Contacts of the helix formed by residues 116 - 138 (chain C) in PDB entry 4O46
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 GLN 116 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C PRO* 4.7 19.0 - - - +
111C ASN 3.5 7.1 - - - +
112C CYS* 3.5 9.0 - - - +
113C SER* 2.7 52.9 + - - +
114C GLU 3.4 0.4 - - - -
115C THR* 1.4 73.8 - - - +
117C TYR* 1.3 62.4 + - - +
118C GLU* 3.5 5.8 + - - -
119C SER* 3.6 16.5 + - - +
120C LYS* 3.2 23.6 + - - +
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Residues in contact with TYR 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C GLU 3.1 24.7 + - - -
115C THR* 3.0 34.8 + - + +
116C GLN* 1.3 68.1 - - - +
118C GLU* 1.4 76.1 + - - +
120C LYS* 3.3 9.1 + - + +
121C VAL* 3.0 30.8 + - + +
160C ILE* 4.0 13.0 - - + -
164C HIS* 3.3 66.1 + + + -
165C MET* 4.8 3.6 - - + -
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Residues in contact with GLU 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C ARG* 4.7 9.9 - - - +
115C THR 4.9 3.1 - - - +
116C GLN* 3.5 2.1 - - - -
117C TYR* 1.4 87.6 + - - +
119C SER* 1.3 58.1 + - - +
121C VAL* 3.5 2.8 + - - +
122C PHE* 2.9 29.7 + - - +
164C HIS 5.3 2.6 - - - +
165C MET* 3.7 31.6 - - + +
169C HIS* 4.2 14.9 + - - +
171C ILE* 4.0 15.0 - - + +
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Residues in contact with SER 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C LEU 4.8 5.9 + - - -
42C ARG* 3.4 23.8 + - - +
112C CYS* 3.7 17.9 - - - -
116C GLN* 3.6 18.2 + - - +
117C TYR 3.4 0.2 - - - -
118C GLU* 1.3 74.2 - - - +
120C LYS* 1.3 59.7 + - - +
122C PHE* 3.3 6.2 + - - +
123C TYR* 2.9 49.7 + - - -
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Residues in contact with LYS 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C ILE* 3.9 33.4 + - + +
112C CYS* 3.8 24.0 + - + +
113C SER 5.0 6.3 - - - +
114C GLU* 5.9 3.1 - - - +
116C GLN 3.2 16.4 + - - +
117C TYR* 3.3 9.6 + - + +
119C SER* 1.3 77.1 - - - +
121C VAL* 1.4 56.4 + - - +
123C TYR* 4.1 1.8 - - - +
124C LEU* 3.0 41.6 + - + +
156C GLU* 4.2 17.6 + - - -
160C ILE* 4.0 23.1 - - + -
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Residues in contact with VAL 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C TYR* 3.0 22.0 + - + +
118C GLU 3.9 3.6 - - - +
120C LYS* 1.4 70.9 - - - +
122C PHE* 1.3 56.4 + - - +
124C LEU* 3.3 1.2 + - - +
125C LYS* 2.8 36.8 + - + +
157C ALA* 3.8 29.5 - - + +
160C ILE* 3.7 25.1 - - + -
161C SER* 3.8 16.8 - - - +
165C MET* 4.4 6.5 - - - -
171C ILE* 3.7 20.4 - - + +
175C LEU* 3.9 20.9 - - + -
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Residues in contact with PHE 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C ARG* 3.4 62.6 - - + +
43C ASN* 4.0 21.8 - - - -
46C SER* 3.8 21.5 - - - -
118C GLU 2.9 19.2 + - - +
119C SER 3.3 4.9 + - - +
121C VAL* 1.3 76.4 - - - +
123C TYR* 1.4 64.2 + + - +
125C LYS* 3.5 13.7 + - + +
126C MET* 3.1 45.2 + - + +
171C ILE* 4.1 20.6 - - + +
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Residues in contact with TYR 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C LEU* 3.6 19.8 + - - +
42C ARG* 3.4 34.4 - - + +
45C LEU* 4.8 5.6 - - + -
104C LEU* 3.6 23.7 - - + +
108C LEU* 3.5 53.0 - - + +
109C ILE* 3.6 21.8 - - + +
112C CYS* 3.7 15.5 - - - -
119C SER* 2.9 40.1 + - - +
120C LYS 4.2 1.8 - - - +
122C PHE* 1.4 76.6 - + - +
124C LEU* 1.4 60.0 + - - +
126C MET* 3.2 6.4 + - - +
