Contacts of the helix formed by residues 67 - 79 (chain B) in PDB entry 3KXK
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 67 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65B GLN* 5.0 13.7 - - + +
66B LEU* 1.3 76.6 - - - +
68B PRO* 1.3 83.4 - - + +
69B ARG* 3.2 31.0 - - + +
70B HIS* 2.8 42.9 + - + +
71B PHE* 3.3 6.1 + - - -
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Residues in contact with PRO 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B LEU 4.4 1.3 - - - +
67B LYS* 1.3 101.7 - - + +
69B ARG* 1.3 56.7 + - - +
71B PHE* 3.1 5.6 + - + +
72B ILE* 2.8 32.7 + - - +
117B PRO* 3.8 28.3 - - + +
118B ILE* 3.9 21.7 - - + +
121B GLU* 3.3 36.6 - - + +
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Residues in contact with ARG 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B VAL* 3.3 38.5 + - - +
40B LYS* 4.2 2.9 - - - +
67B LYS* 4.2 31.9 - - + +
68B PRO* 1.3 80.5 - - + +
70B HIS* 1.3 67.1 + - + +
72B ILE* 3.6 12.9 - - + +
73B ASN* 2.9 40.3 + - - +
121B GLU* 3.9 8.4 + - - +
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Residues in contact with HIS 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ASN 3.6 18.4 - - - -
39B VAL* 3.1 24.4 + - - -
40B LYS 3.3 10.9 + - - -
42B TYR* 3.3 32.4 + + + -
66B LEU* 3.9 24.9 - - + -
67B LYS* 2.8 51.1 + - + +
69B ARG* 1.3 82.4 + - + +
71B PHE* 1.3 59.8 + - - +
74B ILE* 2.8 43.1 + - + +
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Residues in contact with PHE 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B LEU* 3.5 33.9 - - + -
67B LYS 3.3 14.3 + - - -
68B PRO 3.1 7.2 + - - +
70B HIS* 1.3 77.3 - - - +
72B ILE* 1.3 58.2 + - - +
74B ILE* 4.6 4.9 - - - -
75B ARG* 2.8 50.6 + - - +
83B VAL* 3.9 27.4 - - + -
84B LEU* 4.6 0.9 - - - -
85B ASP* 3.3 39.7 - - + -
88B LEU* 3.5 24.2 - - + -
114B TYR* 4.1 6.7 - + - -
118B ILE* 3.6 31.2 - - + -
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Residues in contact with ILE 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B PRO 2.8 24.2 + - - +
69B ARG* 3.6 11.0 - - + +
71B PHE* 1.3 75.6 - - - +
73B ASN* 1.3 64.4 + - - +
75B ARG* 3.9 3.4 - - - +
76B ARG* 2.9 64.9 + - - +
118B ILE* 3.3 30.5 - - + +
121B GLU* 3.1 37.5 - - + +
122B THR* 3.6 7.0 - - - +
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Residues in contact with ASN 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B LYS* 3.2 45.1 - - - +
41B PHE* 3.5 19.9 - - + -
69B ARG* 2.9 24.2 + - - +
72B ILE* 1.3 84.7 - - - +
74B ILE* 1.3 66.3 + - - +
76B ARG* 3.1 13.3 + - - +
77B GLU* 3.0 26.7 + - - +
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Residues in contact with ILE 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B PHE* 3.3 41.1 - - + +
43B ILE* 5.0 2.2 - - + -
48B LEU* 3.9 16.6 - - + -
60B LEU* 4.1 4.9 - - + -
62B ILE* 4.2 11.4 - - + -
66B LEU* 4.2 21.1 - - + -
70B HIS* 2.8 32.7 + - + +
71B PHE* 4.1 1.8 - - - +
73B ASN* 1.3 71.9 - - - +
75B ARG* 1.3 58.6 + - - +
77B GLU* 3.0 3.8 + - - +
78B LEU* 2.8 50.7 + - + +
83B VAL* 3.8 19.3 - - + -
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Residues in contact with ARG 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B PHE* 2.8 40.3 + - - +
72B ILE* 4.1 3.1 - - - +
74B ILE* 1.3 75.0 - - - +
76B ARG* 1.3 61.9 + - - +
78B LEU* 4.5 5.6 - - - +
79B LYS* 3.1 23.7 + - - +
81B LYS 5.7 4.3 - - - +
83B VAL* 3.3 32.6 + - + +
84B LEU* 5.9 0.2 - - - +
88B LEU* 4.0 18.4 - - - +
115B GLU* 2.7 40.3 + - - -
118B ILE* 4.1 10.7 - - - +
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Residues in contact with ARG 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ILE* 2.9 49.1 + - - +
73B ASN* 3.1 16.1 + - - +
75B ARG* 1.3 77.1 - - - +
77B GLU* 1.3 59.0 + - + +
79B LYS* 3.1 23.9 - - + +
122B THR* 3.9 27.9 - - - +
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Residues in contact with GLU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B PHE* 3.8 19.1 - - + -
45B TYR* 3.6 15.9 + - - -
48B LEU* 3.9 19.5 - - + -
49B GLN* 2.9 26.3 + - - +
52B LYS* 3.4 37.8 + - + +
73B ASN 3.0 13.8 + - - +
74B ILE 3.0 7.9 + - - +
76B ARG* 1.3 83.3 - - + +
78B LEU* 1.3 64.7 + - + +
79B LYS* 3.3 5.4 + - - +
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Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B LEU* 3.9 19.7 - - + +
51B ILE* 4.4 10.3 - - + -
52B LYS* 4.3 35.8 - - + +
60B LEU* 4.2 11.0 - - + -
74B ILE* 2.8 41.4 + - + +
75B ARG* 4.4 2.9 - - - +
77B GLU* 1.3 73.4 - - - +
79B LYS* 1.3 71.7 + - - +
80B GLY 3.4 0.3 + - - -
81B LYS* 4.0 35.5 + - + +
82B GLU 4.2 10.5 - - - +
83B VAL* 4.1 17.5 - - + -
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Residues in contact with LYS 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B LYS* 4.7 13.6 - - - +
75B ARG 3.1 13.1 + - - +
76B ARG* 3.1 27.4 - - - +
77B GLU 4.0 7.4 - - - +
78B LEU* 1.3 79.9 - - - +
80B GLY* 1.3 57.3 + - - +
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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