Contacts of the helix formed by residues 141 - 162 (chain A) in PDB entry 1O0W
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 GLY 141 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A ILE 3.2 2.7 + - - +
137A TYR* 2.8 26.0 + - - -
138A LEU 4.9 0.2 + - - -
139A ASP 3.9 0.2 - - - -
140A GLN* 1.3 77.2 - - - +
142A TYR* 1.3 65.7 + - - -
143A GLU 3.3 2.9 - - - -
144A LYS* 3.2 17.5 + - - +
145A ILE* 3.5 9.4 + - - +
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Residues in contact with TYR 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A VAL* 4.5 7.4 - - + -
63A LEU* 3.7 21.9 + - + +
64A PHE* 3.2 41.4 + + + -
67A GLU* 2.7 32.3 + - - +
137A TYR* 3.6 29.1 - + + -
141A GLY* 1.3 69.5 - - - -
143A GLU* 1.3 68.7 + - + +
145A ILE* 3.1 17.6 + - + +
146A LYS* 3.1 50.7 + - + +
63B LEU* 5.1 1.3 - - + -
137B TYR* 3.3 13.9 - + - -
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Residues in contact with GLU 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A GLN 5.7 1.3 - - - +
141A GLY 3.3 1.4 - - - -
142A TYR* 1.3 81.8 - - - +
144A LYS* 1.3 57.1 + - - +
146A LYS* 3.1 37.4 + - - +
147A GLU* 2.9 27.6 + - - +
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Residues in contact with LYS 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ILE* 3.6 18.2 - - + -
140A GLN* 3.4 44.1 + - + +
141A GLY 3.2 11.5 + - - +
142A TYR 3.2 0.4 - - - -
143A GLU* 1.3 78.6 - - - +
145A ILE* 1.3 59.8 + - - +
147A GLU* 3.0 36.3 + - - +
148A LEU* 2.8 56.5 + - + +
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Residues in contact with ILE 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A VAL* 3.2 33.7 - - + -
64A PHE* 4.0 26.9 - - + -
133A LEU* 3.6 18.8 - - + +
136A ILE* 3.9 17.7 - - + -
137A TYR* 3.6 29.6 - - + -
141A GLY 3.8 7.2 - - - +
142A TYR* 3.1 13.4 + - + +
144A LYS* 1.3 77.6 - - - +
146A LYS* 1.3 62.6 + - - +
149A PHE* 2.9 40.7 + - + +
150A GLU 3.9 0.2 + - - -
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Residues in contact with LYS 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A PHE* 4.0 22.2 - - + -
67A GLU* 4.2 17.2 + - - +
71A LYS* 5.0 5.1 - - - +
142A TYR* 3.1 38.3 + - + +
143A GLU* 3.1 43.7 + - - +
144A LYS 3.2 0.2 - - - -
145A ILE* 1.3 76.0 - - - +
147A GLU* 1.3 66.4 + - - +
150A GLU* 2.9 48.6 + - + +
151A GLN 4.7 0.3 + - - -
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Residues in contact with GLU 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A GLU 2.9 14.2 + - - +
144A LYS* 3.0 48.1 + - - +
146A LYS* 1.3 78.7 - - - +
148A LEU* 1.3 69.0 + - + +
150A GLU 4.8 0.3 + - - -
151A GLN* 5.7 1.7 + - - +
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Residues in contact with LEU 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A GLY 5.5 2.9 - - - +
18A ILE* 4.1 31.4 - - + -
136A ILE* 3.9 28.5 - - + -
144A LYS* 2.8 51.3 + - + +
147A GLU* 1.3 82.6 - - + +
149A PHE* 1.3 82.8 + - + +
151A GLN 5.7 0.2 - - - -
152A GLU* 4.7 4.9 - - - +
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Residues in contact with PHE 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ILE* 4.3 18.2 - - + -
