Contacts of the helix formed by residues 63 - 79 (chain E) in PDB entry 1KX3
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 ARG 63 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60E LEU 4.9 8.9 + - - -
61E LEU* 4.0 2.6 + - - +
62E ILE* 1.3 82.5 + - + +
64E LYS* 1.3 66.9 + - - +
66E PRO* 3.5 25.1 - - + +
67E PHE* 3.2 22.0 + - - +
93E GLN* 4.6 0.2 - - - -
28F GLY 5.3 4.0 + - - +
30F THR* 5.7 3.8 - - + +
33F ALA* 5.0 0.8 - - - +
36F ARG* 4.4 6.3 - - - +
17I T 3.2 15.9 + - - +
18I T 2.5 49.7 + - - +
-14J C 4.3 32.1 + - - -
-13J A 3.7 32.7 + - - +
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Residues in contact with LYS 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E LEU* 4.1 19.5 - - + +
62E ILE 4.6 3.6 - - - +
63E ARG* 1.3 71.4 - - - +
65E LEU* 1.3 66.9 + - - +
67E PHE* 3.3 2.9 + - - +
68E GLN* 2.9 22.3 + - - +
89E VAL* 5.5 0.9 - - - +
90E MET* 3.5 33.2 - - + +
93E GLN* 4.0 18.5 - - - +
18I T 2.9 24.4 + - - +
19I T 5.6 7.2 - - - +
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Residues in contact with LEU 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64E LYS* 1.3 72.5 - - - +
66E PRO* 1.3 71.0 - - + +
68E GLN* 3.0 23.8 + - + +
69E ARG* 2.9 44.1 + - + +
17I T 3.5 26.9 - - + +
18I T 2.8 43.8 + - + +
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Residues in contact with PRO 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E ILE* 5.5 0.2 - - + -
63E ARG* 3.5 26.7 - - + +
65E LEU* 1.3 95.9 - - + +
67E PHE* 1.3 61.3 + - - +
69E ARG* 3.3 17.4 + - - +
70E LEU* 3.1 22.0 + - - +
25F ASN* 4.5 5.4 - - - +
28F GLY* 3.7 33.9 - - - +
29F ILE* 5.3 1.8 - - - -
17I T 3.5 35.4 - - - +
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Residues in contact with PHE 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E ILE* 4.0 27.7 - - + +
63E ARG 3.2 17.6 + - - +
64E LYS 3.7 3.1 - - - +
66E PRO* 1.3 78.8 - - - +
68E GLN* 1.3 65.7 + - - +
70E LEU* 3.2 6.5 + - + +
71E VAL* 3.0 36.6 + - + +
89E VAL* 3.9 9.9 - - + -
92E LEU 3.7 3.1 - - - -
93E GLN* 3.4 50.9 - - + +
96E SER* 3.4 33.2 - - - -
29F ILE* 4.3 11.4 - - + -
58F LEU* 4.6 3.8 - - + -
62F LEU* 3.9 24.5 - - + -
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Residues in contact with GLN 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64E LYS 2.9 14.7 + - - +
65E LEU* 3.0 25.9 + - + +
67E PHE* 1.3 79.3 - - - +
69E ARG* 1.3 56.1 + - + +
71E VAL* 3.3 2.9 + - - +
72E ARG* 2.9 64.0 + - - +
86E SER* 5.4 7.1 - - - +
89E VAL* 3.7 38.7 - - + +
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Residues in contact with ARG 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E LEU* 2.9 37.1 + - + +
66E PRO* 3.7 24.7 - - - +
68E GLN* 1.3 73.0 - - + +
70E LEU* 1.3 63.0 + - - +
72E ARG* 3.3 8.9 + - - +
73E GLU* 2.8 31.9 + - - +
22F LEU* 4.5 14.2 - - + +
25F ASN* 3.2 32.9 + - - +
28F GLY* 5.3 5.3 - - - -
16I C 4.9 0.2 - - - -
17I T 2.2 49.1 + - - -
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Residues in contact with LEU 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66E PRO 3.1 13.1 + - - +
67E PHE* 3.2 10.1 + - + +
69E ARG* 1.3 77.2 - - - +
71E VAL* 1.3 62.2 + - - +
73E GLU* 3.6 8.7 - - - +
74E ILE* 3.0 47.4 + - + +
25F ASN* 3.9 13.2 - - + +
26F ILE* 3.7 49.1 - - + +
29F ILE* 3.9 21.3 - - + -
58F LEU* 4.2 3.1 - - + -
59F LYS* 5.7 1.8 - - + -
62F LEU* 3.6 22.4 - - + -
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Residues in contact with VAL 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67E PHE* 3.0 46.5 + - + +
