Contacts of the helix formed by residues 139 - 165 (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 THR 139 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C VAL 4.5 5.8 - - - +
138C ALA* 1.4 78.6 - - - +
140C GLY* 1.3 68.3 + - - +
141C GLU 3.6 0.2 + - - -
142C LYS* 3.4 12.2 + - - +
143C ARG* 3.2 17.2 + - - +
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Residues in contact with GLY 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C THR* 1.3 75.4 - - - +
141C GLU* 1.4 60.8 + - - -
143C ARG* 3.3 6.5 + - - +
144C ALA* 3.3 18.5 + - - +
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Residues in contact with GLU 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C GLY* 1.4 68.4 - - - -
142C LYS* 1.4 62.9 + - - +
144C ALA* 3.3 9.8 + - - +
145C THR* 3.0 29.5 + - - +
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Residues in contact with LYS 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C ALA* 4.3 10.0 - - + +
139C THR 3.4 10.3 + - - +
140C GLY 3.3 0.6 - - - -
141C GLU* 1.4 76.2 - - - +
143C ARG* 1.4 61.1 + - - +
145C THR* 3.4 8.5 + - - -
146C VAL* 3.3 25.5 + - - +
1D MET* 5.9 6.5 - - + -
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Residues in contact with ARG 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C ALA* 3.7 17.7 + - - +
138C ALA* 3.4 29.5 + - + +
139C THR* 3.2 20.0 + - - +
140C GLY 3.4 10.3 - - - +
141C GLU 3.3 0.2 - - - -
142C LYS* 1.4 73.9 - - - +
144C ALA* 1.3 67.0 + - - +
145C THR 3.2 0.2 + - - -
146C VAL* 3.3 3.3 - - - +
147C VAL* 3.0 48.5 + - + +
185C GLU 4.8 1.8 + - - -
186C ILE* 2.8 47.0 + - - +
187C GLN* 5.9 0.4 + - - -
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Residues in contact with ALA 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C GLY 3.3 9.5 + - - +
141C GLU* 3.3 13.2 + - - +
143C ARG* 1.3 78.6 - - - +
145C THR* 1.3 61.4 + - - +
147C VAL* 3.6 6.1 + - - +
148C GLU* 3.1 25.7 + - - +
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Residues in contact with THR 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C GLU* 3.0 15.0 + - - +
142C LYS* 3.6 10.7 - - - -
143C ARG 3.2 0.4 - - - -
144C ALA* 1.3 72.1 - - - +
146C VAL* 1.3 63.8 + - + +
148C GLU* 3.3 15.7 + - - +
149C SER* 3.1 33.3 + - - +
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Residues in contact with VAL 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C GLN* 5.8 0.9 - - - +
131C TYR* 3.6 34.9 - - + +
134C LEU* 3.9 19.5 - - + -
135C ALA* 3.7 27.6 - - - +
138C ALA* 4.2 4.0 - - + -
142C LYS 3.4 11.9 - - - +
143C ARG* 3.3 17.3 - - - +
145C THR* 1.3 76.9 - - + +
147C VAL* 1.4 57.6 + - - +
149C SER* 3.4 7.3 + - - -
150C SER* 2.9 29.5 + - - -
1D MET* 5.0 10.5 - - + -
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Residues in contact with VAL 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C ALA* 3.8 11.7 - - + -
143C ARG* 3.0 43.3 + - - +
144C ALA* 3.8 6.7 - - - +
146C VAL* 1.4 71.7 - - - +
148C GLU* 1.3 60.5 + - - +
150C SER* 3.4 5.2 + - - -
151C GLU* 3.0 28.8 + - - +
182C PHE* 3.5 10.5 - - + -
186C ILE* 3.6 23.6 - - + -
187C GLN* 3.3 34.5 - - - +
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Residues in contact with GLU 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C ALA 3.1 15.1 + - - +
145C THR* 3.4 15.3 - - - +
147C VAL* 1.3 75.3 - - - +
149C SER* 1.4 55.3 + - - +
151C GLU* 3.4 7.5 + - - +
152C LYS* 3.0 31.0 + - + +
