Contacts of the helix formed by residues 118 - 142 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B VAL* 2.7 16.7 + - + +
117B GLY* 1.3 67.8 - - - -
119B ILE* 1.3 65.7 + - + +
120B VAL* 3.1 7.5 + - - -
121B THR* 3.3 30.5 + - + +
122B ILE* 3.3 21.8 + - + +
162B GLY* 5.1 13.0 - - - -
164B ILE* 6.6 0.2 - - + -
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Residues in contact with ILE 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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117B GLY* 3.0 27.3 - - - +
118B VAL* 1.3 80.5 - - + +
120B VAL* 1.3 69.4 + - + +
122B ILE* 3.2 19.5 - - + +
123B VAL* 3.2 28.1 + - + +
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Residues in contact with VAL 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ALA 3.4 26.5 - - - +
31B TRP* 4.6 7.9 - - - -
32B TRP* 5.2 4.0 - - + +
40B LEU* 5.9 4.9 - - + -
117B GLY 3.5 18.6 - - - +
118B VAL* 4.7 0.2 - - - -
119B ILE* 1.3 84.8 - - + +
121B THR* 1.3 72.7 + - + +
123B VAL* 3.1 7.6 + - - +
124B ALA* 2.6 37.9 + - - +
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Residues in contact with THR 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 5.3 11.7 - - + -
42B ALA* 6.0 2.9 - - + -
118B VAL* 3.3 28.8 + - + +
120B VAL* 1.3 88.5 - - + +
122B ILE* 1.3 61.1 + - - +
124B ALA* 3.8 9.3 - - - +
125B LEU* 3.0 27.0 + - - +
160B MET* 3.9 30.2 - - + +
161B ASN 5.5 1.0 - - - -
162B GLY* 4.9 9.6 + - - -
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Residues in contact with ILE 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B VAL* 3.3 21.1 + - + +
119B ILE* 3.2 35.4 - - + +
121B THR* 1.3 79.9 + - - +
123B VAL* 1.3 66.8 + - + +
125B LEU* 3.7 8.7 - - + +
126B ILE* 3.3 27.7 + - - +
162B GLY* 6.0 5.6 - - - -
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Residues in contact with VAL 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LYS* 5.6 2.0 - - + -
30B ALA* 4.9 18.6 - - + -
119B ILE* 3.2 20.0 + - + +
120B VAL* 3.1 6.6 + - - +
122B ILE* 1.3 75.8 - - + +
124B ALA* 1.3 66.9 + - - +
126B ILE* 3.1 7.4 + - - +
127B CYS* 3.0 43.3 + - - -
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Residues in contact with ALA 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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27B LYS* 3.8 41.3 - - + +
120B VAL 2.6 22.1 + - - +
121B THR* 3.8 11.0 - - - +
123B VAL* 1.3 73.3 - - - +
125B LEU* 1.3 60.7 + - - +
127B CYS* 3.4 1.3 + - - +
128B THR* 2.6 33.3 + - - +
160B MET* 3.9 12.3 - - + -
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Residues in contact with LEU 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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121B THR 3.0 19.0 + - - +
122B ILE* 3.7 10.3 - - + +
123B VAL 3.3 0.2 - - - -
124B ALA* 1.3 76.2 - - - +
126B ILE* 1.3 60.1 + - + +
128B THR* 3.3 4.4 + - - -
129B ILE* 2.7 57.7 + - + +
157B ASP 5.8 0.2 - - - -
158B VAL* 3.3 28.8 - - - +
160B MET* 3.7 31.8 - - + +
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Residues in contact with ILE 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 ILE 3.3 14.6 - - - +
123B VAL* 3.1 9.7 + - - +
125B LEU* 1.3 86.7 - - + +
127B CYS* 1.3 66.1 + - - +
129B ILE* 3.2 11.0 + - + +
130B ILE* 2.9 40.7 + - + +
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Residues in contact with CYS 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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23B LEU* 3.9 29.6 - - + +
