Contacts of the helix formed by residues 102 - 124 (chain F) in PDB entry 2OCP
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 GLU 102 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98F MET* 2.9 13.3 + - - +
99F MET 3.7 2.5 - - - -
101F ARG* 1.3 86.9 - - + +
103F PRO* 1.3 60.5 - - - +
104F ALA 3.2 2.2 - - - -
105F ARG* 2.8 35.9 + - + +
106F TRP* 2.9 28.2 + - + -
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Residues in contact with PRO 103 (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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99F MET* 3.1 21.0 - - + +
100F TYR 3.6 10.8 - - - +
101F ARG 3.5 8.3 - - - +
102F GLU* 1.3 88.2 - - - +
104F ALA* 1.3 63.9 + - + +
107F SER* 2.4 38.5 + - - +
155F LEU* 5.3 0.4 - - + -
160F SER* 3.2 22.7 - - - +
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Residues in contact with ALA 104 (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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105E ARG* 3.2 19.6 + - - -
102F GLU 3.2 1.4 + - - -
103F PRO* 1.3 83.2 - - + +
105F ARG* 1.3 57.6 + - + +
107F SER 4.9 0.2 - - - -
159F GLY 4.8 9.4 - - - +
160F SER* 3.5 18.3 - - - +
165F GLU* 4.6 3.1 - - - +
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Residues in contact with ARG 105 (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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104E ALA 3.1 24.7 + - - -
105E ARG* 3.3 48.4 + - - +
165E GLU* 3.3 14.6 + - - -
102F GLU* 2.8 27.8 + - + +
104F ALA* 1.3 82.8 - - - +
106F TRP* 1.3 116.6 + - + +
107F SER 3.8 0.7 - - - -
108F TYR* 5.4 1.0 + - - +
109F THR* 4.3 5.9 + - - -
165F GLU* 5.1 2.7 - - - +
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Residues in contact with TRP 106 (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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162E SER* 4.1 12.6 - - - -
164E ILE* 5.4 5.8 - - + -
165E GLU* 3.8 22.4 - - + -
95F LEU* 4.5 7.6 - - + -
98F MET* 3.8 43.7 - - + +
99F MET* 3.9 23.1 - - - +
102F GLU* 2.9 21.9 + - + -
105F ARG* 1.3 132.6 - - + +
107F SER* 1.3 59.7 + - - +
108F TYR 3.4 2.0 - - - -
109F THR* 3.4 35.4 + - + -
110F PHE* 2.8 31.2 + - - +
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Residues in contact with SER 107 (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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99F MET* 3.9 7.7 - - - +
103F PRO* 2.4 35.1 + - - +
104F ALA 4.9 0.2 - - - -
105F ARG 3.8 0.6 - - - -
106F TRP* 1.3 75.5 - - - +
108F TYR* 1.3 65.2 + - - +
110F PHE* 3.1 7.5 + - - +
111F GLN* 2.9 26.7 + - - +
155F LEU* 3.8 23.0 - - - +
160F SER* 3.4 23.4 - - - -
161F LEU* 3.9 6.5 - - - -
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Residues in contact with TYR 108 (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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108E TYR* 4.0 13.0 - + - -
109E THR* 3.7 25.6 - - + -
112E THR* 2.6 33.0 + - - -
105F ARG 5.9 0.9 - - - +
106F TRP 3.4 0.6 - - - -
107F SER* 1.3 77.4 - - - +
109F THR* 1.3 70.7 + - - +
111F GLN* 3.0 14.7 + - + +
112F THR* 3.0 39.2 + - + +
160F SER 5.2 0.2 + - - -
161F LEU* 3.2 15.2 - - + +
165F GLU* 3.3 58.3 + - + +
168F ILE* 3.0 16.7 - - + +
169F TYR* 3.9 20.9 - + + -
172F TRP* 4.3 4.5 - - - -
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Residues in contact with THR 109 (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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108E TYR* 3.7 27.2 - - + -
164E ILE* 4.6 3.4 - - + -
165E GLU* 4.5 3.6 + - + -
168E ILE* 3.4 26.7 - - + -
95F LEU* 4.4 7.4 - - + -
105F ARG* 4.3 6.5 + - - -
106F TRP* 3.4 43.0 + - + +
107F SER 3.3 0.4 - - - -
108F TYR* 1.3 79.4 - - - +
110F PHE* 1.3 61.6 + - - +
112F THR* 2.8 24.9 + - - -
113F PHE* 3.2 7.3 + - - +