64A PHE* 3.5 13.8 - - + -
97A VAL* 5.2 0.2 - - + -
101A MET* 4.1 12.3 - - + -
129A PHE* 3.9 31.6 - + - -
132A LEU* 5.2 1.8 - - + -
133A LEU* 3.5 29.6 - - + -
136A ILE* 4.0 16.2 - - + -
145A ILE* 2.9 24.5 + - + +
148A LEU* 1.3 101.5 - - + +
150A GLU* 1.3 67.2 + - - +
151A GLN 3.3 2.9 - - - -
152A GLU* 3.3 23.7 + - - +
153A PHE* 2.9 31.9 + + + -
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Residues in contact with GLU 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A PHE* 3.5 12.3 - - + -
68A ILE* 4.0 20.7 - - + +
71A LYS* 6.2 0.2 - - - +
72A LYS* 5.6 1.0 - - - +
146A LYS* 2.9 46.3 + - - +
147A GLU 4.8 0.2 + - - -
149A PHE* 1.3 77.7 - - - +
151A GLN* 1.3 57.5 + - - +
153A PHE* 4.1 0.3 - - - +
154A GLU* 2.8 64.4 + - + +
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Residues in contact with GLN 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A LYS 4.7 0.4 + - - -
147A GLU 5.7 1.9 + - - +
149A PHE 3.3 0.8 - - - -
150A GLU* 1.3 77.7 - - - +
152A GLU* 1.3 65.5 + - - +
154A GLU* 3.7 9.9 - - - -
155A PHE 3.3 6.6 + - - -
218A ARG* 2.8 55.9 + - - +
219A THR* 3.0 36.5 + - - +
222A GLU* 3.8 8.0 + - - +
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Residues in contact with GLU 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A VAL* 3.9 20.5 - - - +
100A LYS* 5.2 6.8 - - - +
101A MET* 5.9 0.2 - - - +
148A LEU 4.7 3.3 - - - +
149A PHE* 3.3 33.0 + - - +
150A GLU 3.3 0.4 - - - -
151A GLN* 1.3 81.2 - - - +
153A PHE* 1.3 63.3 + - + +
155A PHE* 3.3 9.5 + - - +
156A TYR* 2.6 57.8 + - + +
222A GLU* 5.2 1.6 - - - -
225A LYS* 4.5 6.6 + - - +
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Residues in contact with PHE 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A LEU* 4.3 11.2 - - + -
64A PHE* 3.6 27.4 - + + -
65A VAL* 4.4 11.7 - - + -
68A ILE* 4.2 5.4 - - + -
88A ALA* 3.9 24.5 - - + -
93A VAL* 4.3 6.1 - - + -
94A LEU* 4.1 18.6 - - + -
97A VAL* 3.9 35.2 - - + -
129A PHE* 4.3 15.3 - + - -
149A PHE* 2.9 29.7 + + + +
150A GLU 4.1 0.2 - - - +
152A GLU* 1.3 83.4 - - + +
154A GLU* 1.3 62.2 + - - +
155A PHE 3.1 1.3 - - - -
156A TYR* 3.2 11.2 + + + +
157A ILE* 2.8 37.8 + - + +
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Residues in contact with GLU 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ILE* 4.0 24.2 - - + +
72A LYS* 3.9 28.1 + - + +
150A GLU* 2.8 58.4 + - + +
151A GLN* 3.7 8.7 - - - +
153A PHE* 1.3 72.4 - - - +
155A PHE* 1.3 53.2 + - - +
157A ILE* 3.5 2.1 + - - +
158A GLU* 2.7 45.8 + - + +
218A ARG* 2.7 34.6 + - - +
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Residues in contact with PHE 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A GLN 3.3 3.8 + - - +
152A GLU* 3.4 11.0 - - - +
153A PHE 3.1 0.6 - - - -
154A GLU* 1.3 79.4 - - - +
156A TYR* 1.3 82.5 + + - +
158A GLU* 3.2 14.5 + - + +
159A LYS* 3.1 54.2 + - + +
169A TYR* 3.9 19.5 - + - -
218A ARG* 3.8 0.8 - - - +
222A GLU* 3.6 39.0 - - + +
225A LYS* 4.3 19.1 - - + +
226A GLU* 3.6 47.8 - - + -