26B ILE* 5.2 12.8 - - - -
27B LYS* 4.9 9.6 - - + -
123B VAL* 3.0 46.9 + - - +
124B ALA* 3.8 5.2 - - - +
126B ILE* 1.3 78.8 - - - +
128B THR* 1.3 58.9 + - - +
130B ILE* 3.4 13.0 - - - +
131B LEU* 3.0 26.0 + - - +
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Residues in contact with THR 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU* 5.7 0.9 - - - -
24B LEU* 4.6 6.1 - - + +
27B LYS* 4.5 11.8 + - - +
124B ALA* 2.6 25.7 + - - +
125B LEU* 3.7 3.1 - - - -
127B CYS* 1.3 74.7 - - - +
129B ILE* 1.3 67.1 + - - +
130B ILE 3.1 0.2 - - - -
131B LEU* 3.2 7.7 + - + +
132B VAL* 2.8 24.1 + - - +
154B TYR* 3.6 32.3 - - + +
157B ASP* 4.1 18.1 - - + +
158B VAL* 3.6 20.9 - - + +
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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
----------------------------------------------------------
125B LEU* 2.7 52.5 + - + +
126B ILE* 3.4 14.4 - - + +
128B THR* 1.3 71.7 - - - +
130B ILE* 1.3 65.5 + - + +
132B VAL* 3.5 4.8 + - - +
133B SER* 3.1 31.2 + - - +
158B VAL* 3.6 29.6 - - + +
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Residues in contact with ILE 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU* 4.9 9.4 - - + -
126B ILE* 2.9 33.7 + - + +
127B CYS* 3.4 12.3 - - - +
129B ILE* 1.3 77.8 - - + +
131B LEU* 1.3 66.2 + - - +
133B SER* 2.9 19.0 + - - -
134B PHE* 3.1 12.6 + - + +
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Residues in contact with LEU 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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20B ALA* 3.2 38.1 - - + +
21B SER* 3.8 11.2 - - - +
23B LEU* 4.4 11.4 - - + -
24B LEU* 5.1 7.6 - - + -
127B CYS 3.0 11.7 + - - +
128B THR* 3.2 9.8 + - + +
130B ILE* 1.3 79.6 - - - +
132B VAL* 1.3 58.6 + - - +
134B PHE* 2.9 9.1 + - + +
135B GLN* 2.8 51.9 + - + +
154B TYR* 3.8 44.4 - - + -
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Residues in contact with VAL 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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128B THR 2.8 22.6 + - - +
129B ILE* 3.7 7.2 - - - +
131B LEU* 1.3 72.0 - - - +
133B SER* 1.3 53.9 + - - +
135B GLN* 3.4 10.3 + - - +
136B ARG* 2.7 40.9 + - + +
151B MET* 3.9 9.3 - - + +
154B TYR* 3.6 43.5 - - + +
155B GLN* 3.7 23.8 - - + +
158B VAL* 4.1 9.4 - - + -
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Residues in contact with SER 133 (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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129B ILE* 3.1 18.7 + - - +
130B ILE* 2.9 12.5 + - - -
132B VAL* 1.3 74.6 - - - +
134B PHE* 1.3 60.9 + - - +
136B ARG* 3.2 10.1 + - - +
137B TRP* 2.8 29.5 + - - +
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Residues in contact with PHE 134 (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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13B ALA 5.0 0.2 - - - -
16B ALA* 4.4 15.9 - - + -
17B THR* 3.9 17.5 - - - -
20B ALA* 3.5 34.1 - - + -
130B ILE* 3.1 11.5 + - + +
131B LEU* 2.9 11.9 + - + +
133B SER* 1.3 74.1 - - - +
135B GLN* 1.3 60.4 + - + +
137B TRP* 2.9 37.7 + + + +
138B VAL* 2.8 38.9 + - + +
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Residues in contact with GLN 135 (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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17B THR* 3.2 26.4 + - - +
21B SER* 3.0 25.7 + - - -
