Contacts of the helix formed by residues 112 - 133 (chain C) in PDB entry 4CFE
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 112 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110C ARG 4.3 0.4 + - - -
111C VAL* 1.3 72.9 - - - +
113C GLU* 1.3 56.5 + - + +
114C MET* 3.0 33.5 - - + +
115C GLU* 2.8 16.8 + - + +
116C ALA 2.6 32.4 + - - -
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Residues in contact with GLU 113 (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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111C VAL 3.4 2.4 + - - -
112C GLU* 1.3 74.3 - - + +
114C MET* 1.3 66.4 + - + +
116C ALA* 3.7 10.5 - - - -
117C ARG* 3.1 40.7 + - - +
208C LEU* 4.2 15.9 - - + +
238C ASN* 3.3 20.0 + - - -
241C VAL* 5.2 0.5 - - - +
267C TRP* 3.2 28.4 + - + -
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Residues in contact with MET 114 (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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112C GLU* 3.0 29.5 + - + +
113C GLU* 1.3 86.9 - - + +
115C GLU* 1.3 59.0 + - - +
117C ARG* 4.3 11.7 + - - +
118C ARG* 4.0 14.7 + - - +
271C ASP* 4.1 21.5 - - - +
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Residues in contact with GLU 115 (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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104C TYR* 2.9 33.7 + - - -
108C HIS* 5.0 1.2 - - - -
111C VAL* 3.7 13.0 - - + +
112C GLU* 2.8 16.5 + - + +
114C MET* 1.3 78.8 - - + +
116C ALA* 1.3 64.3 + - - +
117C ARG 3.2 2.0 - - - -
118C ARG* 3.3 25.1 + - - +
119C LEU* 3.1 25.8 + - + +
151C MET* 3.3 21.8 - - - +
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Residues in contact with ALA 116 (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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111C VAL* 3.6 19.2 - - + +
112C GLU 2.6 20.1 + - - +
113C GLU* 3.8 2.2 - - - -
115C GLU* 1.3 74.0 - - - +
117C ARG* 1.3 61.0 + - - +
119C LEU* 4.7 0.7 - - - -
120C PHE* 3.0 21.5 + - - +
204C LEU* 4.8 0.6 - - + +
207C LEU* 3.3 26.2 - - + +
208C LEU* 3.8 29.4 - - + -
267C TRP* 4.7 2.9 - - + -
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Residues in contact with ARG 117 (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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113C GLU* 3.1 36.5 + - - +
114C MET* 4.3 12.2 + - - +
116C ALA* 1.3 77.8 - - - +
118C ARG* 1.3 56.6 + - - +
120C PHE* 3.2 2.9 + - - +
121C GLN* 2.8 48.4 + - + +
267C TRP* 2.4 91.7 + - + +
268C PHE* 4.9 1.6 - - + -
270C GLN* 3.2 47.0 + - - +
271C ASP* 4.4 14.7 + - - +
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Residues in contact with ARG 118 (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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114C MET 4.0 10.8 + - - +
115C GLU* 3.3 25.5 + - - +
117C ARG* 1.3 80.7 - - - +
119C LEU* 1.3 74.2 + - - +
121C GLN* 3.3 16.6 + - - +
122C GLN* 3.0 56.5 + - + +
150C HIS 4.3 3.4 + - - -
151C MET* 2.7 45.6 + - - +
152C ASN* 3.5 7.5 + - - -
271C ASP 6.0 0.9 - - - +
273C PRO* 5.8 7.4 - - + -
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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
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101C LEU* 3.9 26.0 - - + -
104C TYR* 4.8 6.3 - - + -
111C VAL* 4.8 2.5 - - + -
115C GLU* 3.1 26.0 + - + +
116C ALA 3.9 4.3 - - - +
118C ARG* 1.3 85.0 - - - +
120C PHE* 1.3 57.9 + - - +
122C GLN* 3.4 13.3 + - - +
123C ILE* 3.0 40.0 + - + +
147C LEU* 4.8 5.4 - - + -
151C MET* 3.7 41.1 - - + +
153C ALA* 4.3 12.9 - - + +
207C LEU* 4.2 17.0 - - + -