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Residues in contact with PHE 110 (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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75F TRP* 4.1 38.4 - + + -
95F LEU* 3.8 36.1 - - + -
96F LEU* 3.7 31.6 - - + -
99F MET* 4.0 15.9 - - + -
106F TRP 2.8 21.4 + - - +
107F SER* 3.1 4.9 + - - +
109F THR* 1.3 73.7 - - - +
111F GLN* 1.3 65.8 + - - +
113F PHE* 2.9 14.1 + + - +
114F SER* 2.9 21.2 + - - -
301F DTP 3.3 51.8 - + - -
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Residues in contact with GLN 111 (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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107F SER 2.9 11.7 + - - +
108F TYR* 3.5 11.7 - - + +
110F PHE* 1.3 76.8 - - - +
112F THR* 1.3 57.9 + - - +
114F SER* 3.1 8.3 + - - -
115F PHE* 2.8 33.9 + - - +
147F ASP* 3.4 10.5 - - - +
151F PHE* 3.8 0.2 - - - +
152F ALA* 3.7 32.5 - - + -
155F LEU* 3.1 26.8 - - + +
161F LEU* 5.1 4.3 - - + -
169F TYR* 3.7 18.6 - - + -
301F DTP 2.8 49.1 + - - -
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Residues in contact with THR 112 (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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108E TYR* 2.6 27.6 + - + +
112E THR* 5.2 2.0 - - + -
168E ILE* 3.6 2.8 - - - +
172E TRP* 3.0 31.2 + - - +
108F TYR* 3.0 52.6 + - + +
109F THR 2.8 13.5 + - - -
111F GLN* 1.3 77.0 - - + +
113F PHE* 1.3 60.3 + - - +
115F PHE* 4.6 4.5 - - - -
116F LEU* 3.3 13.2 + - - +
169F TYR* 5.2 5.6 - - + -
172F TRP* 6.3 1.1 - - + -
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Residues in contact with PHE 113 (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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167E HIS* 4.6 17.7 - + - -
168E ILE* 3.7 30.3 - - + -
171E ASP* 5.0 11.9 - - - -
71F PRO* 5.8 0.4 - - + -
74F THR* 3.9 26.5 - - + -
75F TRP* 3.1 38.6 - + - -
78F ILE* 4.5 11.4 - - + -
95F LEU* 3.9 25.1 - - + -
109F THR 3.2 4.0 + - - +
110F PHE* 2.9 9.2 + + - +
112F THR* 1.3 81.6 + - - +
114F SER* 1.3 63.9 + - - +
116F LEU* 3.7 8.4 + - + +
117F SER* 3.2 27.7 + - - -
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Residues in contact with SER 114 (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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75F TRP* 4.3 17.4 - - - +
110F PHE* 2.9 28.3 + - - -
111F GLN* 3.1 19.2 + - - -
113F PHE* 1.3 75.3 - - - +
115F PHE* 1.3 61.8 + - - +
117F SER* 3.3 5.7 + - - -
118F ARG* 2.9 44.4 + - - +
147F ASP* 2.5 24.1 + - - -
301F DTP 3.7 0.2 + - - -
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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
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172E TRP* 3.6 33.0 - + - -
111F GLN 2.8 18.6 + - - +
112F THR* 4.2 2.9 - - - +
114F SER* 1.3 78.2 + - - +
116F LEU* 1.3 61.7 + - - +
118F ARG* 3.3 1.9 + - - +
119F LEU* 2.9 32.1 + - + +
144F VAL* 3.7 29.6 - - + -
147F ASP* 3.5 19.7 - - + +
169F TYR* 4.3 9.6 - + + -
172F TRP* 4.6 4.0 - - + -
173F HIS* 3.3 56.8 - + - -
176F LEU* 4.2 11.4 - - + -
177F LEU* 4.2 13.2 - - + -
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Residues in contact with LEU 116 (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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171E ASP* 3.1 40.2 - - + +
172E TRP* 3.5 47.5 - - + +
175E PHE* 3.5 35.4 - - + -
112F THR 3.3 16.5 + - - +
113F PHE* 3.9 11.7 - - + +
115F PHE* 1.3 79.1 - - - +
117F SER* 1.3 59.7 + - - +
119F LEU* 3.2 5.0 + - + +
120F LYS* 2.8 37.8 + - + +
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Residues in contact with SER 117 (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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70F GLU* 5.2 0.2 + - - -
71F PRO* 3.0 37.2 - - - +
75F TRP* 4.7 5.2 - - - -
113F PHE* 3.2 22.3 + - - -
114F SER* 3.5 7.0 - - - -
115F PHE 3.2 0.2 - - - -
116F LEU* 1.3 81.8 - - - +
118F ARG* 1.3 64.5 + - - +
120F LYS* 3.2 10.9 + - - +
121F VAL* 3.2 22.9 + - - +