131B LEU* 2.8 31.0 + - + +
132B VAL* 3.6 10.4 - - - +
134B PHE* 1.3 74.5 - - + +
136B ARG* 1.3 57.5 + - - +
138B VAL* 3.2 5.7 + - - +
139B VAL* 2.8 34.5 + - + +
147B VAL* 4.5 5.8 + - + +
150B ASP* 3.9 9.9 + - - +
151B MET* 3.4 41.5 - - + +
154B TYR* 3.7 18.2 - - - +
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Residues in contact with ARG 136 (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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132B VAL* 2.7 28.4 + - - +
133B SER* 3.2 11.0 + - - +
135B GLN* 1.3 73.3 - - - +
137B TRP* 1.3 61.6 + - - +
139B VAL* 4.0 4.8 - - + +
140B ARG* 3.2 55.5 + - - +
151B MET* 3.7 20.6 - - + +
155B GLN* 5.5 6.7 + - - -
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Residues in contact with TRP 137 (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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9B VAL* 5.9 6.7 - - + -
13B ALA* 5.6 7.9 - - + -
133B SER 2.8 13.6 + - - +
134B PHE* 2.9 41.5 + + + +
136B ARG* 1.3 75.8 - - - +
138B VAL* 1.3 72.7 + - + +
140B ARG* 3.4 16.8 + - + +
141B ARG* 3.0 68.3 + - + +
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Residues in contact with VAL 138 (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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13B ALA* 3.4 31.9 - - + +
14B ILE* 4.0 4.9 - - + -
17B THR* 3.5 28.5 - - + -
134B PHE* 2.8 36.3 + - + +
135B GLN 3.7 6.1 - - - +
137B TRP* 1.3 82.7 - - + +
139B VAL* 1.3 58.6 + - - +
141B ARG* 3.2 4.8 + - - +
142B THR* 2.8 52.2 + - + +
147B VAL* 4.4 5.6 - - + -
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Residues in contact with VAL 139 (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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135B GLN 2.8 27.0 + - - +
136B ARG* 4.0 7.2 - - + +
138B VAL* 1.3 72.3 - - - +
140B ARG* 1.3 61.1 + - - +
142B THR 3.2 16.7 - - - +
143B GLN* 2.9 33.7 - - - +
144B SER 4.5 0.2 - - - +
147B VAL* 3.5 23.3 - - + -
148B ARG* 3.9 41.1 - - + -
151B MET* 4.3 11.9 - - + -
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Residues in contact with ARG 140 (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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136B ARG* 3.2 70.4 + - - +
137B TRP* 3.7 17.0 - - + +
138B VAL 3.3 0.6 - - - -
139B VAL* 1.3 78.8 - - - +
141B ARG* 1.3 58.9 + - - +
143B GLN* 4.3 8.3 - - - +
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Residues in contact with ARG 141 (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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8B LEU* 3.9 35.0 - - - +
9B VAL* 4.6 9.0 + - - +
13B ALA* 5.6 6.1 - - + -
137B TRP* 3.0 61.0 + - + +
138B VAL* 3.6 6.7 - - - +
139B VAL 3.2 0.4 - - - -
140B ARG* 1.3 80.2 - - - +
142B THR* 1.3 63.6 + - + +
143B GLN* 5.6 0.7 - - - -
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Residues in contact with THR 142 (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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10B SER 5.6 1.1 - - - -
11B ARG* 2.8 40.0 + - - -
13B ALA* 4.1 15.3 - - + -
14B ILE* 3.6 21.1 - - + +
138B VAL* 2.8 35.1 + - + +
139B VAL* 3.2 8.3 - - - +
141B ARG* 1.3 80.8 - - + +
143B GLN* 1.3 55.3 + - - +
144B SER* 2.7 17.3 + - - -
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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
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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