Contacts of the helix formed by residues 101 - 133 (chain F) in PDB entry 3VBB
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 SER 101 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81F PRO* 5.6 1.7 - - - +
100F VAL* 1.3 80.3 - - - +
102F GLN* 1.3 61.6 + - - +
104F LYS* 4.2 7.7 - - - +
105F LYS* 3.0 37.1 + - - +
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Residues in contact with GLN 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81F PRO* 2.8 54.6 + - + +
82F GLU* 5.9 0.9 - - + -
98F LEU* 2.9 47.0 - - + +
100F VAL 3.0 4.9 + - - +
101F SER* 1.3 81.9 - - - +
103F ILE* 1.3 58.1 + - - +
104F LYS 3.3 0.2 - - - -
105F LYS* 2.9 25.1 + - - +
106F VAL* 3.0 18.7 + - + +
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Residues in contact with ILE 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60F CYS* 4.2 17.9 - - - +
64F ILE* 3.3 46.0 - - + -
68F MET* 3.6 18.8 - - + -
95F LEU* 3.6 17.0 - - + +
96F ALA* 5.4 0.4 - - - -
98F LEU* 3.5 30.1 - - + +
100F VAL* 3.5 12.1 + - + +
102F GLN* 1.3 71.5 - - - +
104F LYS* 1.3 64.5 + - - +
106F VAL* 2.9 30.3 - - + +
107F ARG* 3.3 8.4 + - + +
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Residues in contact with LYS 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68F MET* 5.3 6.1 - - + -
100F VAL 3.2 16.3 + - - +
101F SER* 4.2 7.6 - - - +
103F ILE* 1.3 79.2 - - - +
105F LYS* 1.3 58.7 + - - +
107F ARG* 3.1 37.3 + - - +
108F LEU* 2.9 28.3 + - - +
----------------------------------------------------------
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Residues in contact with LYS 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81F PRO* 3.7 36.5 + - - +
82F GLU* 6.0 1.5 - - - +
101F SER* 3.0 29.5 + - - +
102F GLN* 2.9 14.5 + - - +
104F LYS* 1.3 79.3 - - - +
106F VAL* 1.3 59.1 + - - +
108F LEU* 4.0 14.2 + - + +
109F LEU* 3.5 22.3 + - - +
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Residues in contact with VAL 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60F CYS* 3.7 17.9 - - - -
85F LEU* 5.3 15.0 - - + +
87F PHE* 5.0 0.5 - - - -
98F LEU* 6.1 4.0 - - + -
102F GLN* 3.0 15.8 + - + +
103F ILE* 2.9 30.3 - - + +
105F LYS* 1.3 74.6 - - - +
107F ARG* 1.3 55.6 + - - +
108F LEU 3.1 1.3 - - - -
109F LEU* 2.7 29.9 + - + +
110F ILE* 2.7 23.7 + - + +
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Residues in contact with ARG 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57F LYS* 4.4 13.7 - - + -
60F CYS* 3.9 21.5 - - + -
61F SER* 3.0 35.9 + - - +
64F ILE* 5.7 5.3 - - - +
103F ILE* 3.8 8.7 - - - +
104F LYS* 3.1 40.7 + - - +
106F VAL* 1.3 83.1 - - - +
108F LEU* 1.3 57.6 + - - +
110F ILE* 3.5 7.8 - - - +
111F ASP* 2.8 39.6 + - - +
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Residues in contact with LEU 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104F LYS 2.9 16.1 + - - +
105F LYS* 4.0 14.4 - - + +
107F ARG* 1.3 77.1 - - - +
109F LEU* 1.3 63.7 + - + +
111F ASP* 4.7 5.2 - - + +
112F GLU* 3.0 48.8 + - + +
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Residues in contact with LEU 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85F LEU* 5.2 23.3 - - + +
87F PHE* 4.1 21.8 - - + -
105F LYS 3.5 14.8 - - - +
106F VAL* 2.7 18.1 + - + +
108F LEU* 1.3 83.5 - - + +
110F ILE* 1.3 61.7 + - - +
112F GLU* 3.4 23.3 + - - +
