Contacts of the helix formed by residues 141 - 162 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136B ILE 3.1 3.7 + - - +
137B TYR* 3.0 25.6 + - - -
138B LEU 4.9 0.2 + - - -
140B GLN* 1.3 78.3 - - - +
142B TYR* 1.3 65.7 + - - -
143B GLU* 3.3 3.1 - - - -
144B LYS* 3.2 15.0 + - - +
145B ILE* 3.4 12.3 + - - +
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Residues in contact with TYR 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LEU* 5.3 1.6 - - + -
137A TYR* 3.3 15.2 + + - -
60B VAL* 4.6 12.6 - - + -
63B LEU* 3.7 16.4 + - + -
64B PHE* 3.4 41.9 - + + -
67B GLU* 2.5 32.0 + - - +
137B TYR* 3.9 30.6 - + + -
141B GLY* 1.3 70.2 - - - -
143B GLU* 1.3 72.5 + - + +
145B ILE* 3.0 20.8 + - + +
146B LYS* 3.2 40.5 + - + +
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Residues in contact with GLU 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B GLN 6.0 0.7 - - - +
141B GLY* 3.3 1.0 - - - -
142B TYR* 1.3 82.7 - - + +
144B LYS* 1.3 58.0 + - - +
146B LYS* 3.4 34.1 + - - +
147B GLU* 3.0 29.5 + - - +
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Residues in contact with LYS 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B GLY 5.3 5.9 + - - -
18B ILE* 5.0 6.1 - - - +
136B ILE* 3.9 18.4 - - + -
140B GLN* 3.8 47.0 + - + +
141B GLY 3.2 11.3 + - - +
142B TYR 3.1 0.8 - - - -
143B GLU* 1.3 76.9 - - - +
145B ILE* 1.3 66.4 + - - +
147B GLU* 2.7 36.6 + - - +
148B LEU* 2.9 54.6 + - + +
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Residues in contact with ILE 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B VAL* 4.7 11.4 - - + -
64B PHE* 3.9 29.6 - - + -
133B LEU* 3.5 50.0 - - + +
136B ILE* 3.7 19.5 - - + -
137B TYR* 4.4 7.4 - - + +
141B GLY 3.8 12.3 - - - +
142B TYR* 3.0 16.6 + - + +
144B LYS* 1.3 79.9 - - - +
146B LYS* 1.3 57.4 + - - +
148B LEU* 3.3 1.0 + - - -
149B PHE* 2.8 44.0 + - + +
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Residues in contact with LYS 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B PHE* 3.9 20.9 - - + -
67B GLU* 4.0 19.6 + - - +
71B LYS* 4.7 6.3 - - - +
142B TYR* 3.2 37.0 + - + +
143B GLU* 3.5 39.1 + - - +
145B ILE* 1.3 73.5 - - - +
147B GLU* 1.3 68.0 + - - +
150B GLU* 2.8 53.6 + - + +
151B GLN 4.5 0.3 + - - -
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Residues in contact with GLU 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B GLU 3.0 17.6 + - - +
144B LYS* 2.7 43.1 + - + +
146B LYS* 1.3 78.1 - - - +
148B LEU* 1.3 62.7 + - + +
151B GLN 5.8 0.5 + - - -
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Residues in contact with LEU 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B THR 5.6 1.6 - - - +
17B GLY 6.2 0.7 - - - -
18B ILE* 4.1 26.9 - - + -
136B ILE* 3.8 30.7 - - + -
144B LYS* 2.9 57.3 + - + +
145B ILE* 3.8 2.9 - - - +
147B GLU* 1.3 80.4 - - + +
149B PHE* 1.3 80.2 + - + +
151B GLN 5.7 0.2 - - - -
152B GLU* 4.7 4.5 + - - +
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Residues in contact with PHE 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ILE* 4.9 6.3 - - + -
