Contacts of the helix formed by residues 66 - 92 (chain R) in PDB entry 5L4K
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 66 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64R GLN* 3.3 10.9 + - + +
65R ILE* 1.3 70.6 - - - +
67R VAL* 1.3 66.4 + - - +
68R ASP* 3.3 21.2 + - - +
69R LEU* 3.4 35.3 + - + +
70R LEU* 3.5 18.1 + - - +
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Residues in contact with VAL 67 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65R ILE* 3.5 16.5 + - + +
66R ASP* 1.3 73.7 + - - +
68R ASP* 1.3 65.4 + - - +
69R LEU 3.4 0.3 + - - -
70R LEU* 3.5 11.2 + - + +
71R ASN* 3.1 41.1 + - - +
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Residues in contact with ASP 68 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66R ASP* 3.2 18.3 - - - +
67R VAL* 1.3 80.5 + - - +
69R LEU* 1.3 60.5 + - - +
71R ASN* 4.3 4.9 + - - +
72R LYS* 3.1 35.7 + - - +
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Residues in contact with LEU 69 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42R MET* 4.8 11.4 - - + -
45R VAL* 3.9 35.4 - - + -
46R ARG* 4.5 7.6 - - - +
49R ASN* 6.2 0.9 - - - +
66R ASP* 3.4 24.3 + - + +
67R VAL 3.2 0.2 - - - -
68R ASP* 1.3 77.9 - - - +
70R LEU* 1.3 69.2 + - + +
71R ASN 3.2 1.7 + - - -
72R LYS* 3.3 14.3 + - + +
73R MET* 2.8 38.6 - - + +
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Residues in contact with LEU 70 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49R ASN* 3.7 31.4 - - + +
50R MET* 3.0 25.9 - - + +
55R GLU* 3.0 41.7 - - - +
58R CYS* 5.4 8.7 - - - -
65R ILE* 3.6 18.2 - - + -
66R ASP 3.5 18.8 - - - +
67R VAL* 3.5 9.4 + - + +
69R LEU* 1.3 84.2 - - + +
71R ASN* 1.3 62.7 + - - +
73R MET* 3.7 5.5 + - - +
74R LYS 2.9 20.4 + - - -
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Residues in contact with ASN 71 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50R MET* 4.8 4.2 - - - +
67R VAL* 3.1 38.9 + - - +
68R ASP* 4.9 3.1 - - - +
69R LEU 3.2 1.2 - - - -
70R LEU* 1.3 80.8 - - - +
72R LYS* 1.3 61.6 + - + +
74R LYS* 3.7 17.7 - - + +
75R LYS* 2.9 26.7 + - - +
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Residues in contact with LYS 72 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68R ASP* 3.1 34.7 + - - +
69R LEU* 3.3 11.1 + - + +
71R ASN* 1.3 78.1 - - + +
73R MET* 1.3 73.2 + - + +
75R LYS* 3.3 9.7 + - - +
76R ALA* 3.0 27.0 + - - +
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Residues in contact with MET 73 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45R VAL* 3.7 37.9 - - + +
46R ARG* 4.7 5.8 - - - +
48R ASN* 4.0 15.0 - - - +
49R ASN* 3.4 41.1 - - + +
50R MET* 3.7 3.0 - - - +
69R LEU* 2.8 38.3 + - + +
70R LEU* 4.1 6.3 - - - +
72R LYS* 1.3 91.2 - - + +
74R LYS* 1.3 60.2 + - - +
77R ASN* 2.9 29.6 + - - +
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Residues in contact with LYS 74 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50R MET* 3.5 38.5 - - + +
70R LEU 2.9 19.8 + - - +
71R ASN* 3.8 15.7 - - + +
72R LYS 3.3 0.2 - - - -
73R MET* 1.3 74.4 - - - +
75R LYS* 1.3 59.5 + - - +
77R ASN* 3.4 2.9 - - - +
78R GLU* 2.9 60.9 + - + +
