Contacts of the helix formed by residues 112 - 137 (chain F) in PDB entry 2Y1M
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 112 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108F THR 3.0 8.5 + - - +
109F LEU* 3.0 22.3 + - + +
111F GLU* 1.3 72.6 - - - +
113F GLU* 1.3 65.1 + - - +
114F TYR 4.3 2.0 - - - +
115F PHE* 3.0 41.4 + - + +
116F ARG* 3.1 14.3 + - - +
169F PHE* 3.5 15.5 - - - -
174F PHE* 3.4 40.2 - - - -
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Residues in contact with GLU 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F PRO* 5.8 2.4 - - - +
48F PRO* 4.6 8.1 - - - +
111F GLU 2.9 8.8 + - - +
112F ASN* 1.3 72.4 - - - +
114F TYR* 1.3 62.9 + - - +
116F ARG* 3.3 32.1 + - - +
117F VAL* 3.1 38.0 + - - +
199F ILE* 4.3 19.2 - - + +
235F TYR* 5.1 7.9 + - - -
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Residues in contact with TYR 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112F ASN* 3.4 6.9 + - - +
113F GLU* 1.3 77.2 - - - +
115F PHE* 1.3 63.7 + - - +
117F VAL* 3.3 2.3 + - - +
118F PHE* 2.8 52.8 + + + -
164F GLU* 3.0 47.5 + - + +
165F LEU* 3.6 22.8 - - + -
168F ILE* 3.9 24.0 - - + -
169F PHE* 3.9 13.7 - + - -
174F PHE* 4.4 5.6 - - + -
198F THR* 3.7 33.0 - - + -
199F ILE* 4.1 31.0 - - + +
237F SER* 4.5 1.8 - - - -
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Residues in contact with PHE 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51F VAL* 4.1 20.6 - - + -
56F VAL* 5.0 8.3 - - + -
95F LEU* 3.5 29.8 - - + -
98F ILE* 4.5 11.7 - - + -
99F LEU* 5.4 5.6 - - + -
109F LEU* 3.7 42.8 - - + -
112F ASN* 3.0 29.7 + - + +
114F TYR* 1.3 79.3 - - - +
116F ARG* 1.3 67.2 + - - +
118F PHE* 3.4 3.1 + + + +
119F MET* 3.0 53.3 + - + +
165F LEU* 5.3 5.4 - - + -
169F PHE* 4.2 17.9 - + + -
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Residues in contact with ARG 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48F PRO* 3.1 37.4 + - + -
49F GLY 3.1 25.6 - - - +
50F THR* 3.5 14.4 - - - +
51F VAL* 3.5 20.3 - - + +
55F MET* 5.1 1.2 - - + +
110F GLY 3.2 13.9 + - - +
111F GLU* 3.0 33.7 + - - +
112F ASN 3.1 6.6 + - - +
113F GLU* 3.3 42.6 + - - +
115F PHE* 1.3 77.0 - - - +
117F VAL* 1.3 64.6 + - - +
119F MET* 2.9 5.9 + - - +
120F GLU* 2.9 22.7 + - + +
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Residues in contact with VAL 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48F PRO* 3.9 19.7 - - + -
113F GLU* 3.1 22.5 + - - +
114F TYR* 3.5 9.2 - - + +
116F ARG* 1.3 79.0 - - - +
118F PHE* 1.3 64.4 + - - +
120F GLU* 3.3 5.2 + - - +
121F ASN* 2.9 22.2 + - + +
199F ILE* 4.1 19.1 - - + -
233F ASN* 3.6 26.0 - - + +
235F TYR* 3.7 39.7 - - + -
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Residues in contact with PHE 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91F THR* 4.5 10.3 - - + -
95F LEU* 4.5 6.3 - - + -
114F TYR* 2.8 50.3 + + + +
115F PHE* 3.8 5.4 - + - +
117F VAL* 1.3 76.3 - - - +
119F MET* 1.3 64.5 + - + +
121F ASN* 3.4 7.2 + - - +
122F LEU* 2.7 55.1 + - + +
161F MET* 3.2 49.9 - - + +
164F GLU* 4.1 7.9 - - - +
165F LEU* 3.8 34.5 - - + -
233F ASN* 5.5 1.6 - - - +
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Residues in contact with MET 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51F VAL* 4.4 7.9 - - + -
55F MET* 3.8 18.8 - - + +
56F VAL* 3.7 27.8 - - + +
59F CYS* 3.6 32.8 - - + -
60F TRP* 5.6 0.2 - - - +
95F LEU* 3.9 24.9 - - + -
115F PHE* 3.0 38.7 + - + +
116F ARG 2.9 8.9 + - - +
118F PHE* 1.3 76.4 - - - +
120F GLU* 1.3 68.0 + - - +
122F LEU* 2.8 31.5 + - + +
123F MET* 2.8 15.4 + - - +
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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
----------------------------------------------------------
47F PRO 4.9 0.3 - - - -
