Contacts of the helix formed by residues 113 - 139 (chain F) in PDB entry 1F33
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 ASN 113 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F ARG* 3.5 8.7 - - - +
56F GLY* 5.1 4.7 - - - -
57F ALA 5.6 0.9 + - - -
112F HIS* 1.3 80.1 - - - +
114F VAL* 1.3 66.0 + - - +
115F GLN* 2.8 47.1 - - - +
116F ASP* 3.1 35.4 + - - +
117F HIS* 3.2 12.3 + - - -
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Residues in contact with VAL 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54F MET* 4.3 12.8 - - + -
55F ARG 2.9 38.1 + - - +
56F GLY 3.9 5.2 - - - +
57F ALA 3.4 28.3 - - - +
58F ASN* 4.3 1.8 - - + +
59F PHE* 4.1 11.2 - - - -
62F VAL* 4.3 23.3 - - + -
112F HIS 4.2 0.9 - - - -
113F ASN* 1.3 73.8 + - - +
115F GLN* 1.3 63.0 + - + +
117F HIS* 3.3 4.3 + - - +
118F LEU* 2.9 45.6 + - + +
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Residues in contact with GLN 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57F ALA* 5.2 5.0 + - + +
58F ASN* 5.9 2.8 - - - +
113F ASN* 2.8 23.6 - - - +
114F VAL* 1.3 78.0 - - + +
116F ASP* 1.3 61.1 + - - +
118F LEU* 3.5 13.3 - - - +
119F LYS* 3.0 42.1 + - - +
165F ASN 3.2 20.8 + - - -
166F ILE* 3.2 13.6 - - - +
167F GLU* 2.7 54.4 + - + +
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Residues in contact with ASP 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111F ILE* 4.1 27.8 - - + +
112F HIS 4.8 0.7 + - - -
113F ASN* 3.1 33.4 + - - +
115F GLN* 1.3 79.7 - - - +
117F HIS* 1.3 62.5 + - - +
119F LYS* 3.2 16.2 + - - +
120F GLU* 3.0 26.0 + - + +
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Residues in contact with HIS 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49F GLN* 4.5 4.7 - - - -
50F ALA* 3.5 23.9 - - + -
53F ASN* 3.3 14.9 + - + -
54F MET* 3.7 28.5 - - + -
107F TYR* 2.6 32.4 + + - +
108F PRO 4.9 1.6 - - - -
111F ILE* 3.3 38.8 + - + +
112F HIS* 3.4 24.0 - - - -
113F ASN 3.2 8.7 + - - -
114F VAL 3.6 5.8 - - - +
116F ASP* 1.3 78.6 - - - +
118F LEU* 1.3 57.8 + - - +
120F GLU 3.2 0.2 + - - -
121F LEU* 2.8 37.1 + - - +
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Residues in contact with LEU 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54F MET* 5.0 1.1 - - + -
58F ASN* 5.8 0.4 - - - +
62F VAL* 3.8 27.8 - - + -
65F MET* 5.1 3.8 - - + -
66F LEU* 5.5 0.4 - - + -
114F VAL* 2.9 27.4 + - + +
115F GLN* 3.5 21.1 - - - +
117F HIS* 1.3 77.1 - - - +
119F LYS* 1.3 57.9 + - - +
121F LEU* 3.7 9.6 - - + +
122F ALA* 2.9 24.9 + - - +
162F ILE* 3.3 40.0 - - + +
165F ASN* 3.7 35.2 - - + +
166F ILE* 3.9 10.8 - - + +
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Residues in contact with LYS 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115F GLN* 3.0 34.6 + - - +
116F ASP* 3.6 13.2 + - - +
118F LEU* 1.3 73.2 - - - +
120F GLU* 1.3 66.8 + - + +
122F ALA* 3.3 3.4 + - - +
123F ASP* 3.1 30.0 + - - +
166F ILE* 4.0 36.6 - - + -
167F GLU 5.8 0.4 - - - -
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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
----------------------------------------------------------
107F TYR* 3.4 25.1 - - + +
108F PRO* 3.9 10.8 - - + +
111F ILE* 3.6 21.8 - - + +
116F ASP* 3.0 18.9 + - + +
119F LYS* 1.3 78.8 - - - +
121F LEU* 1.3 63.1 + - - +
123F ASP* 3.4 12.9 + - - +
124F ARG* 2.9 52.6 + - - +
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Residues in contact with LEU 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46F ILE* 3.8 27.6 - - + +
47F THR* 4.3 8.7 - - - -
50F ALA* 3.6 32.1 - - + -
54F MET* 4.7 0.4 - - + -
66F LEU* 3.7 32.5 - - + -
107F TYR* 4.0 2.9 - - + +
117F HIS 2.8 31.2 + - - +
