Contacts of the helix formed by residues 109 - 132 (chain B) in PDB entry 1VGO
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 ASP 109 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B LYS 4.2 0.4 + - - -
108B VAL* 1.3 75.1 - - - +
110B ARG* 1.3 63.9 + - - +
111B VAL* 3.3 15.5 - - + +
112B THR* 2.6 59.6 + - - +
113B ILE* 3.2 10.5 - - - +
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Residues in contact with ARG 110 (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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108B VAL 5.5 0.4 - - - +
109B ASP* 1.3 72.7 - - - +
111B VAL* 1.3 65.6 + - + +
113B ILE* 3.4 15.3 + - + +
114B GLY* 3.0 20.3 + - - -
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Residues in contact with VAL 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ASP* 3.2 10.9 + - + +
110B ARG* 1.3 80.2 - - + +
112B THR* 1.3 64.8 + - - +
114B GLY* 3.2 11.1 + - - -
115B THR* 3.2 22.9 + - - +
310B BNG 4.9 15.0 - - - +
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Residues in contact with THR 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B VAL* 3.4 15.7 - - + -
109B ASP* 2.6 59.7 + - - +
111B VAL* 1.3 76.4 - - - +
113B ILE* 1.3 55.8 + - - +
115B THR* 3.4 7.3 + - - -
116B LEU* 3.0 28.1 + - - +
156B TYR* 5.1 8.2 - - - +
160B SER* 4.3 13.4 - - - -
161B LEU* 4.0 18.4 - - - +
310B BNG 5.3 3.6 - - - -
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Residues in contact with ILE 113 (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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100B LEU* 4.6 15.7 - - + -
103B ALA* 3.8 24.2 - - + +
104B LEU* 5.2 6.3 - - + -
108B VAL* 3.7 27.1 - - + +
109B ASP 3.2 18.3 + - - +
110B ARG* 3.6 14.4 - - + +
111B VAL 3.2 0.2 - - - -
112B THR* 1.3 75.3 - - - +
114B GLY* 1.3 64.3 + - - +
116B LEU* 3.3 7.4 + - - +
117B ILE* 2.8 48.6 + - + +
161B LEU* 6.4 0.2 - - - -
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Residues in contact with GLY 114 (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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110B ARG 3.0 14.5 + - - -
111B VAL 3.2 4.0 + - - -
113B ILE* 1.3 78.4 - - - +
115B THR* 1.3 56.4 + - - +
117B ILE* 3.6 4.4 + - - +
118B GLY* 3.0 25.1 + - - -
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Residues in contact with THR 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B VAL* 3.2 15.8 + - - +
112B THR* 3.7 9.0 - - - -
114B GLY* 1.3 73.2 - - - +
116B LEU* 1.3 67.0 + - - +
118B GLY* 3.2 1.6 + - - -
119B VAL* 2.9 26.8 + - + +
156B TYR* 3.5 34.3 - - + +
310B BNG 3.2 41.5 + - + +
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Residues in contact with LEU 116 (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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99B LEU* 3.6 47.8 - - + +
103B ALA* 4.9 7.4 - - + -
108B VAL* 6.3 0.2 - - + -
112B THR 3.0 14.3 + - - +
113B ILE* 3.3 11.2 - - - +
115B THR* 1.3 78.3 - - - +
117B ILE* 1.3 65.8 + - + +
119B VAL* 3.5 2.1 + - - +
120B ASP* 3.1 19.2 + - - +
153B VAL* 4.2 27.6 - - + +
156B TYR* 4.5 21.1 - - + -
157B LEU* 4.2 16.4 - - + -
161B LEU* 4.5 15.0 - - + -
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Residues in contact with ILE 117 (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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96B PRO* 4.2 41.5 - - + +
99B LEU* 4.8 5.8 - - + -
100B LEU* 5.2 7.6 - - + +