113F ALA* 3.0 23.2 + - - +
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Residues in contact with ILE 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53F LEU* 3.3 23.6 - - + +
56F LEU* 3.9 21.3 - - + +
57F LYS* 3.1 49.1 - - + +
60F CYS* 4.2 15.3 - - + -
87F PHE* 4.0 22.6 - - + -
106F VAL* 2.7 23.0 + - + +
107F ARG* 3.2 6.5 + - - +
109F LEU* 1.3 72.3 - - - +
111F ASP* 1.3 58.7 + - - +
113F ALA* 2.9 8.1 + - - +
114F ILE* 2.8 28.8 + - + +
----------------------------------------------------------
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Residues in contact with ASP 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57F LYS* 4.5 13.5 - - - +
107F ARG* 2.8 26.1 + - - +
108F LEU* 4.7 6.1 - - + +
110F ILE* 1.3 69.6 - - - +
112F GLU* 1.3 60.5 + - - +
113F ALA 3.0 1.6 - - - -
114F ILE* 3.3 18.7 + - - +
115F LEU* 2.9 39.8 + - + +
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Residues in contact with GLU 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108F LEU* 3.0 43.7 + - + +
109F LEU* 3.6 17.8 - - - +
111F ASP* 1.3 76.9 - - - +
113F ALA* 1.3 56.8 + - - +
115F LEU* 3.8 9.7 - - + +
116F LYS* 3.4 20.8 + - - +
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Residues in contact with ALA 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49F ARG* 4.1 13.5 + - - +
53F LEU* 3.7 18.8 - - + -
87F PHE* 4.5 12.3 - - + -
109F LEU 3.0 11.9 + - - +
110F ILE* 2.9 16.2 + - - +
112F GLU* 1.3 74.7 - - - +
114F ILE* 1.3 57.8 + - - +
115F LEU 3.0 1.6 - - - -
116F LYS* 2.9 23.8 + - - +
117F CYS* 3.2 14.7 + - - +
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Residues in contact with ILE 114 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50F ALA* 4.3 11.7 - - + +
53F LEU* 3.6 35.6 - - + +
54F ASN* 2.7 35.9 - - - +
57F LYS* 4.9 2.0 - - + -
110F ILE* 2.8 26.7 + - + +
111F ASP* 3.3 21.3 + - - +
113F ALA* 1.3 72.6 - - - +
115F LEU* 1.3 62.5 + - + +
116F LYS 3.3 0.2 - - - -
117F CYS* 3.7 5.8 + - - +
118F ASP* 3.1 34.6 + - - +
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Residues in contact with LEU 115 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111F ASP* 2.9 27.0 + - + +
112F GLU* 3.8 11.2 - - + +
113F ALA 3.0 0.2 - - - -
114F ILE* 1.3 81.3 - - + +
116F LYS* 1.3 63.8 + - - +
117F CYS 3.2 0.7 - - - -
118F ASP* 4.0 11.7 - - + +
119F ALA* 3.2 23.0 + - - +
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Residues in contact with LYS 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49F ARG* 5.7 4.5 - - - +
112F GLU 3.4 11.8 + - - +
113F ALA* 2.9 12.8 + - - +
115F LEU* 1.3 78.9 - - - +
117F CYS* 1.3 62.8 + - - +
119F ALA* 3.7 5.3 + - + +
120F GLU* 3.2 46.5 + - - +
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Residues in contact with CYS 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46F CYS* 3.8 39.7 - - + +
49F ARG* 3.8 34.1 - - - -
50F ALA* 4.0 16.4 - - + -
53F LEU* 5.4 0.2 - - - -
113F ALA 3.2 12.7 + - - +
114F ILE 3.8 8.5 - - - +
115F LEU 3.2 0.2 - - - -
116F LYS* 1.3 75.3 - - - +
118F ASP* 1.3 56.8 + - - +
120F GLU* 2.9 5.5 + - - +
121F ARG* 2.8 40.7 + - - +
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Residues in contact with ASP 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50F ALA* 5.0 1.9 - - - +
114F ILE* 3.1 28.8 + - - +
115F LEU* 4.0 14.5 - - + +
