Contacts of the helix formed by residues 109 - 133 (chain C) in PDB entry 2FYU
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 PHE 109 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C SER 3.2 15.1 + - - +
107C TYR 3.2 2.6 - - - -
108C THR* 1.3 74.5 + - - +
110C LEU* 1.3 64.9 + - - +
111C GLU* 3.3 3.9 + - - -
112C THR* 3.3 18.0 + - - +
113C TRP* 3.0 22.2 + - - +
200C LEU* 3.9 16.4 - - + -
203C THR* 3.3 32.8 - - + -
204C GLY 3.2 26.5 - - - -
205C SER 4.2 1.3 - - - -
206C ASN* 3.6 17.3 - - + -
313C ARG* 3.3 34.1 - - - -
382C HEM 3.9 13.7 - - + -
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Residues in contact with LEU 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C TYR 4.0 10.3 - - - +
108C THR* 3.1 15.2 + - - +
109C PHE* 1.3 69.7 - - - +
111C GLU* 1.3 65.8 + - + +
113C TRP* 3.5 3.2 - - - +
114C ASN* 2.8 48.4 + - - +
305C PRO* 4.6 22.2 - - + +
306C LEU* 6.3 2.7 - - + -
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Residues in contact with GLU 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C PHE* 3.4 1.2 - - - -
110C LEU* 1.3 87.6 + - + +
112C THR* 1.3 65.6 + - - +
114C ASN* 3.5 4.9 + - - +
115C ILE* 3.1 32.7 + - + +
199C PHE* 3.7 47.2 - - + +
202C GLU* 5.9 1.4 - - - +
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Residues in contact with THR 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C PHE* 3.6 19.4 - - + +
111C GLU* 1.3 78.6 - - - +
113C TRP* 1.3 60.3 + - - +
115C ILE* 3.5 1.1 + - - -
116C GLY 3.1 4.9 + - - -
196C HIS* 2.9 40.7 + - + +
199C PHE* 3.3 12.0 + - - +
200C LEU* 3.2 43.5 + - + -
382C HEM 3.7 34.5 - - + -
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Residues in contact with TRP 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C HIS 5.6 0.2 - - - -
98C VAL* 4.2 16.8 - - + -
101C GLY* 4.0 21.1 - - - -
102C LEU* 4.2 15.7 - - + -
107C TYR* 3.5 36.6 - + + +
109C PHE 3.0 17.1 + - - +
110C LEU 3.5 3.6 - - - +
112C THR* 1.3 78.6 - - - +
114C ASN* 1.3 68.0 + - - +
116C GLY* 3.0 16.3 + - - -
117C VAL* 3.1 20.2 + - + +
301C LEU* 2.8 49.5 + - + -
304C ILE* 4.6 7.4 - - + -
305C PRO* 3.8 17.7 - - + +
382C HEM 3.5 53.6 - - + +
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Residues in contact with ASN 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C LEU* 2.8 32.3 + - + +
111C GLU* 3.5 6.3 + - - +
113C TRP* 1.3 81.4 - - - +
115C ILE* 1.3 61.7 + - + +
117C VAL* 3.6 8.6 - - - +
118C ILE* 3.4 26.3 + - - +
302C ALA* 4.2 33.2 + - - +
305C PRO* 5.5 1.0 - - - +
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Residues in contact with ILE 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C GLU* 3.1 22.7 + - - +
112C THR 3.7 3.1 - - - +
114C ASN* 1.3 74.6 - - + +
116C GLY* 1.3 52.9 + - - +
117C VAL 3.3 0.2 - - - -
118C ILE* 3.1 14.4 + - + +
119C LEU* 2.8 33.1 + - + +
192C ILE* 3.7 27.3 - - + +
195C VAL* 4.5 13.9 - - + -
196C HIS* 3.6 35.4 - - + +
199C PHE* 4.5 17.5 - - + -
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Residues in contact with GLY 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C THR 3.1 7.3 + - - -
113C TRP 3.0 9.3 + - - -
115C ILE* 1.3 75.9 - - - +
117C VAL* 1.3 50.2 + - - +
119C LEU* 3.2 5.7 + - - +
120C LEU 2.8 29.3 + - - -
196C HIS* 3.8 12.0 + - - -
382C HEM 3.1 39.4 - - - +
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Residues in contact with VAL 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C TRP* 3.1 29.5 + - + +
114C ASN* 3.6 13.0 - - - +
116C GLY* 1.3 71.7 - - - +
118C ILE* 1.3 62.3 + - + +
120C LEU* 3.0 10.0 + - + +
121C LEU* 2.9 45.0 + - + +
