Contacts of the helix formed by residues 118 - 142 (chain C) in PDB entry 3H90
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 VAL 118 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C GLY 5.9 0.7 - - - -
116C VAL* 2.5 12.7 + - + +
117C GLY* 1.3 67.4 - - - -
119C ILE* 1.3 62.7 + - + +
120C VAL* 3.0 11.1 + - - -
121C THR* 3.1 42.8 + - + +
122C ILE* 3.1 24.4 + - + +
162C GLY* 4.8 12.1 - - - -
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Residues in contact with ILE 119 (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 GLY* 3.0 26.7 - - - +
118C VAL* 1.3 80.6 - - + +
120C VAL* 1.3 66.8 + - + +
122C ILE* 3.6 19.0 - - + +
123C VAL* 3.2 29.9 + - + +
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Residues in contact with VAL 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LYS* 5.4 0.7 - - - -
30C ALA 4.2 19.7 - - - +
31C TRP* 5.2 6.7 - - - -
32C TRP* 5.4 4.9 - - + +
40C LEU* 5.5 9.2 - - + -
116C VAL* 6.6 0.2 - - + -
117C GLY 3.3 17.7 - - - +
118C VAL* 4.4 0.2 - - - -
119C ILE* 1.3 84.6 - - + +
121C THR* 1.3 75.2 + - + +
123C VAL* 3.1 6.7 + - - +
124C ALA* 2.7 36.1 + - - +
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Residues in contact with THR 121 (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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40C LEU* 5.3 10.8 - - + -
42C ALA* 6.2 1.3 - - + -
118C VAL* 3.1 31.9 + - + +
120C VAL* 1.3 88.8 - - + +
122C ILE* 1.3 56.6 + - - +
124C ALA* 3.5 9.7 - - - +
125C LEU* 3.1 32.1 + - - +
160C MET* 3.8 26.7 - - + +
161C ASN 5.1 1.0 - - - -
162C GLY* 4.3 14.0 + - - -
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Residues in contact with ILE 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C VAL* 3.1 28.3 + - + +
119C ILE* 3.6 24.7 - - + +
121C THR* 1.3 80.2 - - - +
123C VAL* 1.3 70.5 + - + +
125C LEU* 3.4 11.0 + - + +
126C ILE* 3.0 22.6 + - - +
162C GLY* 5.2 13.0 - - - +
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Residues in contact with VAL 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LYS* 5.8 0.9 - - + -
30C ALA* 4.8 18.4 - - + +
119C ILE* 3.2 19.7 - - + +
120C VAL* 3.1 5.7 + - - +
122C ILE* 1.3 78.7 - - + +
124C ALA* 1.3 66.8 + - - +
126C ILE* 2.9 23.6 + - + +
127C CYS* 2.9 34.3 + - - -
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Residues in contact with ALA 124 (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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27C LYS* 3.6 35.9 - - - +
120C VAL 2.7 21.4 + - - +
121C THR* 3.5 13.7 - - - +
123C VAL* 1.3 71.8 - - - +
125C LEU* 1.3 62.2 + - - +
127C CYS* 3.9 3.6 - - - -
128C THR* 2.6 33.2 + - - +
157C ASP 6.0 0.2 - - - -
160C MET* 3.9 15.9 - - + -
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Residues in contact with LEU 125 (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 THR 3.1 17.8 + - - +
122C ILE* 3.5 12.8 - - + +
124C ALA* 1.3 77.1 - - - +
126C ILE* 1.3 55.0 + - - +
128C THR* 3.0 4.9 + - - -
129C ILE* 2.6 62.0 + - + +
157C ASP 5.7 0.7 - - - -
158C VAL* 4.2 13.2 - - + +
160C MET* 3.4 46.1 - - + +
162C GLY* 4.8 8.1 - - - +
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Residues in contact with ILE 126 (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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122C ILE 3.0 7.3 + - - +
123C VAL* 2.9 37.9 + - + +
125C LEU* 1.3 75.1 - - - +
127C CYS* 1.3 60.4 + - + +
129C ILE* 3.8 7.7 - - + +
130C ILE* 2.8 35.0 + - + +
