Contacts of the helix formed by residues 81 - 104 (chain C) in PDB entry 3D29
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 LEU 81 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B PHE* 3.7 27.8 - - + -
19B GLY 5.0 3.8 - - - +
20B ARG* 6.4 0.4 - - - -
21B LEU* 3.9 24.7 - - + -
30C ALA* 4.3 14.4 - - + +
33C ARG* 6.6 0.4 - - - -
78C PHE* 4.0 0.7 - - - -
80C GLY* 1.3 71.8 - - - -
82C ASN* 1.3 65.4 + - - +
83C ALA* 4.7 2.5 - - + +
84C ASP* 3.4 33.6 + - + +
85C SER* 3.3 17.8 + - - -
130C ARG* 4.2 0.2 - - - +
133C GLY* 2.9 16.6 + - - +
134C VAL* 3.5 6.8 - - - +
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Residues in contact with ASN 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ASN* 3.0 38.8 + - - +
158B THR* 5.5 2.9 - - - +
35C THR* 6.4 0.2 - - - +
53C ARG* 4.6 11.1 + - - +
66C LYS* 3.9 11.8 - - - +
78C PHE* 3.3 25.8 - - + -
80C GLY 3.4 7.9 + - - -
81C LEU* 1.3 69.3 - - - +
83C ALA* 1.3 67.2 + - - +
85C SER* 2.5 26.1 + - - -
86C ARG* 3.3 10.0 + - - +
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Residues in contact with ALA 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ASP* 5.4 0.3 - - - +
121B GLN* 3.4 31.1 - - + +
154B SER* 3.5 20.4 - - - +
155B GLY 3.6 16.6 - - - +
156B ASN* 4.0 4.8 - - + +
81C LEU* 3.4 2.4 - - + -
82C ASN* 1.3 80.1 - - - +
84C ASP* 1.3 65.9 + - - +
86C ARG* 3.3 29.0 + - - +
87C ILE* 3.9 4.2 + - - +
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Residues in contact with ASP 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B GLN* 3.0 18.5 - - - +
124B THR* 4.7 0.3 - - - +
125B GLN* 4.5 0.9 - - - -
81C LEU* 3.4 17.6 + - + +
82C ASN 3.2 0.8 - - - -
83C ALA* 1.3 79.2 - - - +
85C SER* 1.3 62.2 + - - +
87C ILE* 3.2 19.1 + - - +
88C LEU* 3.5 4.0 + - - +
130C ARG* 2.7 46.3 + - - -
132C PHE* 3.6 20.0 - - + -
133C GLY 3.0 14.9 + - - -
134C VAL* 3.5 20.2 - - + -
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Residues in contact with SER 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C LEU* 5.9 0.7 - - - -
78C PHE* 3.2 52.5 - - - -
81C LEU 3.3 3.2 + - - -
82C ASN* 2.5 20.9 + - - +
84C ASP* 1.3 76.4 - - - +
86C ARG* 1.3 67.8 + - - +
88C LEU* 3.2 7.9 + - - +
89C ILE* 2.9 33.5 + - - +
134C VAL* 3.8 10.5 - - - +
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Residues in contact with ARG 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ARG* 3.9 19.5 - - - +
117B SER* 3.1 20.6 + - - -
118B ASP* 2.8 36.1 + - - +
121B GLN* 4.6 1.2 - - - +
155B GLY* 2.6 30.1 + - - -
156B ASN* 4.2 8.1 - - - +
157B TYR* 3.8 32.8 - - - -
64C PRO* 6.4 1.6 - - - -
82C ASN* 3.9 6.2 + - - +
83C ALA* 3.3 25.9 + - - +
84C ASP 3.3 0.8 - - - -
85C SER* 1.3 82.2 + - - +
87C ILE* 1.3 58.9 + - + +
89C ILE* 3.3 9.3 + - + +
90C GLU* 2.9 32.2 + - - +
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Residues in contact with ILE 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ASP* 5.1 19.5 - - + +
121B GLN* 3.7 35.2 - - + +
125B GLN* 4.7 3.4 - - - +
83C ALA 4.0 3.8 - - - +
84C ASP 3.5 11.0 - - - +
85C SER 3.2 0.4 - - - -
86C ARG* 1.3 77.7 - - + +
88C LEU* 1.3 61.6 + - - +
90C GLU* 3.4 4.9 + - + +
91C LYS* 3.1 47.1 + - + +
123C TYR* 5.1 3.6 - - - +
132C PHE* 3.9 22.0 - - + -
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Residues in contact with LEU 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C LEU* 5.7 4.5 - - + -
84C ASP 3.5 3.3 + - - +
85C SER* 3.2 8.3 + - - +
87C ILE* 1.3 78.8 - - - +
89C ILE* 1.3 60.2 + - + +