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Residues in contact with SER 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C LYS* 5.4 1.6 - - - -
131C TYR* 3.6 40.2 + - - -
145C THR* 3.1 19.5 + - - +
146C VAL 3.6 7.9 - - - -
148C GLU* 1.4 75.4 - - - +
150C SER* 1.4 55.2 + - - +
152C LYS* 3.4 10.1 + - - +
153C ALA* 3.1 28.4 + - - +
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Residues in contact with SER 150 (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 GLY* 2.8 26.9 + - - -
131C TYR* 3.7 12.7 - - - +
132C ARG* 3.8 6.7 + - - -
135C ALA* 5.9 0.2 - - - -
146C VAL 2.9 18.7 + - - -
147C VAL* 3.6 5.8 - - - -
149C SER* 1.4 72.9 - - - +
151C GLU* 1.4 63.8 + - - +
153C ALA* 3.3 2.9 + - - +
154C TYR* 3.0 40.6 + - - -
182C PHE* 3.4 17.6 - - - -
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Residues in contact with GLU 151 (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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147C VAL 3.0 16.9 + - - +
148C GLU* 3.6 7.9 - - - +
150C SER* 1.4 74.1 - - - +
152C LYS* 1.4 55.8 + - - +
154C TYR* 3.4 3.5 + - - +
155C SER* 2.8 44.0 + - - -
179C TYR* 2.7 25.5 + - - -
182C PHE* 3.7 19.8 - - + -
183C TYR* 3.8 14.3 + - - -
187C GLN* 3.4 23.1 + - - +
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Residues in contact with LYS 152 (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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148C GLU* 3.0 18.2 + - + +
149C SER* 3.6 10.3 - - - +
150C SER 3.4 0.2 - - - -
151C GLU* 1.4 75.7 - - - +
153C ALA* 1.3 60.0 + - - +
155C SER* 4.0 5.0 - - - -
156C GLU* 3.3 27.3 + - - +
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Residues in contact with ALA 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C LEU* 3.4 35.1 - - + +
127C LYS* 3.8 21.1 - - + -
128C GLY* 3.5 15.9 - - - +
149C SER 3.1 16.8 + - - +
150C SER 3.7 2.2 - - - +
151C GLU 3.3 0.2 - - - -
152C LYS* 1.3 74.1 - - - +
154C TYR* 1.4 62.9 + - - +
156C GLU* 3.4 3.0 + - - +
157C ALA* 3.1 22.2 + - - +
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Residues in contact with TYR 154 (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 LYS* 3.7 24.9 - - + -
128C GLY* 3.4 10.3 - - - -
129C ASP* 2.6 27.2 + - - -
132C ARG* 2.9 20.8 + - - -
150C SER* 3.0 41.0 + - - +
151C GLU 3.9 0.7 - - - +
153C ALA* 1.4 72.7 - - - +
155C SER* 1.4 55.4 + - - +
157C ALA* 3.3 5.2 + - - +
158C HIS* 2.8 36.4 + - - +
175C LEU* 3.7 18.9 - - + +
178C ASN* 3.8 16.4 - - + +
179C TYR* 3.5 38.5 - + + -
182C PHE* 3.7 22.7 - + + -
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Residues in contact with SER 155 (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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151C GLU* 2.8 30.0 + - - -
152C LYS* 4.0 5.8 - - - -
154C TYR* 1.4 71.9 - - - +
156C GLU* 1.4 61.0 + - - +
158C HIS* 3.4 3.4 + - - +
159C GLU* 3.1 23.6 + - - +
179C TYR* 3.7 18.8 + - - -
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Residues in contact with GLU 156 (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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109C ILE* 6.0 0.5 - - - +
120C LYS* 4.2 15.2 + - - -
124C LEU* 3.5 32.2 - - + +
152C LYS* 3.3 19.0 + - - +
153C ALA* 3.8 4.2 - - - +
154C TYR 3.3 0.2 - - - -
155C SER* 1.4 76.3 - - - +
157C ALA* 1.3 61.2 + - - +
159C GLU* 3.3 7.9 + - + +
160C ILE* 3.2 34.3 + - + +
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Residues in contact with ALA 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C VAL* 3.8 21.5 - - + +