68E GLN* 3.5 9.9 - - - +
70E LEU* 1.3 77.2 - - - +
72E ARG* 1.3 58.6 + - + +
74E ILE* 3.8 2.2 - - - +
75E ALA* 2.9 28.1 + - - +
84E PHE* 3.7 24.7 - - + -
89E VAL* 4.6 10.5 - - + -
92E LEU* 3.7 31.0 - - + -
62F LEU* 4.3 10.3 - - + -
66F ILE* 3.9 10.9 - - + +
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Residues in contact with ARG 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E GLN* 2.9 55.2 + - + +
69E ARG* 3.8 7.0 - - - +
71E VAL* 1.3 75.3 - - + +
73E GLU* 1.3 60.0 + - - +
75E ALA* 3.9 4.6 - - - +
76E GLN* 2.8 32.4 + - - +
82E LEU 4.7 5.5 + - - -
84E PHE* 4.0 33.2 + - + +
89E VAL* 5.3 0.4 - - + -
19F ARG* 4.2 16.6 - - - +
22F LEU* 3.8 15.3 - - + +
-23J A 2.7 49.6 + - - -
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Residues in contact with GLU 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69E ARG 2.8 20.4 + - - +
70E LEU* 3.6 12.9 - - - +
72E ARG* 1.3 73.0 - - - +
74E ILE* 1.3 67.3 + - + +
76E GLN* 3.6 5.2 - - - +
77E ASP* 3.1 34.6 + - - +
22F LEU* 3.8 24.6 - - + +
23F ARG* 3.4 9.8 - - - -
24F ASP* 3.8 13.0 + - - -
25F ASN* 2.7 45.1 + - - +
26F ILE* 4.9 1.9 + - - +
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Residues in contact with ILE 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E LEU* 3.0 43.9 + - + +
71E VAL 3.8 2.9 - - - +
73E GLU* 1.3 82.6 - - + +
75E ALA* 1.3 63.8 + - - +
77E ASP* 3.2 18.2 + - - +
78E PHE* 3.4 31.8 + - + -
59F LYS* 4.4 21.5 - - + +
62F LEU* 3.8 26.9 - - + -
63F GLU* 3.9 19.3 - - + +
66F ILE* 3.8 16.2 - - + -
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Residues in contact with ALA 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E VAL 2.9 17.9 + - - +
72E ARG 3.9 2.5 - - - +
74E ILE* 1.3 77.0 - - - +
76E GLN* 1.3 57.8 + - - +
78E PHE* 2.9 7.4 + - - +
79E LYS* 2.8 29.1 + - - +
82E LEU* 3.9 11.9 - - + +
84E PHE* 3.5 32.8 - - + -
66F ILE* 3.7 21.3 - - + +
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Residues in contact with GLN 76 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72E ARG 2.8 17.4 + - - +
73E GLU* 3.6 3.5 - - - +
75E ALA* 1.3 76.9 - - - +
77E ASP* 1.3 61.2 + - - +
78E PHE 3.3 0.7 + - - -
79E LYS* 3.4 22.0 + - - +
80E THR* 3.8 20.3 + - + +
81E ASP 5.7 2.7 - - - +
82E LEU* 5.5 0.7 - - - -
946E MN 4.1 14.9 + - - +
19F ARG* 2.5 36.4 - - - +
20F LYS 5.4 1.0 + - - -
21F VAL* 6.2 0.4 - - - +
22F LEU* 3.8 26.8 + - - +
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Residues in contact with ASP 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E GLU* 3.1 19.6 + - - +
74E ILE* 3.2 10.5 + - - +
76E GLN* 1.3 75.9 - - - +
78E PHE* 1.3 63.9 + - + +
946E MN 2.0 38.1 + - - -
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Residues in contact with PHE 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74E ILE* 3.4 21.5 + - + -
75E ALA* 2.9 7.2 + - - +
77E ASP* 1.3 84.9 - - + +
79E LYS* 1.3 65.5 + - + +
63F GLU* 3.2 45.5 - - + -
66F ILE* 3.8 17.3 - - + -
67F ARG* 3.6 49.6 - - + -
70F VAL* 5.2 8.5 - - + -
74F GLU* 5.2 0.5 - - - +
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Residues in contact with LYS 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75E ALA 2.8 14.8 + - - +
76E GLN* 3.4 11.5 + - - +
78E PHE* 1.3 79.8 - - - +
80E THR* 1.3 99.8 + - - +
81E ASP* 4.0 5.7 + - - +
82E LEU* 3.6 34.4 + - + +
70F VAL* 4.0 7.4 - - + -
74F GLU* 3.0 33.7 - - - +
79F LYS* 6.3 1.2 - - - +
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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