48F PRO* 3.3 46.6 - - + +
55F MET* 3.9 13.1 - - + +
116F ARG* 2.9 14.9 + - + +
117F VAL* 3.7 8.0 - - - +
119F MET* 1.3 73.5 - - - +
121F ASN* 1.3 61.5 + - - +
123F MET* 3.4 3.8 + - - +
124F LYS* 3.2 37.7 + - + +
235F TYR* 5.0 6.4 - - - -
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Residues in contact with ASN 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117F VAL* 2.9 16.7 + - + +
118F PHE* 3.8 6.1 + - - +
120F GLU* 1.3 75.3 + - - +
122F LEU* 1.3 63.6 + - - +
124F LYS* 4.4 10.9 + - + +
125F LYS* 2.9 54.2 + - - +
161F MET* 3.8 26.3 - - - +
231F THR* 3.2 23.1 + - - +
232F CYS 3.8 0.2 - - - +
233F ASN* 3.6 27.7 - - + +
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Residues in contact with LEU 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59F CYS* 3.7 12.3 - - - -
63F MET* 4.4 17.3 - - + -
88F LEU* 6.0 0.9 - - + -
91F THR* 4.5 12.1 - - + -
95F LEU* 3.4 33.0 - - + -
118F PHE* 2.7 32.1 + - + +
119F MET* 2.8 27.3 + - + +
121F ASN* 1.3 72.8 - - - +
123F MET* 1.3 54.7 - - - +
125F LYS* 4.4 1.0 - - - +
126F THR* 2.6 39.8 + - - +
158F PHE* 4.7 7.4 - - + -
161F MET* 3.5 22.2 - - + -
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Residues in contact with MET 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55F MET* 3.8 28.0 - - + -
58F LYS* 3.8 25.1 - - + -
59F CYS* 3.8 31.6 - - + -
62F LEU* 3.6 16.8 - - + -
119F MET 2.8 12.4 + - - +
120F GLU* 3.8 5.4 - - - +
122F LEU* 1.3 76.5 - - - +
124F LYS* 1.3 60.3 + - + +
126F THR* 3.0 5.1 + - - -
127F LYS* 2.9 54.9 + - + +
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Residues in contact with LYS 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120F GLU* 3.2 28.3 + - + +
121F ASN* 3.9 12.7 + - + +
123F MET* 1.3 77.9 - - + +
125F LYS* 1.3 74.2 + - - +
127F LYS* 3.5 6.4 + - - +
128F GLN* 2.8 33.6 + - - +
232F CYS 5.1 4.2 + - - -
233F ASN* 5.5 5.5 + - - +
234F ASP* 5.6 4.0 + - - -
386F GLU* 5.9 2.7 - - - -
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Residues in contact with LYS 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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121F ASN* 2.9 44.2 + - - +
122F LEU 4.5 0.2 - - - +
124F LYS* 1.3 90.4 - - - +
126F THR* 1.3 54.0 + - - +
128F GLN* 3.7 19.7 + - - +
129F THR* 2.6 34.0 + - - -
154F LEU* 4.0 19.4 - - + +
157F ILE* 4.0 17.9 - - + -
158F PHE* 4.2 19.7 - - + -
161F MET* 4.1 9.2 - - + -
231F THR 3.6 8.7 - - - -
232F CYS* 3.2 34.7 + - - -
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Residues in contact with THR 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59F CYS* 5.4 0.8 - - - -
62F LEU* 3.4 47.6 - - + +
63F MET* 3.8 12.5 - - + +
66F VAL* 3.6 9.6 - - + +
88F LEU* 5.3 0.6 - - + +
122F LEU* 2.6 31.9 + - - +
123F MET* 3.0 8.6 + - - -
125F LYS* 1.3 76.5 - - - +
127F LYS* 1.3 60.9 + - - +
129F THR* 2.9 21.4 + - - -
130F ILE* 3.0 16.3 + - + +
158F PHE* 4.3 12.3 - - + -
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Residues in contact with LYS 127 (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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58F LYS* 5.0 8.8 - - - +
62F LEU* 3.7 21.5 - - + -
123F MET* 2.9 46.3 + - + +
124F LYS* 3.9 6.1 - - - +
126F THR* 1.3 76.5 - - - +
128F GLN* 1.3 51.7 + - - +
130F ILE* 2.7 16.7 + - + +
131F SER* 2.6 38.1 + - - -
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Residues in contact with GLN 128 (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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124F LYS* 2.8 23.9 + - - +
125F LYS* 3.7 26.7 + - - +
127F LYS* 1.3 72.1 - - - +
129F THR* 1.3 57.5 + - - +
131F SER* 4.2 7.1 - - - -
132F LEU* 3.3 24.9 + - - +
150F ASN* 4.9 4.2 + - - -
154F LEU* 3.9 28.1 - - + +
157F ILE* 6.3 0.4 - - - +