124C LEU* 3.7 23.9 - - + +
125C LYS 4.1 2.7 - - - +
153C ALA 3.1 17.9 + - - +
154C TYR 3.6 4.7 - - - +
156C GLU* 1.3 74.6 - - - +
158C HIS* 1.3 56.0 + - - +
160C ILE* 3.5 0.8 + - - -
161C SER* 3.0 31.9 + - - -
175C LEU* 3.5 23.0 - - + +
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Residues in contact with HIS 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C TYR 2.8 17.7 + - - +
155C SER* 3.6 5.6 - - - +
156C GLU 3.3 0.2 - - - -
157C ALA* 1.3 74.3 - - - +
159C GLU* 1.4 58.9 + - - +
161C SER* 3.1 8.9 + - - -
162C LYS* 3.1 60.5 + - + +
172C ARG* 5.9 2.0 + - + -
175C LEU* 3.5 14.8 - - + +
176C ALA* 5.3 7.7 - - + +
179C TYR* 4.0 21.1 - + + -
196C LEU* 3.4 30.9 - - + +
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Residues in contact with GLU 159 (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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155C SER 3.1 13.8 + - - +
156C GLU* 3.3 11.0 + - + +
158C HIS* 1.4 75.7 + - - +
160C ILE* 1.4 62.0 + - + +
162C LYS* 3.7 7.4 + - - +
163C GLU* 3.3 27.5 + - - +
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Residues in contact with ILE 160 (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 TYR* 4.0 23.1 - - + +
120C LYS* 4.0 24.0 - - + -
121C VAL* 3.7 20.2 - - + -
124C LEU* 3.8 24.9 - - + -
156C GLU* 3.2 26.5 + - + +
157C ALA* 4.7 0.7 - - - -
159C GLU* 1.4 73.2 - - + +
161C SER* 1.4 59.2 + - - +
163C GLU* 3.2 3.8 + - - -
164C HIS* 2.9 48.5 + - + +
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Residues in contact with SER 161 (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 VAL* 3.8 23.0 - - - +
157C ALA 3.0 16.6 + - - -
158C HIS* 3.1 15.2 + - - -
160C ILE* 1.4 75.4 - - - +
162C LYS* 1.3 59.1 + - - +
165C MET* 2.9 46.7 + - - +
172C ARG* 3.6 26.6 + - - +
175C LEU* 3.6 11.9 - - - +
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Residues in contact with LYS 162 (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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158C HIS* 3.1 48.9 + - + +
159C GLU* 3.9 7.2 - - - +
161C SER* 1.3 81.9 + - - +
163C GLU* 1.3 60.2 + - - +
165C MET 4.2 2.1 - - - +
172C ARG* 4.0 32.1 + - - +
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Residues in contact with GLU 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C GLU* 3.3 17.5 + - - +
160C ILE* 3.2 4.9 + - - +
162C LYS* 1.3 80.2 - - - +
164C HIS* 1.4 89.1 + - + +
165C MET 3.9 0.2 - - - -
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Residues in contact with HIS 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C TYR* 3.3 71.2 + + + -
118C GLU* 5.3 2.8 - - - +
160C ILE* 2.9 29.4 + - + +
163C GLU* 1.4 110.3 + - + +
165C MET* 1.4 62.0 + - + +
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Residues in contact with MET 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C TYR* 4.8 2.7 - - + +
118C GLU* 3.7 42.4 - - + +
121C VAL* 4.4 8.7 - - + -
161C SER* 2.9 42.1 + - - +
162C LYS 4.2 3.1 - - - +
163C GLU 3.9 0.2 - - - -
164C HIS* 1.4 79.4 - - + +
166C GLN* 1.4 58.4 + - - +
167C PRO* 4.3 0.2 - - - +
169C HIS* 3.6 37.9 - - + -
171C ILE* 3.8 14.6 - - + -
172C ARG* 2.7 47.4 + - - -
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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
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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