116F LYS 3.5 0.2 - - - -
117F CYS* 1.3 76.2 - - - +
119F ALA* 1.3 63.3 + - - +
121F ARG* 3.4 19.6 + - - +
122F ILE* 3.1 35.1 + - + +
----------------------------------------------------------
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Residues in contact with ALA 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115F LEU 3.2 16.6 + - - +
116F LYS* 3.8 7.2 - - + +
117F CYS 3.2 0.6 - - - -
118F ASP* 1.3 77.7 - - - +
120F GLU* 1.3 63.9 + - + +
122F ILE* 3.8 10.5 - - - +
123F LYS* 3.4 18.7 + - - +
----------------------------------------------------------
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Residues in contact with GLU 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46F CYS* 4.4 18.4 - - - -
116F LYS* 3.2 45.3 + - - +
117F CYS* 2.9 5.6 + - - +
119F ALA* 1.3 80.9 - - + +
121F ARG* 1.3 53.8 + - - +
123F LYS* 3.0 10.2 + - + +
124F LEU* 2.7 48.0 + - + +
----------------------------------------------------------
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Residues in contact with ARG 121 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43F TRP* 3.8 35.2 - - + +
46F CYS* 3.6 30.6 + - + -
47F ARG* 3.1 58.0 - - - +
50F ALA* 5.0 6.7 - - - +
117F CYS* 2.8 27.8 + - - +
118F ASP* 3.9 17.5 + - - +
120F GLU* 1.3 69.1 - - - +
122F ILE* 1.3 65.8 + - + +
124F LEU* 4.2 2.9 - - - +
125F GLU* 2.8 39.9 + - - +
----------------------------------------------------------
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Residues in contact with ILE 122 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118F ASP* 3.1 23.5 + - + +
119F ALA* 3.8 9.6 - - - +
121F ARG* 1.3 78.3 - - + +
123F LYS* 1.3 63.4 + - - +
125F GLU* 3.6 14.4 + - - +
126F ALA* 3.4 18.9 + - - +
----------------------------------------------------------
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Residues in contact with LYS 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119F ALA 3.4 10.6 + - - +
120F GLU* 3.0 15.9 + - + +
122F ILE* 1.3 81.9 - - + +
124F LEU* 1.3 64.5 + - + +
126F ALA* 3.6 6.9 + - - +
127F GLU* 3.2 45.6 + - + +
----------------------------------------------------------
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Residues in contact with LEU 124 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F ALA* 4.2 23.1 - - + +
42F GLU* 3.7 29.2 - - + +
43F TRP* 3.6 35.9 - - + +
46F CYS* 5.0 3.6 - - - -
120F GLU* 2.7 35.2 + - + +
121F ARG* 3.8 4.3 - - - +
123F LYS* 1.3 73.9 - - + +
125F GLU* 1.3 60.4 + - - +
126F ALA 3.1 1.3 - - - -
127F GLU* 3.0 23.3 + - - +
128F ARG* 2.8 32.5 + - - +
----------------------------------------------------------
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Residues in contact with GLU 125 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43F TRP* 3.1 36.2 + - + +
121F ARG* 2.8 30.3 + - - +
122F ILE* 3.9 13.2 - - - +
124F LEU* 1.3 72.0 - - - +
126F ALA* 1.3 57.2 + - - +
128F ARG* 3.4 21.0 + - - +
129F PHE* 2.9 30.9 + - - +
----------------------------------------------------------
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Residues in contact with ALA 126 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122F ILE 3.4 10.7 + - - +
123F LYS* 3.8 10.1 - - - +
124F LEU 3.1 1.0 - - - -
125F GLU* 1.3 76.5 - - - +
127F GLU* 1.3 61.9 + - + +
129F PHE* 4.1 5.8 - - - +