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Residues in contact with LYS 75 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71R ASN 2.9 18.3 + - - +
72R LYS* 3.3 9.8 + - + +
74R LYS* 1.3 73.1 - - - +
76R ALA* 1.3 67.2 + - - +
78R GLU* 3.3 6.3 + - - +
79R ASP* 2.9 31.1 + - + +
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Residues in contact with ALA 76 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48R ASN* 2.9 35.2 - - - +
72R LYS 3.0 14.8 + - - +
73R MET* 4.0 0.9 - - - +
75R LYS* 1.3 77.7 - - - +
77R ASN* 1.3 63.5 + - - +
79R ASP* 3.0 17.7 + - - +
80R GLU* 3.0 22.1 + - - +
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Residues in contact with ASN 77 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48R ASN* 4.1 6.1 - - + +
50R MET* 3.7 20.6 + - + +
73R MET 2.9 21.3 + - - +
74R LYS* 3.4 8.9 + - - +
76R ALA* 1.3 76.3 - - - +
78R GLU* 1.3 76.8 + - - +
80R GLU* 3.5 0.9 + - - -
81R LEU* 3.0 46.6 + - - +
110R TYR* 3.7 13.9 + - - -
114R ILE* 3.7 32.1 - - - +
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Residues in contact with GLU 78 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74R LYS* 2.9 47.5 + - + +
75R LYS* 3.8 4.9 - - - +
77R ASN* 1.3 88.5 + - - +
79R ASP* 1.3 63.7 + - - +
81R LEU* 3.7 12.8 - - - +
82R LYS* 2.9 29.3 + - - +
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Residues in contact with ASP 79 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75R LYS* 2.9 27.1 + - + +
76R ALA* 3.0 8.7 + - - +
78R GLU* 1.3 78.6 - - - +
80R GLU* 1.3 63.7 + - + +
82R LYS* 3.9 17.8 + - - +
83R ARG* 2.9 31.8 + - - +
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Residues in contact with GLU 80 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48R ASN* 3.7 13.1 + - - -
76R ALA* 3.0 14.1 + - - +
79R ASP* 1.3 81.9 - - - +
81R LEU* 1.3 61.2 + - - +
82R LYS 3.3 0.4 - - - -
83R ARG* 3.7 32.6 + - - +
84R LEU* 3.0 33.6 + - - +
110R TYR* 3.2 45.7 - - + +
113R ARG* 5.1 1.0 + - - -
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Residues in contact with LEU 81 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77R ASN* 3.0 41.1 + - - +
78R GLU* 3.9 15.5 - - - +
80R GLU* 1.3 75.5 - - - +
82R LYS* 1.3 60.2 + - - +
84R LEU* 4.1 3.6 - - + -
85R ASP* 3.5 21.5 + - - +
107R LYS* 4.0 28.0 - - + +
110R TYR* 4.4 16.4 - - + -
111R LEU* 4.0 32.1 - - + -
114R ILE* 6.3 0.2 - - + -
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Residues in contact with LYS 82 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78R GLU* 2.9 15.2 + - - +
79R ASP* 4.1 21.8 + - - +
81R LEU* 1.3 75.3 - - - +
83R ARG* 1.3 65.7 + - - +
84R LEU 3.2 1.1 - - - -
85R ASP* 3.5 3.8 + - - +
86R GLU* 3.0 33.0 + - + +
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Residues in contact with ARG 83 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79R ASP* 2.9 24.0 + - - +
80R GLU* 3.7 33.7 + - - +
82R LYS* 1.3 76.8 - - - +
84R LEU* 1.3 86.6 + - - +
86R GLU* 3.4 5.6 + - - +
87R GLU* 2.9 32.5 + - - +
110R TYR* 6.0 0.2 - - - -
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Residues in contact with LEU 84 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80R GLU 3.0 22.5 + - - +
81R LEU* 4.5 4.5 - - + +