127C LYS* 2.9 27.2 + - - +
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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
----------------------------------------------------------
109C ILE* 4.4 23.3 - - + -
120C LYS* 3.0 31.2 + - + +
123C TYR* 1.4 73.2 - - - +
125C LYS* 1.4 58.8 + - - +
127C LYS* 3.4 11.4 + - + +
128C GLY* 3.0 22.3 + - - -
153C ALA* 3.4 38.2 - - - +
156C GLU* 3.5 42.8 - - + +
157C ALA* 3.7 13.0 - - + +
160C ILE* 3.8 20.6 - - + -
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Residues in contact with LYS 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C SER* 5.8 1.8 + - - -
121C VAL* 2.8 19.5 + - + +
122C PHE* 3.5 14.2 - - + +
124C LEU* 1.4 73.1 - - - +
126C MET* 1.4 57.1 + - - +
128C GLY* 3.2 2.6 + - - -
129C ASP* 2.9 57.9 + - - +
154C TYR* 3.7 9.2 - - + -
157C ALA* 4.1 0.8 - - - +
171C ILE* 4.9 7.0 - - + +
174C GLY* 3.8 17.0 - - - -
175C LEU* 3.9 43.7 - - + +
178C ASN* 3.5 20.3 - - + +
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Residues in contact with MET 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C LEU* 4.5 14.8 - - + +
46C SER* 4.2 28.0 - - - +
49C TYR* 5.2 0.2 - - + -
100C VAL* 3.7 30.3 - - + -
104C LEU* 3.9 17.9 - - + -
122C PHE* 3.1 41.8 + - + +
123C TYR* 3.2 13.2 + - - +
125C LYS* 1.4 78.2 - - - +
127C LYS* 1.4 57.7 + - - +
129C ASP* 3.1 10.7 + - - +
130C TYR* 2.9 53.5 + - + +
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Residues in contact with LYS 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C LEU* 3.7 21.0 - - + +
104C LEU* 3.7 7.1 - - + +
105C ASP* 2.7 38.3 + - - +
109C ILE* 3.8 15.5 - - + +
123C TYR 2.9 13.1 + - - +
124C LEU* 3.5 19.0 - - + +
126C MET* 1.4 75.1 - - - +
128C GLY* 1.3 61.6 - - - +
131C TYR* 3.2 49.5 + - + -
149C SER* 5.4 1.8 - - - -
153C ALA* 3.8 15.7 - - + +
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Residues in contact with GLY 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C LEU 3.0 12.0 + - - -
125C LYS 3.2 4.0 + - - -
127C LYS* 1.3 76.3 - - - +
129C ASP* 1.3 55.1 + - - +
131C TYR 3.5 0.9 + - - -
132C ARG* 3.0 17.5 + - - +
150C SER* 2.8 28.9 + - - -
153C ALA* 3.5 15.6 - - - +
154C TYR* 3.4 18.4 - - - -
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Residues in contact with ASP 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C LYS* 6.1 0.2 - - - +
125C LYS* 2.9 44.1 + - - +
126C MET* 3.4 12.6 - - - +
128C GLY* 1.3 76.4 - - - +
130C TYR* 1.3 61.1 + - + +
132C ARG* 3.1 10.9 + - - +
133C TYR* 2.9 50.7 + - + +
154C TYR* 2.6 27.0 + - - -
178C ASN* 2.7 26.1 + - - +
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Residues in contact with TYR 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C SER* 4.1 4.3 + - - -
49C TYR* 3.3 12.4 - - + +
50C LYS* 3.2 32.3 + - + +
53C VAL* 3.7 23.1 - - + -
96C VAL* 5.2 1.3 - - + -
97C CYS* 3.7 19.7 - - - -
100C VAL* 3.3 29.4 - - + -
101C LEU* 4.0 24.5 - - + -
104C LEU* 5.0 1.3 - - + -
126C MET* 2.9 59.0 + - + +
129C ASP* 1.3 73.5 - - + +
131C TYR* 1.3 59.9 + - - +
133C TYR* 3.4 20.8 + + - -
134C LEU* 3.1 30.5 + - - +
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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
----------------------------------------------------------
98C GLN* 5.2 6.6 + - - -
101C LEU* 3.6 32.0 - - + +
105C ASP* 4.5 8.8 + - - -
127C LYS* 3.2 47.3 + - + +
130C TYR* 1.3 74.3 - - - +
