + +
69K THR* 1.3 76.8 - - - +
71K THR* 1.3 69.3 + - - +
79K ALA* 5.5 0.9 - - + -
80K TYR 3.5 7.2 - - - +
81K LEU* 3.7 17.7 - - + -
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Residues in contact with THR 71 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19K LYS* 5.4 3.5 + - - -
51K ILE* 4.0 4.7 - - - -
69K THR* 4.1 18.9 + - + -
70K ILE* 1.3 79.0 - - - +
72K THR* 1.3 57.5 + - - +
79K ALA* 3.9 0.7 - - - +
80K TYR* 2.6 52.0 + - - +
82K GLN* 5.7 2.6 + - - +
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Residues in contact with THR 72 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29K ILE* 3.4 19.9 - - - +
34K MET* 6.5 0.2 - - - -
51K ILE* 3.8 21.7 - - + +
52K ASP 5.4 0.2 - - - +
53K PRO* 4.2 24.5 - - + +
56K GLY* 5.8 4.0 - - - -
71K THR* 1.3 77.8 - - - +
73K ASP* 1.3 58.2 + - - +
74K THR* 4.0 10.3 + - + +
78K THR 2.9 21.3 + - - -
79K ALA* 3.8 9.0 - - - +
80K TYR* 4.4 2.9 - - - +
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Residues in contact with ASP 73 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72K THR* 1.3 71.9 + - - +
74K THR* 1.3 66.1 + - - +
75K PHE* 3.3 20.1 + - - +
76K SER* 2.8 30.7 + - - +
77K ASN 3.0 16.8 + - - -
78K THR 2.8 17.6 + - - +
80K TYR* 4.0 20.5 + - + -
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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