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Residues in contact with PHE 120 (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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116C ALA 3.0 18.2 + - - +
117C ARG* 3.5 6.3 - - - +
119C LEU* 1.3 74.9 - - - +
121C GLN* 1.3 59.6 + - - +
123C ILE* 3.8 9.4 - - + +
124C LEU* 3.0 39.0 + - + +
200C CYS* 3.4 32.1 - - + -
203C ILE* 5.3 6.5 - - + -
204C LEU* 3.7 36.3 - - + -
207C LEU* 4.5 3.7 - - + +
244C LEU* 4.8 3.4 - - + -
248C MET* 3.7 30.1 - - + -
262C ILE* 4.1 11.0 - - + -
267C TRP* 4.4 9.0 - + - -
268C PHE* 3.7 32.8 - + - -
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Residues in contact with GLN 121 (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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117C ARG* 2.8 28.9 + - + +
118C ARG* 3.3 19.1 + - - +
120C PHE* 1.3 77.7 - - - +
122C GLN* 1.3 61.4 + - - +
124C LEU* 4.1 0.9 - - - +
125C SER* 3.1 24.1 + - - -
268C PHE* 2.9 49.2 + - + +
270C GLN 3.3 18.8 + - - -
271C ASP 3.6 12.0 + - - +
272C LEU* 3.5 21.4 - - + +
273C PRO* 3.7 8.3 - - - +
276C LEU* 4.0 16.4 - - + +
277C PHE* 4.5 4.2 - - - -
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Residues in contact with GLN 122 (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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75C HIS* 3.3 47.0 + - + +
118C ARG* 3.0 56.1 + - + +
119C LEU* 3.7 7.6 - - - +
120C PHE 3.3 0.2 - - - -
121C GLN* 1.3 75.3 - - - +
123C ILE* 1.3 63.7 + - - +
125C SER* 3.4 5.3 + - - -
126C ALA* 3.2 15.9 + - - +
151C MET 4.0 2.1 - - - +
152C ASN* 3.4 13.8 + - - -
153C ALA* 2.9 30.4 + - + +
275C TYR* 4.6 6.6 + - - +
276C LEU* 4.7 9.0 - - + -
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Residues in contact with ILE 123 (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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101C LEU* 4.2 13.9 - - + -
119C LEU* 3.0 25.1 + - + +
120C PHE* 3.8 10.1 - - + +
122C GLN* 1.3 75.7 - - - +
124C LEU* 1.3 60.4 + - - +
126C ALA* 2.9 20.1 + - - +
127C VAL* 3.0 21.5 + - + +
140C LEU* 5.6 2.0 - - + -
145C VAL* 3.9 27.1 - - + -
153C ALA* 3.7 16.2 - - + -
155C ILE* 3.9 23.7 - - + +
200C CYS* 4.4 13.2 - - + -
203C ILE* 4.2 22.0 - - + -
207C LEU* 5.7 2.0 - - + -
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Residues in contact with LEU 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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120C PHE* 3.0 25.1 + - + +
121C GLN 4.2 2.7 - - - +
123C ILE* 1.3 78.3 - - - +
125C SER* 1.3 57.1 + - - +
127C VAL* 3.3 8.6 + - + +
128C ASP* 2.9 29.1 + - - +
197C ILE* 4.8 4.7 - - + -
200C CYS* 4.2 24.7 - - + -
259C ILE* 4.3 31.4 - - + +
262C ILE* 3.6 47.8 - - + -
268C PHE* 3.8 19.5 - - + -
277C PHE* 4.6 3.1 - - + -
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Residues in contact with SER 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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73C HIS* 3.0 25.4 + - - -
121C GLN 3.1 20.8 + - - -
122C GLN 3.5 5.8 - - - -
123C ILE 3.1 0.2 - - - -
124C LEU* 1.3 78.0 - - - +
126C ALA* 1.3 61.2 + - - +
128C ASP* 3.6 2.3 + - - +
129C TYR* 3.2 16.6 + - - +
276C LEU* 3.0 44.1 + - - +
277C PHE* 4.2 13.8 - - - -
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Residues in contact with ALA 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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73C HIS* 3.5 12.7 - - - +
75C HIS 3.6 23.3 - - - +
76C ILE* 3.7 15.6 - - + +
122C GLN 3.2 8.9 + - - +
123C ILE 2.9 9.9 + - - +
125C SER* 1.3 78.4 - - - +
127C VAL* 1.3 65.0 + - - +
