Contacts of the helix formed by residues 65 - 76 (chain A) in PDB entry 2KK0
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 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A LEU* 4.4 8.5 - - - -
29A LEU* 3.3 34.1 - - + +
62A GLN* 2.9 27.1 + - - -
63A VAL* 2.9 10.1 + - - +
64A LEU* 1.3 68.2 - - - +
66A LEU* 1.3 56.4 + - - +
67A PHE 3.3 2.0 - - - -
68A MET* 3.1 27.6 + - + -
69A LEU* 2.8 35.3 + - - +
95A LEU* 4.5 14.6 - - + +
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Residues in contact with LEU 66 (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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26A LEU* 3.8 31.1 - - + +
38A PHE* 5.0 0.2 - - - -
39A LEU* 4.6 5.4 - - + -
42A LEU* 5.1 4.9 - - + -
43A PHE* 4.2 18.6 - - + -
53A VAL* 4.8 8.3 - - + -
56A ILE* 4.1 22.2 - - + -
57A PRO* 5.4 2.7 - - + -
64A LEU* 2.6 32.7 + - + +
65A ASP* 1.3 70.5 - - - +
67A PHE* 1.3 63.4 + - - +
69A LEU* 3.4 1.5 + - + -
70A TYR* 3.0 21.5 + - - +
111A GLN* 6.4 1.3 - - + -
115A TYR* 4.8 18.4 - - + -
116A LEU* 3.1 36.9 - - + +
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Residues in contact with PHE 67 (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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26A LEU* 5.4 1.0 - - - +
29A LEU* 5.4 1.8 - - + -
34A LYS* 3.3 42.4 - - + -
35A ARG* 3.3 60.8 - - - +
38A PHE* 3.4 41.0 - + + -
39A LEU* 3.9 11.5 - - + +
65A ASP 3.3 0.4 - - - -
66A LEU* 1.3 78.8 - - - +
68A MET* 1.3 67.6 + - - +
70A TYR* 3.4 3.1 + - - +
71A VAL* 3.1 44.1 + - + +
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Residues in contact with MET 68 (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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29A LEU* 5.1 0.2 - - + -
35A ARG* 2.9 40.4 - - - +
65A ASP* 3.1 24.5 + - + +
67A PHE* 1.3 78.1 - - - +
69A LEU* 1.3 66.6 + - - +
71A VAL* 3.1 9.8 + - + +
72A LEU* 3.0 39.1 + - + +
94A GLY 5.2 6.5 - - - +
95A LEU* 3.4 21.1 - - + -
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Residues in contact with LEU 69 (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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64A LEU* 3.8 32.3 - - + -
65A ASP 2.8 21.1 + - - +
66A LEU* 3.6 5.6 - - + +
68A MET* 1.3 73.8 - - - +
70A TYR* 1.3 62.4 + - - +
72A LEU* 3.4 2.6 + - - +
73A VAL* 3.0 32.2 + - + +
88A TRP* 4.9 1.6 - - + -
91A ILE* 3.5 30.5 - - + -
95A LEU* 3.7 22.7 - - + +
108A LEU* 4.8 11.2 - - + +
112A TYR* 3.6 35.2 - - + +
116A LEU* 3.9 9.2 - - + -
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Residues in contact with TYR 70 (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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38A PHE* 3.5 34.1 - + + -
66A LEU 3.0 17.0 + - - +
67A PHE 3.7 4.7 - - - +
69A LEU* 1.3 76.3 - - - +
71A VAL* 1.3 60.3 + - + +
74A THR* 2.8 60.6 + - + +
112A TYR* 3.7 19.7 - + - -
116A LEU* 3.9 22.1 - - + +
119A TYR* 3.2 31.8 + + + -
120A GLU* 3.3 34.9 - - + +
123A LYS* 5.1 0.9 - - - +
124A ARG* 4.9 7.3 - - - +
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Residues in contact with VAL 71 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A PHE* 3.1 42.9 + - + +
68A MET* 3.1 14.1 + - + +
70A TYR* 1.3 78.5 - - + +
72A LEU* 1.3 70.9 + - + +
74A THR* 3.1 17.3 + - - -
75A GLU* 3.1 29.6 + - - +
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Residues in contact with LEU 72 (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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68A MET* 3.0 41.9 + - + +
69A LEU* 3.9 3.6 - - - +
71A VAL* 1.3 86.8 - - + +
73A VAL* 1.3 61.3 + - - +
75A GLU* 3.1 38.4 - - - +
76A LYS* 3.4 18.1 - - + +
90A GLU* 5.0 5.4 - - + +
91A ILE* 3.8 25.2 - - + +
94A GLY* 4.4 26.0 - - - +
95A LEU* 4.7 7.0 - - + -
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Residues in contact with VAL 73 (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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69A LEU* 3.0 21.8 + - + +
72A LEU* 1.3 74.2 - - - +
74A THR* 1.3 62.9 + - - +
76A LYS* 3.1 11.6 + - - +
77A GLY 3.2 1.0 + - - -
78A GLY 3.0 20.9 + - - -
79A LEU* 3.5 26.5 - - + +
82A VAL* 3.6 14.4 - - + +
88A TRP* 4.5 9.2 - - + -
91A ILE* 4.1 24.2 - - + -
112A TYR* 3.4 40.6 - - + +
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Residues in contact with THR 74 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A TYR* 2.8 62.7 + - + +
71A VAL* 3.1 9.4 + - - -
73A VAL* 1.3 75.4 - - - +
75A GLU* 1.3 60.0 + - - +
77A GLY* 3.0 18.7 + - - -
78A GLY 3.9 6.9 + - - +
112A TYR* 3.9 7.9 - - - +
120A GLU* 4.4 1.8 - - + +
124A ARG* 6.0 1.3 - - + -
126A LEU* 4.0 25.0 - - + +
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Residues in contact with GLU 75 (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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71A VAL* 3.2 27.7 - - + +
72A LEU* 3.1 38.7 - - - +
74A THR* 1.3 80.8 + - - +
76A LYS* 1.3 73.6 + - + +
77A GLY 3.3 0.4 + - - -
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Residues in contact with LYS 76 (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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72A LEU* 3.4 16.4 - - + +
73A VAL 3.1 9.5 + - - +
74A THR 3.1 0.8 - - - -
75A GLU* 1.3 90.4 - - + +
77A GLY* 1.3 56.9 + - - +
78A GLY 3.8 0.4 - - - -
81A GLU* 3.1 19.9 - - + +
82A VAL* 3.9 13.9 - - + -
85A LYS* 5.5 2.1 - - + +
87A LEU* 3.7 34.4 - - + +
90A GLU* 4.8 16.8 + - - -
91A ILE* 4.6 9.2 - - + -
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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