298C ILE* 5.2 7.9 - - + +
299C LEU* 5.1 8.3 - - + -
301C LEU* 4.1 18.4 - - + -
302C ALA* 4.3 20.2 - - + +
382C HEM 3.7 13.7 - - + -
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Residues in contact with ILE 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C ASN* 3.4 16.4 + - - +
115C ILE* 3.1 18.5 + - + +
117C VAL* 1.3 74.3 - - + +
119C LEU* 1.3 56.7 + - - +
121C LEU* 3.2 21.6 + - + +
122C THR* 2.6 42.9 + - - +
192C ILE* 4.0 26.9 - - + -
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Residues in contact with LEU 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C LEU* 5.3 0.2 - - - -
115C ILE* 2.8 20.5 + - + +
116C GLY* 3.2 8.5 + - - +
118C ILE* 1.3 71.6 - - - +
120C LEU* 1.3 55.2 + - - +
122C THR* 3.3 4.3 + - - -
123C VAL* 3.0 35.9 + - - +
189C ILE* 3.6 34.1 - - + +
192C ILE* 3.8 13.5 - - + -
193C ALA* 3.8 11.2 - - - +
196C HIS* 3.8 36.3 - - + +
382C HEM 3.6 46.9 - - + -
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Residues in contact with LEU 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C PHE* 4.5 1.1 - - + -
94C LEU* 3.7 32.5 - - + -
95C TYR* 4.3 20.4 - - + -
98C VAL* 4.7 11.0 - - + -
116C GLY 2.8 15.6 + - - +
117C VAL* 3.0 9.6 + - + +
119C LEU* 1.3 72.7 - - - +
121C LEU* 1.3 56.0 + - - +
123C VAL* 3.4 3.0 + - - +
124C MET* 3.1 51.3 + - + +
298C ILE* 4.1 17.7 - - + -
301C LEU* 3.8 29.4 - - + -
382C HEM 3.9 10.2 - - + +
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Residues in contact with LEU 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C VAL* 2.9 33.9 + - + +
118C ILE* 3.7 20.4 - - + +
120C LEU* 1.3 71.8 - - - +
122C THR* 1.3 56.8 + - - +
124C MET* 3.8 11.8 - - + +
125C ALA* 3.2 26.9 + - - +
298C ILE* 3.9 28.0 - - + -
299C LEU* 4.1 28.3 - - + -
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Residues in contact with THR 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C ILE* 2.6 35.5 + - - +
119C LEU* 3.6 5.6 - - - -
121C LEU* 1.3 75.4 - - - +
123C VAL* 1.3 55.4 + - - +
125C ALA* 3.7 4.9 + - + +
126C THR* 2.7 35.6 + - - -
185C LEU* 3.7 28.0 - - + +
188C ILE* 4.9 9.4 - - + -
189C ILE* 3.7 23.6 - - + -
192C ILE* 4.6 6.7 - - + +
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Residues in contact with VAL 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C PHE* 3.8 39.7 - - + -
91C PHE* 4.0 13.7 - - + -
94C LEU* 3.7 27.1 - - + -
119C LEU 3.0 27.3 + - - +
120C LEU 4.7 0.2 - - - +
122C THR* 1.3 72.4 - - - +
124C MET* 1.3 56.4 + - - +
126C THR* 3.2 7.1 + - - -
127C ALA* 2.8 34.1 + - - +
189C ILE* 4.1 14.1 - - + -
381C HEM 4.5 7.8 - - + +
382C HEM 4.3 10.3 - - + -
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Residues in contact with MET 124 (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 PHE* 3.7 25.8 - - + -
95C TYR* 5.4 4.7 - - - +
120C LEU* 3.1 38.9 + - + +
121C LEU* 3.8 11.2 - - + +
123C VAL* 1.3 75.6 - - - +
125C ALA* 1.3 56.2 + - - +
128C PHE* 3.0 27.3 + - - +
274C PHE* 4.0 15.5 - - + -
298C ILE* 3.8 41.1 - - + -
400C FDN 3.3 42.1 - - - -
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Residues in contact with ALA 125 (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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121C LEU 3.2 17.5 + - - +
122C THR* 3.9 6.5 - - - +
124C MET* 1.3 76.3 - - - +
126C THR* 1.3 63.7 + - - +
128C PHE* 3.6 9.5 + - + +
129C MET* 3.2 32.9 + - + +
185C LEU* 4.4 16.2 - - + -
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Residues in contact with THR 126 (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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122C THR 2.7 23.0 + - - -