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Residues in contact with ARG 118 (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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70F GLU* 3.0 40.7 + - - +
71F PRO* 6.4 0.2 - - - -
75F TRP* 3.9 10.7 - - + -
114F SER* 2.9 24.6 + - - +
115F PHE* 3.8 3.6 - - - +
117F SER* 1.3 74.0 - - - +
119F LEU* 1.3 59.1 + - - +
121F VAL* 3.0 27.2 - - + +
122F GLN* 3.2 14.0 + - - +
142F ARG* 3.8 20.5 - - - +
143F SER* 3.4 23.6 + - - +
144F VAL* 3.9 17.5 - - + +
147F ASP* 2.8 38.7 + - - +
151F PHE* 4.8 0.6 - - - -
301F DTP 2.8 48.5 + - - -
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Residues in contact with LEU 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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172E TRP* 5.1 2.9 - - + -
175E PHE* 4.2 13.0 - - + -
115F PHE* 2.9 26.4 + - + +
116F LEU* 3.6 4.9 - - + +
118F ARG* 1.3 73.8 - - - +
120F LYS* 1.3 67.1 + - - +
122F GLN* 3.2 2.5 + - - -
123F LEU* 3.1 39.7 + - + +
144F VAL* 3.6 16.3 - - + +
176F LEU* 4.0 23.6 - - + -
177F LEU* 4.2 9.9 - - + -
180F PHE* 4.0 28.3 - - + -
184F ILE* 3.9 27.1 - - + -
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Residues in contact with LYS 120 (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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171E ASP* 2.7 33.9 + - - -
175E PHE* 3.6 53.1 - - + +
116F LEU* 2.8 25.1 + - + +
117F SER* 3.5 9.0 - - - +
119F LEU* 1.3 76.0 - - - +
121F VAL* 1.3 64.1 + - - +
123F LEU* 2.9 13.9 + - - +
124F GLU* 3.1 20.3 + - - +
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Residues in contact with VAL 121 (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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68F ALA* 3.6 29.4 - - + -
69F THR* 4.8 11.7 - - + +
70F GLU* 6.1 0.9 - - - +
71F PRO* 6.4 2.9 - - + -
117F SER 3.2 7.0 + - - +
118F ARG* 3.0 23.8 - - + +
120F LYS* 1.3 79.4 - - - +
122F GLN* 1.3 66.8 + - + +
123F LEU 3.4 0.3 + - - -
124F GLU* 3.5 34.1 + - - +
138F GLN* 5.6 1.9 + - - -
140F PHE* 3.6 22.0 - - + -
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Residues in contact with GLN 122 (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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40F ARG* 2.9 35.2 + - - +
118F ARG* 3.5 16.2 - - - +
119F LEU* 3.2 6.6 + - - +
120F LYS 3.2 0.8 - - - -
121F VAL* 1.3 81.6 - - - +
123F LEU* 1.3 60.4 + - - +
124F GLU 4.3 2.7 - - - +
140F PHE* 3.8 24.5 - - + -
142F ARG 4.9 0.7 - - - +
143F SER* 4.1 6.6 - - - -
144F VAL* 3.4 32.9 + - - +
145F TYR* 4.5 3.6 - - - -
183F ARG 3.3 8.8 - - - +
184F ILE* 3.2 34.7 + - + +
186F LEU* 3.8 25.4 - - + +
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Residues in contact with LEU 123 (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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175E PHE* 3.7 28.0 - - + -
179E GLU* 4.3 9.2 - - - +
119F LEU* 3.1 17.2 + - + +
120F LYS* 2.9 9.1 + - - +
122F GLN* 1.3 77.3 - - - +
124F GLU* 1.3 67.5 + - - +
125F PRO* 4.1 3.8 - - - +
180F PHE* 3.9 40.6 - - + -
183F ARG* 3.7 48.7 + - + +
184F ILE* 3.6 27.1 - - + -
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Residues in contact with GLU 124 (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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40F ARG* 5.5 1.2 + - - -
120F LYS* 3.1 15.3 + - + +
121F VAL* 3.5 38.1 + - - +
122F GLN 4.3 4.2 - - - +
123F LEU* 1.3 82.0 - - - +
125F PRO* 1.3 77.5 - - + +
126F PHE* 4.0 5.9 + - - -
138F GLN* 5.4 2.9 + - - +
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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
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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) + - + + + + + -
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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