130F GLU* 3.0 33.8 + - + +
----------------------------------------------------------
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Residues in contact with GLU 127 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F ALA* 4.7 10.6 - - + +
123F LYS* 3.2 43.8 + - + +
124F LEU* 3.0 24.8 + - - +
126F ALA* 1.3 79.1 - - + +
128F ARG* 1.3 57.6 + - - +
130F GLU* 3.9 5.3 - - - +
131F ASN* 3.1 36.4 + - - +
----------------------------------------------------------
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Residues in contact with ARG 128 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F LEU* 3.6 26.6 - - + +
9F ARG* 3.8 0.4 - - - +
36F LEU* 4.0 22.7 - - + +
39F ALA* 4.5 8.3 - - + +
40F ASP* 2.8 45.8 + - + +
43F TRP* 3.2 48.3 - - - -
124F LEU 2.8 15.5 + - - +
125F GLU* 3.6 18.2 + - - +
127F GLU* 1.3 76.6 - - - +
129F PHE* 1.3 59.7 - - - +
131F ASN* 3.5 4.6 + - - +
132F LEU* 2.9 33.5 + - + +
----------------------------------------------------------
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Residues in contact with PHE 129 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2F VAL* 6.4 1.6 - - + -
125F GLU 2.9 18.2 + - - +
126F ALA* 4.1 6.3 - - - +
128F ARG* 1.3 75.3 - - - +
130F GLU* 1.3 76.2 + - + +
131F ASN 3.2 0.3 + - - -
132F LEU* 3.4 10.0 + - + +
133F ARG* 3.3 52.1 + - + +
405F ARG* 5.8 7.6 - - - -
----------------------------------------------------------
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Residues in contact with GLU 130 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126F ALA* 3.0 22.1 + - + +
127F GLU* 3.9 7.0 - - - +
129F PHE* 1.3 85.6 - - + +
131F ASN* 1.3 63.5 + - - +
133F ARG* 3.2 42.4 + - - +
134F GLU* 3.9 12.3 - - - +
----------------------------------------------------------
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Residues in contact with ASN 131 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F LEU* 3.6 32.8 - - + +
35F GLN* 3.3 40.5 + - - +
36F LEU* 3.5 24.9 - - + +
39F ALA* 5.4 0.2 - - - +
127F GLU* 3.1 23.8 + - - +
128F ARG 3.7 4.0 - - - +
130F GLU* 1.3 76.0 - - - +
132F LEU* 1.3 67.1 + - - +
134F GLU* 3.2 12.3 + - - -
135F ILE* 3.6 14.4 + - - +
----------------------------------------------------------
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Residues in contact with LEU 132 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2F VAL* 3.4 38.2 - - + +
3F LEU* 3.8 22.0 - - + +
5F LEU* 3.5 29.4 - - + -
8F PHE* 4.2 15.5 - - + -
36F LEU* 3.4 22.0 - - + +
128F ARG* 2.9 21.3 + - + +
129F PHE* 3.4 10.3 + - + +
131F ASN* 1.3 76.7 - - - +
133F ARG* 1.3 61.1 + - - +
135F ILE* 3.2 23.4 + - + +
401F TYR* 4.4 0.2 + - - -
----------------------------------------------------------
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Residues in contact with ARG 133 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2F VAL* 4.4 9.6 - - + -
129F PHE* 3.3 44.3 + - + +
130F GLU* 3.2 36.1 + - - +
131F ASN 3.2 0.2 + - - -
132F LEU* 1.3 78.3 - - + +
134F GLU* 1.3 84.3 + - - +
135F ILE 3.4 0.6 + - - -
371F HIS* 4.4 11.3 + - - -
401F TYR* 4.1 11.6 + - - -
405F ARG* 5.6 8.5 - - - +
----------------------------------------------------------
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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