91C LYS* 3.5 4.5 + - + +
92C ALA* 3.0 29.3 + - - +
116C VAL* 4.4 17.3 - - + +
119C VAL* 3.8 21.8 - - + -
120C GLN* 3.8 35.0 - - + +
132C PHE* 3.8 41.1 - - + -
134C VAL* 4.2 20.4 - - + -
136C THR* 4.3 9.4 - - + -
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Residues in contact with ILE 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C SER* 3.5 24.2 - - - +
70C ILE* 4.0 13.2 - - + -
76C LEU* 3.6 32.8 - - + +
78C PHE* 4.7 7.2 - - + -
85C SER* 2.9 35.7 + - - +
86C ARG* 3.7 8.1 - - + +
88C LEU* 1.3 74.2 - - + +
90C GLU* 1.3 67.3 + - - +
92C ALA* 3.4 2.4 + - - +
93C ARG* 3.0 56.4 + - - +
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Residues in contact with GLU 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C ARG 2.9 17.8 + - - +
87C ILE* 3.8 6.5 - - + +
89C ILE* 1.3 77.3 - - - +
91C LYS* 1.3 67.0 + - + +
93C ARG* 3.2 12.4 + - - +
94C VAL* 2.9 43.5 + - + +
65J LEU* 4.5 1.3 - - - +
69J ARG* 2.8 49.0 + - - +
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Residues in contact with LYS 91 (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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87C ILE* 3.1 32.8 + - + +
88C LEU* 3.8 4.9 - - + +
90C GLU* 1.3 80.8 - - + +
92C ALA* 1.3 62.7 + - - +
94C VAL* 3.3 8.5 + - - +
95C GLU* 2.9 24.3 + - - +
115C TYR* 3.6 26.2 + - + +
119C VAL* 4.1 22.8 - - + +
122C ARG* 4.9 7.9 - - - +
123C TYR* 3.7 27.1 + - - -
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Residues in contact with ALA 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ILE* 3.6 26.6 - - + +
76C LEU* 5.3 1.1 - - + -
88C LEU 3.0 17.7 + - - +
89C ILE* 3.7 4.3 - - - +
90C GLU 3.2 0.2 - - - -
91C LYS* 1.3 76.2 - - - +
93C ARG* 1.3 58.3 + - - +
95C GLU* 3.2 2.9 + - - +
96C ALA* 2.9 28.9 + - - +
112C LEU* 3.9 6.6 - - + +
115C TYR* 4.0 12.3 - - - -
116C VAL* 3.9 22.7 - - + -
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Residues in contact with ARG 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C SER* 3.9 10.1 + - - +
69C LYS* 2.7 36.5 + - - +
70C ILE* 3.5 29.9 - - + +
89C ILE* 3.0 38.3 + - - +
90C GLU* 3.6 12.8 + - - +
92C ALA* 1.3 75.9 - - - +
94C VAL* 1.3 62.7 + - - +
96C ALA* 3.2 4.9 + - - +
97C GLN* 3.2 25.5 + - - +
65J LEU* 3.8 14.4 - - + -
68J ILE* 3.2 25.6 + - + +
69J ARG* 3.4 35.3 + - - +
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Residues in contact with VAL 94 (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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90C GLU* 2.9 38.7 + - + +
91C LYS* 3.5 10.8 - - - +
93C ARG* 1.3 77.3 - - - +
95C GLU* 1.3 63.6 + - - +
97C GLN* 3.2 6.1 + - - +
98C SER* 3.1 24.1 + - - -
65J LEU* 4.1 20.4 - - + -
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Residues in contact with GLU 95 (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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91C LYS 2.9 17.0 + - - +
92C ALA 3.6 4.3 - - - +
94C VAL* 1.3 78.9 - - - +
96C ALA* 1.3 58.2 + - - +
98C SER* 4.3 12.6 + - - -
99C HIS* 2.8 34.0 + - - +
107C VAL* 5.2 0.4 - - + -
111C TYR* 2.6 39.2 + - + -
112C LEU* 4.9 4.3 - - + -
115C TYR* 3.7 42.7 - - + +
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Residues in contact with ALA 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ILE* 4.0 23.6 - - + +
71C ASP* 4.1 16.6 - - + +
92C ALA 2.9 14.0 + - - +
93C ARG 3.2 9.8 + - - +
95C GLU* 1.3 78.4 - - - +
97C GLN* 1.3 62.6 + - + +
99C HIS* 3.6 2.3 + - - +