384F CYS 5.1 1.8 + - - +
385F ALA 3.7 10.9 + - - -
386F GLU* 3.2 52.9 - - + +
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Residues in contact with THR 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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66F VAL* 3.8 27.1 - - + -
125F LYS 2.6 19.5 + - - -
126F THR 2.9 9.2 + - - -
128F GLN* 1.3 77.1 - - - +
130F ILE* 1.3 64.5 + - - +
131F SER 3.3 0.2 - - - -
132F LEU* 3.6 5.0 + - + +
133F PHE* 3.0 35.7 + - + -
151F LEU* 3.3 34.1 - - + -
154F LEU* 3.8 15.9 - - + +
158F PHE* 3.8 13.3 - - + -
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Residues in contact with ILE 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62F LEU* 3.8 44.9 - - + +
65F LYS* 4.6 16.8 - - + -
66F VAL* 3.6 13.9 - - + +
69F LEU* 4.6 16.9 - - + +
126F THR 3.0 17.0 + - - +
127F LYS* 2.7 16.8 + - + +
129F THR* 1.3 76.7 - - - +
131F SER* 1.3 62.1 + - - +
133F PHE* 3.2 7.3 + - - +
134F LYS* 3.1 22.2 + - + +
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Residues in contact with SER 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127F LYS 2.6 18.4 + - - -
128F GLN* 4.2 8.8 + - - +
130F ILE* 1.3 69.8 - - - +
132F LEU* 1.3 60.7 + - - -
133F PHE 3.0 2.0 - - - -
134F LYS* 2.8 26.4 + - - +
135F GLU* 2.9 38.8 + - - +
386F GLU* 5.3 4.1 + - - -
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Residues in contact with LEU 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128F GLN 3.3 19.2 + - - +
129F THR 3.8 4.9 - - - +
130F ILE 3.4 0.2 - - - -
131F SER* 1.3 78.5 + - - +
133F PHE* 1.3 57.7 + - + +
135F GLU* 4.9 2.9 - - - -
136F GLY* 3.1 21.4 + - - +
140F MET* 3.3 14.4 - - + +
147F PRO* 3.4 40.8 - - + +
150F ASN* 3.7 20.0 - - + +
151F LEU* 3.5 37.0 - - + +
154F LEU* 4.1 10.8 - - + -
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Residues in contact with PHE 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310D ALA* 4.1 4.9 - - - +
66F VAL* 5.1 0.9 - - + -
69F LEU* 3.8 58.3 - - + -
70F CYS* 4.1 7.9 - - - -
75F LEU* 3.7 14.8 - - + -
129F THR* 3.0 28.0 + - + -
130F ILE 3.2 8.2 + - - +
131F SER 3.0 0.8 - - - -
132F LEU* 1.3 76.5 - - + +
134F LYS* 1.3 57.0 + - - +
135F GLU 3.2 5.2 - - - -
137F LYS* 3.1 26.9 + - - +
140F MET* 3.4 39.6 - - + +
141F TYR* 5.7 3.8 - + - -
151F LEU* 3.8 35.0 - - + -
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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
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310D ALA* 3.7 20.6 - - - +
311D ASP* 3.5 42.5 + - - +
130F ILE* 3.1 14.8 + - + +
131F SER* 2.8 11.9 + - - +
133F PHE* 1.3 77.6 - - - +
135F GLU* 1.3 70.8 + - - +
137F LYS* 3.2 24.4 + - - -
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Residues in contact with GLU 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131F SER* 2.9 36.0 + - - +
132F LEU* 4.7 2.6 - - - +
134F LYS* 1.3 98.1 + - + +
136F GLY* 1.3 65.9 + - - +
137F LYS* 3.1 13.2 + - - +
139F ARG* 5.2 3.3 + - - -
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Residues in contact with GLY 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132F LEU* 3.1 18.7 + - - +
135F GLU* 1.3 77.3 - - - +
137F LYS* 1.3 63.5 + - - +
139F ARG* 2.8 39.0 + - - +
140F MET* 4.1 2.5 - - - -
147F PRO* 4.2 23.3 - - - -
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Residues in contact with LYS 137 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310D ALA* 3.4 23.3 - - + -
311D ASP* 2.9 38.4 + - - -
133F PHE 3.1 15.4 + - - -
134F LYS 3.2 16.9 + - - +
135F GLU* 3.1 11.4 + - - +
136F GLY* 1.3 77.9 - - - +
138F GLU* 1.3 76.4 + - + +
139F ARG* 5.7 0.2 - - + -
140F MET* 2.8 37.1 + - - +
141F TYR* 4.2 6.4 - - - -
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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