113B ILE* 2.8 44.7 + - + +
114B GLY* 4.1 4.5 - - - +
116B LEU* 1.3 90.4 - - + +
118B GLY* 1.3 58.4 + - - +
120B ASP* 3.2 7.3 + - - +
121B ALA* 2.8 32.0 + - + +
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Residues in contact with GLY 118 (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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114B GLY 3.0 16.4 + - - -
115B THR* 3.2 4.5 + - - -
116B LEU 3.2 0.4 - - - -
117B ILE* 1.3 79.6 - - - +
119B VAL* 1.3 62.1 + - - +
121B ALA* 3.2 7.3 + - - +
122B LEU* 3.0 22.3 + - - +
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Residues in contact with VAL 119 (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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115B THR* 2.9 23.9 + - + +
116B LEU* 4.1 2.9 - - - +
118B GLY* 1.3 73.8 - - - +
120B ASP* 1.3 57.1 + - - +
122B LEU* 3.3 8.2 + - - +
123B MET* 2.9 26.3 + - - +
149B ALA* 3.1 42.0 - - + +
152B PHE* 3.7 10.1 - - + -
153B VAL* 4.1 5.4 - - + -
156B TYR* 4.0 16.6 - - + -
310B BNG 3.7 34.1 - - + -
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Residues in contact with ASP 120 (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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95B THR* 2.6 26.2 + - - -
96B PRO* 3.6 14.6 - - - +
99B LEU* 3.3 28.4 - - + +
116B LEU 3.1 17.7 + - - +
117B ILE* 3.4 6.1 - - - +
119B VAL* 1.3 76.2 - - - +
121B ALA* 1.3 64.2 + - - +
123B MET* 3.2 31.8 + - - +
124B ILE* 3.3 15.1 + - - +
153B VAL* 4.1 11.9 - - + +
187B TRP* 3.7 9.9 - - - -
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Residues in contact with ALA 121 (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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92B LEU* 4.0 26.6 - - + +
96B PRO* 5.7 1.8 - - + -
117B ILE* 2.8 22.2 + - + +
118B GLY* 3.7 6.5 - - - +
120B ASP* 1.3 76.3 + - - +
122B LEU* 1.3 60.7 + - - +
124B ILE* 3.3 3.6 + - - +
125B VAL* 3.0 29.6 + - - +
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Residues in contact with LEU 122 (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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118B GLY 3.0 13.3 + - - +
119B VAL* 3.3 12.3 - - - +
121B ALA* 1.3 77.8 - - - +
123B MET* 1.3 57.3 + - - +
125B VAL* 3.1 24.2 - - + +
126B THR* 2.9 43.2 + - + +
145B PHE* 4.4 15.0 - - + +
149B ALA* 4.0 17.0 - - + -
310B BNG 4.3 18.6 - - + -
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Residues in contact with MET 123 (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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95B THR* 4.9 1.3 - - + +
119B VAL 2.9 12.8 + - - +
120B ASP* 3.3 33.2 - - - +
121B ALA 3.2 0.2 - - - -
122B LEU* 1.3 77.5 - - - +
124B ILE* 1.3 78.4 + - + +
126B THR* 2.9 11.7 + - - -
127B GLY* 3.1 5.0 + - - -
146B SER* 2.8 36.8 + - - +
149B ALA* 3.9 13.5 - - + -
150B PHE* 3.4 38.8 - - - -
153B VAL* 4.8 2.7 - - + -
187B TRP* 4.4 6.5 - - + -
261B RET 3.7 36.8 - - + +
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Residues in contact with ILE 124 (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 TYR* 3.3 42.2 - - + +
91B TRP* 3.6 44.4 - - + +
92B LEU* 4.0 14.1 - - + +
95B THR* 4.0 5.6 - - - +
120B ASP 3.3 13.6 + - - +
121B ALA* 3.3 5.4 + - - +
123B MET* 1.3 95.9 - - + +
125B VAL* 1.3 59.4 + - - +
127B GLY* 3.2 2.6 + - - -
128B LEU* 2.9 26.2 + - - +
261B RET 4.3 14.6 - - + -