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Residues in contact with CYS 127 (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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23C LEU* 3.8 21.3 - - + +
26C ILE* 5.7 10.3 - - + -
27C LYS* 4.2 20.6 - - - -
123C VAL* 2.9 45.8 + - - -
124C ALA* 3.9 6.7 - - - -
126C ILE* 1.3 79.2 - - + +
128C THR* 1.3 66.3 + - - +
130C ILE* 3.5 12.5 - - + +
131C LEU* 3.2 20.1 + - - +
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Residues in contact with THR 128 (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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27C LYS* 4.8 11.8 + - - +
124C ALA* 2.6 25.6 + - - +
125C LEU* 3.0 3.7 + - - -
127C CYS* 1.3 76.4 - - - +
129C ILE* 1.3 64.7 + - - +
131C LEU* 3.1 6.8 + - + +
132C VAL* 2.9 28.2 + - + +
154C TYR* 3.7 37.0 - - + +
157C ASP* 4.1 17.6 + - + +
158C VAL* 3.7 12.6 - - + +
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Residues in contact with ILE 129 (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 LEU* 2.6 50.6 + - + +
126C ILE* 3.8 9.2 - - + +
128C THR* 1.3 73.9 - - - +
130C ILE* 1.3 67.4 + - + +
132C VAL* 3.6 3.1 + - - +
133C SER* 3.3 25.6 + - - +
158C VAL* 3.8 32.5 - - + +
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Residues in contact with ILE 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C LEU* 5.6 6.5 - - + -
126C ILE* 2.8 29.4 - - + +
127C CYS* 3.5 13.9 - - + +
128C THR 3.2 0.4 - - - -
129C ILE* 1.3 83.1 - - + +
131C LEU* 1.3 65.2 + - - +
133C SER* 3.5 4.0 + - - -
134C PHE* 3.3 17.9 + - + +
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Residues in contact with LEU 131 (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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20C ALA* 3.3 43.1 - - + +
21C SER* 4.0 5.8 - - - +
23C LEU* 4.6 9.0 - - + -
24C LEU* 5.2 4.0 - - + -
127C CYS 3.2 10.1 + - - +
128C THR* 3.1 10.9 + - - +
130C ILE* 1.3 79.4 - - - +
132C VAL* 1.3 54.0 + - + +
134C PHE* 2.7 29.1 + - + +
135C GLN* 2.8 38.6 + - + +
154C TYR* 3.7 46.4 - - + -
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Residues in contact with VAL 132 (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 THR 2.9 23.1 + - - +
129C ILE* 4.0 3.8 - - - +
131C LEU* 1.3 72.0 - - - +
133C SER* 1.3 53.6 + - - +
135C GLN* 3.5 11.8 - - - +
136C ARG* 2.7 40.7 + - + +
151C MET* 4.1 4.1 - - + +
154C TYR* 3.7 42.8 - - + +
155C GLN* 3.8 24.2 - - + +
158C VAL* 3.9 13.9 - - + -
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Residues in contact with SER 133 (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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129C ILE* 3.3 19.0 + - - +
130C ILE* 3.9 4.7 - - - -
131C LEU 3.0 1.4 - - - -
132C VAL* 1.3 78.7 - - - +
134C PHE* 1.3 59.8 + - - +
135C GLN 3.2 0.2 - - - -
136C ARG* 3.3 8.0 + - - +
137C TRP* 2.8 28.1 + - - +
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Residues in contact with PHE 134 (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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13C ALA 5.0 1.8 - - - -
16C ALA* 4.1 19.3 - - + -
17C THR* 3.7 20.2 - - - -
20C ALA* 3.5 33.9 - - + -
130C ILE* 3.3 11.4 + - + +
131C LEU* 2.7 16.2 + - + +
133C SER* 1.3 73.6 - - - +
135C GLN* 1.3 59.0 + - - +
137C TRP* 3.0 38.3 + + + +
138C VAL* 2.9 33.7 + - + +
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Residues in contact with GLN 135 (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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17C THR* 3.7 17.5 + - - +