83R ARG* 1.3 95.2 - - - +
85R ASP* 1.3 60.5 + - - +
87R GLU* 3.1 24.2 + - - +
88R LEU* 2.9 26.3 + - - +
103R ALA* 4.8 4.1 - - - +
106R ALA* 3.4 49.6 - - + +
107R LYS* 4.2 18.6 - - + +
110R TYR* 3.9 25.6 - - + -
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Residues in contact with ASP 85 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81R LEU 3.5 17.3 + - - +
82R LYS* 3.5 4.8 + - - +
83R ARG 3.5 0.4 - - - -
84R LEU* 1.3 78.1 - - - +
86R GLU* 1.3 58.0 + - - +
88R LEU* 3.6 21.6 - - - +
89R GLU* 2.9 28.8 + - - +
107R LYS* 4.0 18.7 - - - +
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Residues in contact with GLU 86 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82R LYS* 3.0 27.4 + - + +
83R ARG* 3.8 6.3 - - - +
85R ASP* 1.3 75.3 - - - +
87R GLU* 1.3 65.9 + - - +
88R LEU 3.1 0.2 - - - -
89R GLU* 4.3 13.5 - - + +
90R ASP* 2.9 28.4 + - + +
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Residues in contact with GLU 87 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83R ARG* 2.9 26.2 + - - +
84R LEU* 3.2 27.3 - - - +
86R GLU* 1.3 76.1 - - - +
88R LEU* 1.3 55.5 + - - +
90R ASP* 3.8 4.1 - - - +
91R ALA* 2.9 30.5 + - + +
102R ASP 4.2 1.0 - - - +
103R ALA* 3.3 29.8 + - + +
106R ALA* 4.1 8.5 - - - +
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Residues in contact with LEU 88 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84R LEU 2.9 12.7 + - - +
85R ASP* 3.6 25.1 - - - +
86R GLU 3.1 0.2 - - - -
87R GLU* 1.3 73.7 - - - +
89R GLU* 1.3 62.1 + - - +
91R ALA* 2.7 20.1 + - + +
92R GLU* 3.0 28.9 + - + +
100R ILE* 4.3 15.9 - - + -
103R ALA* 3.9 24.5 - - + -
104R MET* 4.2 31.4 - - + -
107R LYS* 4.9 12.6 - - + -
126R LYS* 5.4 6.7 - - - +
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Residues in contact with GLU 89 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85R ASP* 2.9 21.2 + - - +
86R GLU* 3.9 14.0 - - - +
88R LEU* 1.3 75.1 - - - +
90R ASP* 1.3 63.6 + - - +
92R GLU* 3.2 26.5 + - - +
93R LYS* 3.5 35.9 + - - +
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Residues in contact with ASP 90 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86R GLU* 2.9 20.6 + - + +
87R GLU* 3.8 4.5 - - - +
89R GLU* 1.3 77.2 + - - +
91R ALA* 1.3 58.8 + - - +
92R GLU 3.4 0.2 - - - -
93R LYS* 3.6 20.6 + - - +
94R ASN* 3.2 34.0 + - - +
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Residues in contact with ALA 91 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87R GLU* 2.9 20.5 + - + +
88R LEU* 2.7 18.2 + - + +
90R ASP* 1.3 71.8 - - - +
92R GLU* 1.3 56.4 + - - -
93R LYS 3.3 3.6 - - - -
94R ASN 4.1 2.2 + - - +
95R LEU 3.4 12.8 - - - +
99R GLU* 3.9 31.4 - - + +
100R ILE* 3.3 21.1 + - + +
103R ALA* 4.5 12.1 - - + -
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Residues in contact with GLU 92 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88R LEU* 3.0 30.7 + - + +
89R GLU* 3.2 17.8 + - - +
91R ALA* 1.3 77.2 - - - +
93R LYS* 1.3 64.3 + - + +
94R ASN 5.1 0.2 - - - -
95R LEU 4.9 1.8 - - - -
100R ILE* 4.1 24.1 - - + +
104R MET* 5.6 4.9 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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