123C VAL* 3.2 9.4 + - - -
125C ALA* 1.3 77.5 - - - +
127C ALA* 1.3 56.4 + - - +
129C MET* 3.3 1.8 + - - -
130C GLY 3.1 9.0 + - - -
182C HIS* 2.7 35.5 + - + +
185C LEU* 3.4 18.4 - - + +
186C PRO* 3.7 20.4 - - + -
189C ILE* 3.3 12.2 - - + +
381C HEM 3.6 33.4 - - + -
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Residues in contact with ALA 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C ALA* 5.2 1.1 - - + -
91C PHE* 3.6 24.7 - - + -
123C VAL 2.8 19.4 + - - +
124C MET 4.1 1.8 - - - +
126C THR* 1.3 71.3 - - - +
128C PHE* 1.3 64.9 + - - +
130C GLY 4.0 0.2 - - - -
131C TYR* 3.2 24.1 + - - +
273C TYR* 3.9 11.4 - - - +
381C HEM 3.9 31.6 - - + +
400C FDN 4.0 5.7 - - + +
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Residues in contact with PHE 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C MET 3.0 18.2 + - - +
125C ALA* 3.7 8.3 - - + +
127C ALA* 1.3 75.1 - - - +
129C MET* 1.3 74.6 + - + +
131C TYR* 3.3 13.2 + - - +
132C VAL* 3.4 24.1 + - + +
142C GLY 3.9 2.2 - - - -
143C ALA* 3.8 18.2 - - - -
146C ILE* 3.6 44.6 - - + -
147C THR* 3.9 13.7 - - + -
164C ILE* 5.8 1.1 - - + -
178C PHE* 3.5 35.2 - + - -
400C FDN 3.5 38.1 - - + -
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Residues in contact with MET 129 (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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125C ALA* 3.2 20.9 + - + +
126C THR* 3.3 3.8 + - - +
128C PHE* 1.3 87.2 - - + +
130C GLY* 1.3 60.9 + - - +
132C VAL* 3.5 11.8 - - - +
133C LEU* 3.4 20.8 - - - +
164C ILE* 5.1 5.6 - - + -
178C PHE* 3.6 56.4 - - + +
181C PHE* 3.6 39.9 - - + -
182C HIS* 4.0 7.2 - - + +
185C LEU* 4.6 12.8 - - + -
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Residues in contact with GLY 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C THR 3.1 10.7 + - - -
127C ALA 3.8 1.1 + - - -
129C MET* 1.3 73.6 - - - +
131C TYR* 1.3 58.2 - - - +
133C LEU* 3.0 29.4 + - - +
134C PRO* 3.5 1.0 - - - +
182C HIS* 3.2 29.4 + - - -
381C HEM 3.4 22.0 - - - +
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Residues in contact with TYR 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C ALA 3.2 19.2 + - - +
128C PHE 3.3 4.7 + - - +
130C GLY* 1.3 70.8 - - - +
132C VAL* 1.3 55.5 + - - +
134C PRO* 3.4 8.8 - - - +
138C MET* 3.7 34.7 - - + +
139C SER* 2.6 35.7 + - - -
251C GLY* 5.9 1.3 - - - -
252C ASP* 3.9 14.7 + - - +
255C ASN* 3.9 17.4 - - + +
269C LYS 5.6 1.0 + - - -
271C GLU* 3.3 36.7 + - + -
381C HEM 3.7 33.0 - - + -
400C FDN 3.6 44.6 - + + -
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Residues in contact with VAL 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C PHE* 3.4 24.2 - - + +
129C MET 3.5 8.7 - - - +
131C TYR* 1.3 75.1 - - - +
133C LEU* 1.3 63.7 + - - +
135C TRP* 3.1 44.6 + - + -
139C SER* 3.3 16.7 - - - +
143C ALA* 3.7 24.9 - - + +
170C VAL* 5.2 1.3 - - + -
174C THR* 5.8 0.4 - - + -
175C LEU* 4.5 7.4 - - + -
178C PHE* 3.7 34.5 - - + -
400C FDN 4.8 2.0 - - - +
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Residues in contact with LEU 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C TYR* 2.6 37.0 + - + +
62C ALA* 3.7 3.5 - - - +
129C MET 3.4 19.1 - - - +
130C GLY* 3.0 13.8 + - - +
132C VAL* 1.3 73.6 - - - +
134C PRO* 1.4 60.9 - - + +
135C TRP 3.2 1.6 + - - -
175C LEU* 3.5 20.9 - - + +
178C PHE* 3.7 5.6 - - + -
179C PHE* 3.4 54.3 - - + +
182C HIS* 3.8 22.7 - - + -
381C HEM 3.8 25.8 - - + -
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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