21C SER* 4.9 0.7 - - - -
131C LEU* 2.8 29.6 + - + +
132C VAL* 3.5 20.2 - - - +
134C PHE* 1.3 75.3 - - - +
136C ARG* 1.3 62.1 + - - +
138C VAL* 3.1 11.2 + - - +
139C VAL* 2.9 26.4 + - + +
147C VAL* 4.3 4.8 - - + +
150C ASP* 3.6 13.2 - - - +
151C MET* 3.2 48.6 + - + +
154C TYR* 3.5 29.6 - - - +
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Residues in contact with ARG 136 (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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132C VAL* 2.7 28.7 + - + +
133C SER* 3.3 8.9 + - - +
135C GLN* 1.3 72.1 - - - +
137C TRP* 1.3 62.1 + - - +
139C VAL* 3.5 4.3 + - + +
140C ARG* 3.0 44.0 + - - +
151C MET* 3.6 23.5 - - + +
155C GLN* 3.9 20.4 + - - +
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Residues in contact with TRP 137 (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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9C VAL* 5.9 6.5 - - + -
13C ALA* 5.7 6.7 - - + -
133C SER 2.8 14.2 + - - +
134C PHE* 3.0 41.4 + + + +
136C ARG* 1.3 77.8 - - - +
138C VAL* 1.3 64.8 + - + +
140C ARG* 3.4 16.7 + - + +
141C ARG* 3.0 79.8 + - + +
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Residues in contact with VAL 138 (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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13C ALA* 3.4 45.8 - - + +
14C ILE* 4.0 3.1 - - - +
17C THR* 3.8 28.9 - - + -
134C PHE* 2.9 28.9 + - + +
135C GLN* 3.4 7.0 - - - +
137C TRP* 1.3 79.6 - - + +
139C VAL* 1.3 57.1 + - - +
141C ARG* 4.2 4.7 - - + -
142C THR* 2.7 46.8 + - + +
147C VAL* 4.7 5.6 - - + -
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Residues in contact with VAL 139 (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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135C GLN 2.9 20.3 + - - +
136C ARG* 3.8 7.6 - - + +
138C VAL* 1.3 74.9 - - - +
140C ARG* 1.3 58.9 + - - +
142C THR 3.0 18.7 - - - +
143C GLN* 3.1 26.7 - - - +
144C SER 5.0 2.5 - - - +
147C VAL* 3.5 23.5 - - + +
148C ARG* 4.0 32.3 - - + -
151C MET* 3.8 23.8 - - + -
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Residues in contact with ARG 140 (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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136C ARG* 3.0 39.4 + - - +
137C TRP* 3.7 15.8 - - + +
139C VAL* 1.3 80.0 - - - +
141C ARG* 1.3 63.6 + - + +
142C THR* 3.5 0.3 + - - -
143C GLN* 4.4 8.0 + - - +
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Residues in contact with ARG 141 (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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8C LEU* 4.5 27.9 - - - +
9C VAL* 5.0 7.7 + - - +
13C ALA* 5.6 3.1 - - + -
137C TRP* 3.0 73.0 + - + +
138C VAL* 3.7 7.0 - - + +
140C ARG* 1.3 79.0 - - + +
142C THR* 1.3 66.1 + - + +
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Residues in contact with THR 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ARG* 3.1 44.2 + - - -
13C ALA* 4.2 9.2 - - + -
14C ILE* 3.5 18.8 - - + +
138C VAL* 2.7 50.0 + - + +
139C VAL* 3.0 8.8 - - - +
141C ARG* 1.3 80.0 - - + +
143C GLN* 1.3 52.6 + - - +
144C SER* 2.5 18.3 + - - -
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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) + - + + + + + -
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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