118F LEU* 3.7 11.9 - - + +
120F GLU* 1.3 72.0 - - - +
122F ALA* 1.3 60.8 - - - +
124F ARG* 3.2 4.1 + - - +
125F TYR* 2.8 46.2 + - + -
162F ILE* 4.1 12.6 - - + -
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Residues in contact with ALA 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118F LEU 2.9 18.7 + - - +
119F LYS* 3.3 9.8 + - - +
121F LEU* 1.3 74.6 - - - +
123F ASP* 1.3 61.3 + - - +
125F TYR* 4.6 0.7 - - - -
126F ALA* 2.8 32.5 + - - +
159F LEU* 3.5 10.4 - - + +
162F ILE* 3.9 14.8 - - + +
163F GLU* 4.3 17.0 - - + +
166F ILE* 4.3 11.0 - - + -
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Residues in contact with ASP 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119F LYS* 3.1 16.5 + - - +
120F GLU* 3.5 16.3 - - - +
121F LEU 3.1 0.2 - - - -
122F ALA* 1.3 80.5 - - - +
124F ARG* 1.3 69.3 + - - +
126F ALA* 3.3 7.2 + - - +
127F ILE* 3.1 29.8 + - + +
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Residues in contact with ARG 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43F LEU* 3.8 18.6 - - + -
46F ILE* 4.1 12.1 - - + +
104F LEU* 3.8 17.6 - - + +
105F LYS* 2.9 51.4 + - - +
106F SER 3.7 6.1 + - - -
107F TYR* 2.8 36.1 - - - +
108F PRO* 3.5 15.4 - - - +
120F GLU* 2.9 41.5 + - - +
121F LEU* 3.2 5.7 + - - +
123F ASP* 1.3 80.3 - - - +
125F TYR* 1.3 64.3 + - - +
127F ILE* 3.2 10.2 + - - +
128F VAL* 3.1 25.6 + - - +
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Residues in contact with TYR 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F LEU* 3.5 37.0 - - + -
47F THR* 2.7 31.6 + - + +
69F PHE* 3.6 18.8 - + - +
73F LEU* 3.5 12.2 - - + +
121F LEU* 2.8 41.4 + - + +
122F ALA 3.9 2.9 - - - +
124F ARG* 1.3 72.4 - - - +
126F ALA* 1.3 53.5 + - - +
128F VAL* 3.3 1.0 + - - +
129F ALA* 2.6 40.0 + - - +
155F LEU* 4.2 9.3 - - + +
158F PHE* 3.8 35.4 - + + -
159F LEU* 4.2 13.7 - - + -
162F ILE* 3.6 28.9 - - + -
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Residues in contact with ALA 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122F ALA 2.8 20.2 + - - +
123F ASP* 3.4 7.6 - - - +
125F TYR* 1.3 77.1 - - - +
127F ILE* 1.3 57.4 + - + +
129F ALA* 4.1 0.4 - - - -
130F ASN* 2.7 48.1 + - - +
159F LEU* 4.0 23.3 - - + +
163F GLU* 5.7 1.6 - - - +
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Residues in contact with ILE 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F GLN* 4.3 10.5 - - - +
103F PRO* 4.5 17.7 - - + +
104F LEU* 3.8 24.9 - - + -
105F LYS* 5.5 3.4 - - + +
123F ASP* 3.1 17.9 + - + +
124F ARG* 3.2 14.5 + - - +
126F ALA* 1.3 76.7 - - + +
128F VAL* 1.3 57.5 + - - +
130F ASN* 4.1 3.6 - - - +
131F ASP* 3.0 33.0 + - + +
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Residues in contact with VAL 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F GLN* 3.4 35.4 - - + +
40F PHE* 3.6 28.3 - - + -
43F LEU* 3.9 17.3 - - + -
104F LEU* 3.9 17.9 - - + -
124F ARG 3.1 13.3 + - - +
125F TYR 3.8 3.1 - - - +
127F ILE* 1.3 71.4 - - - +
129F ALA* 1.3 66.2 + - - +
131F ASP* 3.7 0.2 - - - +
132F VAL* 2.9 25.1 + - - +
155F LEU* 3.4 23.1 - - + -
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Residues in contact with ALA 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125F TYR 2.6 25.2 + - - +
126F ALA* 3.7 6.1 - - - +
128F VAL* 1.3 73.6 - - - +
130F ASN* 1.3 63.8 + - - +
132F VAL* 3.3 6.9 - - - +
133F ARG* 3.0 30.4 + - - +
152F SER* 4.8 0.2 + - - -
155F LEU* 3.8 25.1 - - + +
156F ASP* 3.7 18.1 - - - +
159F LEU* 4.4 10.5 - - + -
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Residues in contact with ASN 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126F ALA* 2.7 40.0 + - - +