100C ARG* 3.2 29.9 + - - +
107C VAL* 4.0 21.6 - - + +
112C LEU* 4.9 0.7 - - + -
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Residues in contact with GLN 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ILE 5.6 0.5 - - - +
71C ASP* 4.5 9.4 - - - +
93C ARG 3.2 12.6 + - - +
94C VAL* 3.2 7.6 + - - +
96C ALA* 1.3 76.4 - - + +
98C SER* 1.3 66.0 + - - +
100C ARG* 3.3 20.3 + - - +
101C LEU* 3.1 23.4 + - - +
61J ALA* 3.8 32.1 + - + +
64J GLN* 3.0 51.9 + - - +
65J LEU* 3.9 17.6 - - + -
68J ILE* 4.6 7.1 - - - +
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Residues in contact with SER 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C VAL* 3.1 20.0 + - - -
95C GLU* 3.6 15.5 + - - -
97C GLN* 1.3 77.7 - - - +
99C HIS* 1.3 62.1 + - - +
101C LEU* 3.0 12.5 + - - +
102C THR* 2.9 33.5 + - - +
61J ALA* 6.0 0.2 - - - -
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Residues in contact with HIS 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C GLU* 2.8 23.0 + - - +
96C ALA 3.9 0.7 - - - +
98C SER* 1.3 75.8 + - - +
100C ARG* 1.3 57.6 + - - +
102C THR* 3.9 5.8 - - - -
103C LEU* 2.9 65.9 + - + +
105C ASP* 2.7 31.4 + - + -
106C PRO 3.8 11.2 - - - -
107C VAL* 3.4 27.4 + - + -
108C THR* 5.2 2.0 - - + -
111C TYR* 3.9 37.5 - + - -
66K HIS* 6.2 0.4 - - - -
70K GLU* 6.3 0.2 - - - -
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Residues in contact with ARG 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C ASP* 2.9 29.0 + - - -
72C SER* 4.8 6.9 + - - -
73C HIS* 4.4 2.0 + - - -
96C ALA 3.2 18.0 + - - +
97C GLN* 3.5 23.5 + - - +
98C SER 3.2 0.4 - - - -
99C HIS* 1.3 76.8 - - - +
101C LEU* 1.3 59.0 + - + +
104C GLU* 3.0 27.7 - - - +
105C ASP 3.6 8.9 + - - +
106C PRO* 2.8 58.4 - - + +
64J GLN* 3.8 20.6 + - - +
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Residues in contact with LEU 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C GLN 3.1 9.6 + - - +
98C SER* 3.0 14.2 + - - +
100C ARG* 1.3 81.2 - - + +
102C THR* 1.3 63.9 + - + +
104C GLU 4.0 0.5 + - - -
57J GLU* 3.4 50.9 - - + +
58J TYR* 4.6 8.1 - - + -
60J GLN* 5.2 5.4 - - - +
61J ALA* 4.1 22.4 - - + +
81K LYS* 3.1 32.5 + - - +
85K ASN* 5.1 0.4 - - - +
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Residues in contact with THR 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C SER* 2.9 27.2 + - - +
99C HIS* 3.9 1.9 - - - -
101C LEU* 1.3 80.3 - - + +
103C LEU* 1.3 80.5 + - - +
104C GLU 3.7 0.3 + - - -
78K ALA* 4.6 4.9 - - - +
81K LYS* 3.8 22.3 - - - +
82K ILE* 5.5 3.8 - - - +
85K ASN* 4.3 18.8 - - - +
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Residues in contact with LEU 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C HIS* 2.9 58.7 + - + +
102C THR* 1.3 91.6 - - - +
104C GLU* 1.3 71.6 + - - +
105C ASP* 3.3 8.5 + - + +
66K HIS* 4.0 29.2 - - + +
74K ILE* 4.9 2.2 - - + -
75K SER* 4.6 3.1 + - - -
77K ALA* 5.3 0.7 - - - +
78K ALA* 3.9 31.9 + - + +
82K ILE* 6.0 5.6 - - + -
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Residues in contact with GLU 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C ARG 3.0 17.1 + - - +
101C LEU 4.2 0.9 - - - +
102C THR 3.3 0.2 - - - -
103C LEU* 1.3 80.0 - - - +
105C ASP* 1.3 62.9 + - - +
57J GLU* 4.4 3.5 - - - +
77K ALA* 3.8 15.0 - - + +
81K LYS* 3.1 33.1 + - + +
111K TYR* 4.0 5.2 + - - -
119K ARG* 2.6 46.9 + - - -
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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