64B PHE* 3.4 13.5 - - + -
97B VAL* 5.0 0.2 - - + -
101B MET* 4.3 19.5 - - + -
129B PHE* 3.8 28.9 - + - -
132B LEU* 5.0 1.3 - - + -
133B LEU* 3.4 29.8 - - + -
136B ILE* 4.2 13.0 - - + -
145B ILE* 2.8 26.4 + - + +
148B LEU* 1.3 103.4 - - + +
150B GLU* 1.3 65.6 + - - +
151B GLN 3.4 2.2 - - - -
152B GLU* 3.4 24.4 + - - +
153B PHE* 3.0 34.9 + + + -
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Residues in contact with GLU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B PHE* 3.4 13.4 - - + -
68B ILE* 4.2 18.7 - - + +
71B LYS* 6.2 0.2 - - - +
146B LYS* 2.8 53.0 + - - +
148B LEU 3.9 0.2 - - - -
149B PHE* 1.3 71.6 - - - +
151B GLN* 1.3 65.0 + - - +
153B PHE* 3.3 0.7 + - - +
154B GLU* 2.8 55.3 + - + +
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Residues in contact with GLN 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B LYS 4.5 0.6 + - - -
147B GLU 5.8 0.6 + - - -
148B LEU 5.7 0.2 - - - -
149B PHE 3.4 0.6 - - - -
150B GLU* 1.3 80.7 - - - +
152B GLU* 1.3 62.8 + - - +
154B GLU* 3.2 9.9 + - - -
155B PHE* 3.2 6.8 + - - +
218B ARG* 2.9 55.9 + - - +
219B THR* 3.2 33.2 - - - +
222B GLU* 4.3 4.4 - - - +
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Residues in contact with GLU 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B VAL* 4.0 15.3 - - - +
100B LYS* 3.5 17.3 - - - +
101B MET* 6.0 0.9 - - - +
148B LEU 4.7 3.8 + - - +
149B PHE* 3.4 34.4 + - - +
150B GLU 3.3 0.2 - - - -
151B GLN* 1.3 79.2 + - - +
153B PHE* 1.3 63.0 + - + +
155B PHE* 3.2 10.6 + - - +
156B TYR* 2.6 60.9 + - + +
222B GLU* 5.5 0.9 - - - -
225B LYS* 4.8 4.1 + - - +
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Residues in contact with PHE 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B LEU* 4.1 15.0 - - + -
64B PHE* 3.5 29.8 - + + -
65B VAL* 4.3 11.4 - - + -
68B ILE* 4.1 6.3 - - + -
88B ALA* 3.9 23.8 - - + -
93B VAL* 4.5 6.3 - - + -
94B LEU* 4.2 7.6 - - + -
97B VAL* 4.1 25.6 - - + -
129B PHE* 4.1 31.2 - + - -
133B LEU* 6.1 0.7 - - + -
149B PHE* 3.0 29.8 + + + +
150B GLU 4.0 1.3 - - - +
152B GLU* 1.3 77.2 - - + +
154B GLU* 1.3 60.1 + - - +
155B PHE 3.1 1.8 - - - -
156B TYR* 3.8 11.8 - + + +
157B ILE* 2.8 39.6 + - + +
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Residues in contact with GLU 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B ILE* 3.9 23.3 - - + +
72B LYS* 3.6 26.9 + - + +
73B TYR* 4.4 2.6 + - - -
150B GLU* 2.8 47.6 + - + +
151B GLN* 3.5 11.6 - - - +
153B PHE* 1.3 72.5 - - - +
155B PHE* 1.3 57.6 + - - +
157B ILE* 3.8 6.0 - - - +
158B GLU* 2.9 30.3 + - - +
218B ARG* 2.7 34.5 + - - +
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Residues in contact with PHE 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B GLN 3.2 7.2 + - - +
152B GLU* 3.2 11.2 - - - +
153B PHE 3.1 0.4 - - - -
154B GLU* 1.3 74.8 - - - +
156B TYR* 1.3 86.3 + + - +
158B GLU* 3.2 4.8 + - + +
159B LYS* 3.2 61.6 + - + +
166B LEU* 5.0 0.7 - - + -
169B TYR* 4.3 12.8 - + - -
216B LYS 5.6 0.2 - - - -
218B ARG* 3.8 3.3 - - - +
222B GLU* 3.4 44.9 - - + +