127F ILE* 4.1 3.1 - - - +
129F ALA* 1.3 74.2 - - - +
131F ASP* 1.3 60.3 + - - +
133F ARG* 2.4 36.7 + - - +
134F LYS* 3.3 46.1 + - - +
159F LEU* 5.3 5.0 - - - +
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Residues in contact with ASP 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F ARG* 2.9 40.3 + - - -
36F GLN* 3.7 2.3 - - - +
39F GLN* 3.0 26.0 + - - +
103F PRO* 5.8 0.5 - - - +
127F ILE* 3.0 22.3 + - + +
128F VAL 3.7 3.1 - - - +
130F ASN* 1.3 74.1 - - - +
132F VAL* 1.3 66.2 + - - +
134F LYS* 3.0 11.8 + - - +
135F ALA 3.0 17.2 + - - -
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Residues in contact with VAL 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F GLN* 3.6 32.5 + - - +
40F PHE* 4.3 19.5 - - + -
128F VAL 2.9 23.9 + - - +
129F ALA* 3.3 11.9 - - - +
131F ASP* 1.3 73.4 + - - +
133F ARG* 1.3 67.2 + - - +
135F ALA* 3.1 10.0 + - - +
136F ILE* 3.3 13.9 + - - +
148F LEU* 3.9 31.4 - - + +
151F ALA* 4.7 1.8 - - + -
152F SER* 3.9 20.9 - - - +
155F LEU* 4.8 2.9 - - + -
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Residues in contact with ARG 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129F ALA* 3.0 20.3 + - - +
130F ASN* 2.4 36.8 + - - +
131F ASP 3.1 0.2 - - - -
132F VAL* 1.3 77.2 - - - +
134F LYS* 1.3 67.1 + - + +
136F ILE* 3.4 24.8 - - + +
137F GLY 4.3 0.9 + - - -
152F SER* 3.6 16.6 - - - +
156F ASP* 2.6 45.7 + - - -
159F LEU* 6.2 0.4 - - - +
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Residues in contact with LYS 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130F ASN* 3.3 36.2 + - - +
131F ASP* 3.0 9.4 + - - +
133F ARG* 1.3 79.4 - - + +
135F ALA* 1.3 67.1 + - - +
136F ILE 3.0 3.3 + - - -
137F GLY* 3.2 11.6 + - - -
138F GLU* 3.2 14.3 + - - +
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Residues in contact with ALA 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F LEU* 3.9 20.3 - - + +
35F ARG* 4.3 3.4 - - - +
36F GLN* 3.6 22.4 - - - +
131F ASP 3.0 8.1 + - - +
132F VAL* 3.1 10.3 + - - +
134F LYS* 1.3 78.3 - - - +
136F ILE* 1.3 56.2 + - - +
138F GLU* 3.1 13.6 + - - +
139F ALA* 2.8 32.2 + - - +
148F LEU* 3.8 12.9 - - + +
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Residues in contact with ILE 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132F VAL 3.4 8.5 - - - +
133F ARG* 3.4 21.1 - - + +
134F LYS 3.0 0.4 - - - -
135F ALA* 1.3 80.2 - - - +
137F GLY* 1.3 63.6 + - - +
139F ALA* 3.2 17.9 + - - +
145F ALA* 4.0 14.5 - - + +
148F LEU* 4.0 22.2 - - + +
149F THR* 3.4 42.2 - - + +
152F SER* 3.7 19.1 - - - +
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Residues in contact with GLY 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133F ARG 4.3 0.8 + - - -
134F LYS* 3.2 7.2 + - - +
136F ILE* 1.3 81.0 - - - +
138F GLU* 1.3 60.2 + - - +
139F ALA 3.4 5.2 + - - +
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Residues in contact with GLU 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F LEU* 3.7 28.3 - - + +
35F ARG* 3.8 14.6 + - - -
134F LYS* 3.2 12.8 + - - +
135F ALA* 3.1 13.0 + - - +
137F GLY* 1.3 76.1 - - - +
139F ALA* 1.3 62.2 + - - +
140F LYS* 3.5 11.6 + - - +
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Residues in contact with ALA 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F LEU* 4.0 15.9 - - + -
135F ALA 2.8 10.6 + - - +
136F ILE 3.4 16.9 - - - +
137F GLY 3.2 6.0 - - - +
138F GLU* 1.3 77.2 - - - +
140F LYS* 1.3 64.8 + - - +
141F ASP 4.4 1.1 - - - +
144F THR* 4.3 7.2 - - + -
145F ALA* 4.0 29.9 - - + +
148F LEU* 4.1 5.4 - - + -
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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