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Residues in contact with VAL 125 (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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92B LEU* 5.2 4.6 - - + +
121B ALA 3.0 21.1 + - - +
122B LEU* 3.1 32.5 - - + +
124B ILE* 1.3 78.0 - - - +
126B THR* 1.3 57.9 + - + +
128B LEU* 3.0 15.8 + - + +
129B ILE* 2.9 40.9 + - + +
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Residues in contact with THR 126 (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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122B LEU* 2.9 34.9 + - + +
123B MET 2.9 7.1 + - - -
125B VAL* 1.3 74.4 - - + +
127B GLY* 1.3 73.3 + - - +
129B ILE* 3.0 12.7 + - + +
130B GLY* 2.9 21.8 + - - -
142B TRP* 3.8 30.5 - - + +
145B PHE* 3.7 28.0 - - + -
146B SER* 3.1 16.3 - - - -
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Residues in contact with GLY 127 (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 TYR* 3.7 9.8 + - - -
123B MET 3.1 10.7 + - - -
124B ILE 3.2 4.7 + - - -
126B THR* 1.3 83.2 + - - +
128B LEU* 1.3 59.8 + - - +
130B GLY* 3.6 1.6 + - - -
131B ALA* 3.2 23.4 + - - +
142B TRP 5.0 2.0 - - - -
143B TRP* 6.0 0.4 - - - -
146B SER* 4.1 4.7 - - - -
194B TRP* 4.2 6.3 + - - -
261B RET 4.1 24.2 - - - -
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Residues in contact with LEU 128 (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 ILE* 4.8 2.0 - - + -
85B TYR* 4.1 27.4 - - + -
88B TYR* 3.7 42.4 - - + -
124B ILE 2.9 12.8 + - - +
125B VAL* 3.1 17.9 - - + +
126B THR 3.0 0.2 - - - -
127B GLY* 1.3 76.2 - - - +
129B ILE* 1.3 70.2 + - + +
131B ALA* 3.3 3.1 + - - +
132B LEU* 3.1 45.9 + - + +
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Residues in contact with ILE 129 (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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125B VAL* 2.9 31.6 + - + +
126B THR* 3.5 10.5 - - + +
128B LEU* 1.3 78.6 - - + +
130B GLY* 1.3 63.3 + - - +
132B LEU* 3.1 21.7 + - + +
133B SER* 3.1 15.5 + - - +
142B TRP* 3.4 50.7 - - + +
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Residues in contact with GLY 130 (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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126B THR 2.9 12.1 + - - -
127B GLY* 4.0 1.8 - - - -
129B ILE* 1.3 78.1 - - - +
131B ALA* 1.3 53.8 + - - +
133B SER* 2.7 34.4 + - - -
139B ARG* 3.2 14.4 - - - +
142B TRP* 3.4 23.7 - - - +
194B TRP* 4.0 11.0 - - - -
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Residues in contact with ALA 131 (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 VAL* 4.7 4.2 - - - +
75B LEU* 6.0 0.5 - - - +
81B LEU* 5.0 0.9 - - - +
83B ILE* 3.9 21.9 - - + +
88B TYR* 3.6 23.8 - - + +
127B GLY 3.2 14.5 + - - +
128B LEU 3.5 9.0 - - - +
130B GLY* 1.3 74.7 - - - +
132B LEU* 1.3 60.0 + - - +
133B SER 3.5 4.3 + - - +
194B TRP* 3.6 5.1 - - + -
199B GLU* 2.9 40.5 - - - +
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Residues in contact with LEU 132 (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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71B THR* 4.6 2.0 - - - +
73B VAL* 3.7 26.3 - - + +
83B ILE* 3.7 35.4 - - + -
85B TYR* 4.2 31.6 - - + +
128B LEU* 3.1 27.1 - - + +
129B ILE* 3.1 13.7 + - + +
130B GLY 3.0 1.0 - - - -
131B ALA* 1.3 76.0 - - - +
133B SER* 1.3 58.6 + - - +
134B LYS* 3.9 3.1 + - - +
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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