Contacts of the helix formed by residues 60 - 70 (chain C) in PDB entry 3KXC
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 ASP 60 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58C PHE 3.1 3.4 + - - -
59C LYS* 1.3 81.5 - - - +
61C GLU* 1.3 75.1 + - - +
62C LEU* 3.1 29.3 + - - +
63C ASP* 3.2 23.8 + - + +
64C ILE* 3.1 32.7 + - - +
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Residues in contact with GLU 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C ASP* 1.3 74.6 + - - +
62C LEU* 1.3 61.3 + - + +
64C ILE* 3.0 11.5 + - - +
65C MET* 2.9 29.2 + - + +
90C GLY* 5.0 5.8 + - - -
92C TYR* 2.6 33.2 + - + +
135C ILE* 4.1 15.0 - - + +
155C ILE* 3.3 35.7 - - + +
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Residues in contact with LEU 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C ASP* 3.1 20.1 + - - +
61C GLU* 1.3 78.0 - - + +
63C ASP* 1.3 59.2 + - - +
65C MET* 3.5 4.4 + - - +
66C LYS* 3.0 46.7 + - - +
84C LEU* 5.4 3.4 - - + +
86C THR* 5.1 2.7 - - + -
88C HIS* 4.5 27.8 - - + +
92C TYR* 3.3 33.2 - - + +
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Residues in contact with ASP 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C PHE* 4.5 15.2 - - + -
59C LYS* 4.1 14.2 + - - +
60C ASP* 3.2 27.2 + - + +
61C GLU 3.2 0.8 - - - -
62C LEU* 1.3 76.3 - - - +
64C ILE* 1.3 65.9 + - - +
66C LYS* 3.3 15.3 + - - +
67C PHE* 3.0 23.2 + - - +
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Residues in contact with ILE 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C PHE* 3.7 34.3 - - + +
60C ASP 3.1 18.9 + - - +
61C GLU* 3.0 10.8 + - - +
63C ASP* 1.3 75.8 - - - +
65C MET* 1.3 61.5 + - - +
67C PHE* 3.2 5.8 + - - +
68C ILE* 3.1 21.3 + - - +
130C LEU* 3.6 26.9 - - + -
133C LEU* 3.6 44.9 - - + +
135C ILE* 3.8 22.2 - - + -
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Residues in contact with MET 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C GLU* 2.9 19.1 + - + +
62C LEU 3.9 4.5 - - - +
63C ASP 3.3 0.2 - - - -
64C ILE* 1.3 75.1 - - - +
66C LYS* 1.3 64.6 + - - +
68C ILE* 3.4 8.4 + - + +
69C CYS* 3.1 28.6 + - - -
84C LEU* 4.3 9.4 - - + -
92C TYR* 3.7 50.3 - - + -
94C LEU* 3.8 34.1 - - + -
130C LEU* 3.8 29.2 - - + -
135C ILE* 5.2 1.3 - - - -
153C VAL* 4.2 17.0 - - + -
155C ILE* 4.7 6.1 - - - -
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Residues in contact with LYS 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C LEU* 3.0 34.5 + - - +
63C ASP* 3.3 15.4 + - - +
65C MET* 1.3 76.3 - - - +
67C PHE* 1.3 56.2 + - - +
69C CYS* 3.3 6.4 + - - +
70C LYS* 2.8 59.9 + - + +
84C LEU* 4.6 15.3 - - + -
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Residues in contact with PHE 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C ILE* 3.7 24.9 - - + -
51C PHE* 5.3 3.1 - - + -
52C THR* 2.8 34.5 - - + -
58C PHE* 3.7 25.1 - + + -
63C ASP 3.0 13.4 + - - +
64C ILE 3.2 7.6 + - - +
66C LYS* 1.3 76.1 - - - +
68C ILE* 1.3 67.7 + - + +
71C ASP* 3.0 64.7 + - + +
72C PHE* 3.0 21.1 + + + -
133C LEU* 4.0 17.0 - - + -
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Residues in contact with ILE 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C ILE 3.1 15.6 + - - +
65C MET* 3.6 12.3 - - + +
67C PHE* 1.3 82.4 - - + +
69C CYS* 1.3 59.4 + - - +
72C PHE* 3.5 32.3 - - + -
73C TRP* 2.9 33.5 + - + +
94C LEU* 3.9 23.3 - - + -
126C ILE* 4.5 17.9 - - + +
129C GLY* 4.5 6.5 - - - -
130C LEU* 3.7 41.7 - - + +
133C LEU* 4.7 3.8 - - + -
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Residues in contact with CYS 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C MET 3.1 20.1 + - - +
66C LYS* 3.6 7.4 - - - +
68C ILE* 1.3 77.9 - - - +
70C LYS* 1.3 63.1 + - + +
73C TRP* 3.5 2.4 - - - +
80C GLN* 3.4 7.7 - - - +
81C ILE* 2.9 59.5 + - + +
84C LEU* 3.5 30.7 - - + -
94C LEU* 3.9 17.0 - - - -
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Residues in contact with LYS 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C LYS* 2.8 42.2 + - + +
67C PHE* 3.1 1.4 + - - -
69C CYS* 1.3 81.1 - - + +
71C ASP* 1.3 71.5 + - - +
74C THR* 2.7 34.8 + - - -
80C GLN* 4.0 28.5 - - + +
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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