132C ARG* 1.4 60.0 + - - +
134C LEU* 3.3 14.6 + - + +
135C ALA* 2.9 27.2 + - - +
146C VAL* 3.6 37.2 - - + +
149C SER* 3.6 36.9 + - - -
150C SER* 3.7 11.9 - - - -
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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
----------------------------------------------------------
57C ARG* 4.3 4.4 - - - +
128C GLY 3.0 13.4 + - - +
129C ASP* 3.1 28.6 + - - +
131C TYR* 1.4 74.1 - - - +
133C TYR* 1.4 81.6 + - - +
135C ALA* 3.1 8.3 + - - +
136C GLU* 3.0 49.3 + - - +
150C SER* 3.8 9.1 + - - +
154C TYR* 2.9 16.7 + - - -
178C ASN* 3.4 20.8 + - - +
181C VAL* 3.8 23.1 - - - +
182C PHE* 3.8 33.7 - - + +
185C GLU* 5.1 1.2 + - - -
186C ILE* 3.7 18.1 - - + +
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Residues in contact with TYR 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C LYS* 3.3 26.3 - - + +
53C VAL* 3.9 17.5 - - + -
57C ARG* 3.3 47.5 - - - +
93C LEU* 3.8 17.0 - - + +
97C CYS* 4.0 9.2 - - - -
129C ASP* 2.9 43.1 + - + +
130C TYR* 3.7 41.3 - + - +
131C TYR 3.3 0.2 - - - -
132C ARG* 1.4 96.9 + - - +
134C LEU* 1.4 61.0 + - - +
136C GLU* 3.5 23.5 - - - +
137C VAL* 3.9 4.2 + - - +
178C ASN* 4.8 2.1 + - - -
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Residues in contact with LEU 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C LEU* 4.9 0.9 - - + -
94C GLU* 3.7 33.1 - - + +
97C CYS* 3.7 21.3 - - + -
98C GLN* 3.9 14.8 - - - +
101C LEU* 3.8 24.0 - - + -
130C TYR 3.1 18.8 + - - +
131C TYR* 3.4 22.4 - - + +
133C TYR* 1.4 75.3 - - - +
135C ALA* 1.4 57.1 + - - +
137C VAL* 3.4 9.6 + - - +
138C ALA* 3.1 28.6 + - + +
146C VAL* 3.9 18.4 - - + -
1D MET* 4.0 14.2 - - + +
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Residues in contact with ALA 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C TYR 2.9 14.1 + - - +
132C ARG* 3.1 12.5 + - - +
134C LEU* 1.4 74.1 - - - +
136C GLU* 1.3 61.4 + - - +
137C VAL 3.3 0.9 + - - -
138C ALA* 3.4 16.4 + - - +
143C ARG* 3.7 14.2 + - - +
146C VAL* 3.7 12.1 - - + +
147C VAL* 3.8 29.8 - - + +
182C PHE* 5.8 0.2 - - + -
186C ILE* 4.0 16.5 - - + +
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Residues in contact with GLU 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C ARG* 3.1 44.6 + - - +
60C TRP* 3.5 21.0 - - + -
61C ARG* 4.6 5.3 + - - -
132C ARG* 3.0 32.4 + - - +
133C TYR* 3.5 16.0 - - - +
134C LEU 3.3 0.2 - - - -
135C ALA* 1.3 76.5 - - - +
137C VAL* 1.4 62.3 + - + +
138C ALA 5.0 0.9 - - - +
185C GLU* 4.2 13.0 - - - +
186C ILE* 3.8 17.1 - - + +
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Residues in contact with VAL 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C TRP* 3.4 45.0 - - + +
90C GLU* 3.8 31.4 - - + +
93C LEU* 4.3 25.8 - - + -
94C GLU* 3.8 24.6 - - + +
133C TYR 4.1 9.4 - - - +
134C LEU 3.4 13.4 + - - +
136C GLU* 1.4 79.0 - - + +
138C ALA* 1.4 64.1 + - - +
139C THR* 4.1 6.1 + - - +
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Residues in contact with ALA 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C GLU* 5.3 5.4 - - - +
134C LEU* 3.1 17.7 + - + +
135C ALA 3.4 4.9 + - - +
136C GLU 4.9 1.0 - - - +
137C VAL* 1.4 81.2 - - + +
139C THR* 1.4 65.2 + - - +
142C LYS* 4.3 7.4 - - + -
143C ARG* 3.4 46.0 + - + +
146C VAL* 4.2 7.6 - - + -
1D MET* 6.0 4.3 - - + -
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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