129C TYR* 3.4 4.3 + - - +
130C CYS* 3.2 27.3 + - - -
155C ILE* 3.9 15.0 - - + -
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Residues in contact with VAL 127 (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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123C ILE* 3.0 18.1 + - + +
124C LEU* 3.6 11.9 - - + +
126C ALA* 1.3 74.8 - - + +
128C ASP* 1.3 66.0 + - - +
130C CYS* 3.1 10.3 + - + +
131C HIS* 3.0 50.7 + - + +
137C HIS* 6.4 0.7 - - + -
140C LEU* 3.7 26.9 - - + -
155C ILE* 5.2 3.4 - - + -
196C ASP* 4.1 13.5 - - + +
197C ILE* 5.1 1.6 - - + -
200C CYS* 3.9 16.8 - - - -
259C ILE* 4.5 5.4 - - + -
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Residues in contact with ASP 128 (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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124C LEU 2.9 17.4 + - - +
125C SER 3.9 4.9 - - - +
127C VAL* 1.3 75.5 - - - +
129C TYR* 1.3 57.9 + - - +
131C HIS* 3.2 4.6 + - - +
132C ARG* 2.6 74.8 + - - +
259C ILE* 3.4 40.2 - - + +
263C ARG* 3.5 5.9 + - - -
277C PHE* 4.1 10.9 - - + -
278C PRO* 4.2 3.6 - - - +
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Residues in contact with TYR 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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70C LEU 3.8 4.2 + - - -
71C PHE* 3.5 37.5 - + + -
72C ARG* 2.9 37.7 + - - +
73C HIS* 3.5 31.4 - + + -
76C ILE* 3.8 17.3 - - + -
125C SER 3.2 4.1 + - - +
126C ALA 3.5 9.0 - - - +
128C ASP* 1.3 79.0 + - - +
130C CYS* 1.3 62.2 + - - +
132C ARG* 3.5 8.9 + - - +
133C HIS* 2.8 59.8 + + - -
283C TYR* 5.5 7.9 - - - -
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Residues in contact with CYS 130 (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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71C PHE* 4.2 11.7 - - - -
76C ILE* 3.9 16.2 - - - -
126C ALA 3.2 17.4 + - - -
127C VAL* 3.1 11.8 + - - +
129C TYR* 1.3 82.2 - - - +
131C HIS* 1.3 59.6 + - + +
133C HIS* 2.9 13.5 + - - -
135C VAL* 2.8 41.0 + - + +
137C HIS* 5.1 8.7 - - + +
155C ILE* 5.5 3.6 - - - -
158C PHE* 3.9 29.2 - - - -
196C ASP* 5.8 0.2 - - - +
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Residues in contact with HIS 131 (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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127C VAL* 3.0 33.3 + - + +
128C ASP* 3.2 9.8 + - - +
130C CYS* 1.3 77.0 - - + +
132C ARG* 1.3 61.4 + - + +
134C MET* 3.3 13.7 + - - +
135C VAL 3.4 16.4 - - - -
136C VAL* 4.4 4.4 - - + -
164C MET* 3.6 18.2 - - + +
193C PRO* 3.5 47.1 - - + +
196C ASP* 2.9 27.8 + - + +
197C ILE* 4.4 6.5 - - + +
259C ILE* 3.8 15.9 - - + +
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Residues in contact with ARG 132 (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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128C ASP* 2.6 43.3 + - - +
129C TYR* 3.8 9.4 - - - +
131C HIS* 1.3 77.0 - - + +
133C HIS* 1.3 67.7 + - + +
134C MET* 3.3 9.0 + - - +
263C ARG* 3.0 34.1 - - - +
278C PRO* 3.6 32.2 - - - +
279C GLU* 6.0 2.0 - - - +
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Residues in contact with HIS 133 (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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67C ASN* 4.7 3.0 - - - +
70C LEU* 5.4 4.9 + - + -
71C PHE* 3.7 31.4 - + + -
129C TYR* 2.8 55.3 + + - +
130C CYS 2.9 5.3 + - - +
132C ARG* 1.3 84.8 - - + +
134C MET* 1.3 70.8 + - - +
135C VAL* 3.1 12.4 + - - +
163C MET* 4.5 4.9 - - - +
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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