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Residues in contact with TYR 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A ALA* 5.8 1.8 - - + -
93A VAL* 4.2 15.9 - - + -
96A MET* 3.6 19.1 - - + +
97A VAL* 3.5 22.2 - - + +
100A LYS* 5.2 5.0 - - - +
152A GLU* 2.6 49.9 + - + -
153A PHE* 3.2 20.7 + + + +
155A PHE* 1.3 87.5 - + - +
157A ILE* 1.3 64.1 + - + +
159A LYS* 3.2 5.4 + - - +
160A ILE* 3.0 31.1 + - + +
166A LEU* 3.7 34.1 - - + -
225A LYS* 3.0 27.8 + - + -
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Residues in contact with ILE 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A VAL* 3.9 28.9 - - + +
68A ILE* 3.8 33.7 - - + -
69A LEU* 3.7 17.7 - - + -
73A TYR* 3.5 28.9 - - + +
84A VAL* 3.8 10.0 - - + +
88A ALA* 3.8 21.1 - - + -
153A PHE* 2.8 23.6 + - + +
154A GLU* 3.9 4.7 - - - +
156A TYR* 1.3 77.5 - - + +
158A GLU* 1.3 51.3 + - - +
160A ILE* 3.4 2.8 + - - +
161A MET* 2.8 33.7 + - + +
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Residues in contact with GLU 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A LYS* 5.7 9.1 - - - -
73A TYR* 3.1 22.8 + - - +
154A GLU* 2.7 38.8 + - + +
155A PHE* 3.6 10.6 - - + +
157A ILE* 1.3 75.0 - - - +
159A LYS* 1.3 73.5 + - - +
161A MET* 3.3 1.4 + - - +
162A LYS* 3.0 45.6 + - - +
218A ARG* 4.0 18.9 + - - -
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Residues in contact with LYS 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A PHE* 3.1 53.6 + - + +
156A TYR 3.5 6.1 - - - +
158A GLU* 1.3 84.9 - - - +
160A ILE* 1.3 61.7 + - - +
162A LYS* 3.3 12.6 + - - +
163A GLY 3.2 3.3 + - - -
164A GLU* 2.8 65.2 + - - +
166A LEU* 4.2 11.2 - - + -
169A TYR* 3.6 24.7 - - - +
226A GLU* 2.9 29.7 + - - -
229A ARG* 3.6 11.5 - - - +
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Residues in contact with ILE 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ARG* 3.3 23.3 + - - +
84A VAL* 3.8 15.5 - - + -
87A ALA* 3.7 27.8 - - + +
88A ALA* 3.8 36.6 - - + +
93A VAL* 4.6 0.7 - - + -
156A TYR* 3.0 19.5 + - + +
157A ILE* 3.8 3.6 - - - +
159A LYS* 1.3 74.2 - - - +
161A MET* 1.3 66.2 + - - +
163A GLY* 2.9 12.6 + - - -
164A GLU 4.4 4.0 - - - +
166A LEU* 3.9 28.9 - - + -
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Residues in contact with MET 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A LEU* 3.8 13.9 - - + -
73A TYR* 3.8 50.9 - - + -
76A ALA* 4.2 14.4 - - + -
80A ASP* 4.3 14.4 - - - +
81A LEU* 4.3 4.3 - - + -
83A ARG* 3.4 21.7 + - - +
84A VAL* 3.5 26.0 - - + +
157A ILE 2.8 22.0 + - - +
158A GLU 3.8 3.4 - - - +
160A ILE* 1.3 73.4 - - - +
162A LYS* 1.3 61.5 + - + +
163A GLY 3.2 3.5 + - - -
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Residues in contact with LYS 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A GLU* 3.0 35.2 + - - +
159A LYS* 4.6 10.5 - - - +
160A ILE 3.1 0.2 - - - -
161A MET* 1.3 77.6 - - + +
163A GLY* 1.3 62.3 + - - +
164A GLU* 3.2 36.2 + - + +
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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
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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