225B LYS* 4.1 33.4 - - + -
226B GLU* 3.8 28.5 - - + -
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Residues in contact with TYR 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B ALA* 5.8 1.6 - - + -
93B VAL* 4.1 15.9 - - + -
96B MET* 3.6 11.9 - - + -
97B VAL* 3.5 20.7 - - + +
100B LYS* 2.4 36.4 + - - +
152B GLU* 2.6 51.4 + - + +
153B PHE* 3.3 19.9 + + + +
155B PHE* 1.3 89.9 - + - +
157B ILE* 1.3 65.1 + - + +
159B LYS* 3.1 8.2 + - - +
160B ILE* 3.0 30.8 + - + +
166B LEU* 3.5 35.0 - - + -
225B LYS* 4.3 1.1 - - + -
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Residues in contact with ILE 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B VAL* 4.0 24.5 - - + +
68B ILE* 3.9 33.7 - - + -
69B LEU* 3.5 17.5 - - + -
73B TYR* 3.5 28.3 - - + +
84B VAL* 4.1 10.1 - - + +
88B ALA* 3.9 21.5 - - + -
153B PHE* 2.8 28.6 + - + +
154B GLU* 3.8 4.3 - - - +
156B TYR* 1.3 77.9 - - + +
158B GLU* 1.3 52.4 + - - +
160B ILE* 3.7 3.1 - - - +
161B MET* 2.7 38.1 + - - +
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Residues in contact with GLU 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B TYR* 2.4 47.9 + - - -
154B GLU 2.9 19.3 + - - +
155B PHE* 3.5 7.4 - - + +
157B ILE* 1.3 77.3 - - - +
159B LYS* 1.3 66.9 + - - +
161B MET* 3.3 1.7 + - - +
162B LYS* 2.8 72.7 + - - +
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Residues in contact with LYS 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B PHE* 3.2 49.3 + - + +
156B TYR 3.1 7.0 + - - +
158B GLU* 1.3 90.1 - - - +
160B ILE* 1.3 61.1 + - - +
162B LYS* 3.3 3.0 + - - +
163B GLY 3.0 3.6 + - - -
164B GLU* 2.6 74.7 + - + +
166B LEU* 4.1 14.8 - - + -
169B TYR* 3.5 24.7 - - - +
226B GLU* 3.6 17.4 + - - +
229B ARG* 3.8 10.8 - - - -
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Residues in contact with ILE 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B ARG* 3.3 26.6 + - - +
84B VAL* 3.9 15.7 - - + -
87B ALA* 3.6 27.6 - - + +
88B ALA* 3.7 35.9 - - + +
93B VAL* 4.5 3.1 - - + -
156B TYR* 3.0 19.3 + - + +
157B ILE* 3.9 3.4 - - - +
159B LYS* 1.3 72.8 - - - +
161B MET* 1.3 56.6 + - - +
163B GLY* 2.7 23.6 + - - +
164B GLU 4.4 4.5 - - - +
166B LEU* 4.0 26.7 - - + -
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Residues in contact with MET 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B LEU* 4.2 10.1 - - + -
73B TYR* 3.7 50.7 - - + -
76B ALA* 4.1 18.6 - - + -
80B ASP* 4.2 13.7 - - + +
81B LEU* 4.2 6.5 - - + -
83B ARG* 3.7 16.2 + - - +
84B VAL* 3.6 28.2 - - + +
157B ILE 2.7 23.1 + - - +
158B GLU 3.7 3.8 - - - +
160B ILE* 1.3 73.5 - - - +
162B LYS* 1.3 62.7 + - + +
163B GLY 3.3 0.9 + - - -
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Residues in contact with LYS 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B GLU* 2.8 53.5 + - + +
159B LYS* 4.7 2.0 - - - +
160B ILE 3.1 0.4 - - - -
161B MET* 1.3 77.3 - - + +
163B GLY* 1.3 61.6 - - - +
164B GLU* 3.4 38.8 + - + +
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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