Contacts of the helix formed by residues 118 - 142 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A GLY 5.9 0.9 - - - -
116A VAL* 2.5 12.9 + - + +
117A GLY* 1.3 67.2 - - - -
119A ILE* 1.3 63.2 + - + +
120A VAL* 3.0 10.9 + - - -
121A THR* 3.1 43.1 + - + +
122A ILE* 3.1 24.7 + - + +
162A GLY* 4.8 12.1 - - - -
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Residues in contact with ILE 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A GLY* 3.0 26.3 - - - +
118A VAL* 1.3 81.1 - - + +
120A VAL* 1.3 65.9 + - + +
122A ILE* 3.6 19.5 - - + +
123A VAL* 3.2 30.1 + - + +
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Residues in contact with VAL 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LYS* 5.5 0.3 - - - -
30A ALA 4.2 18.6 - - - +
31A TRP* 5.2 6.1 - - - -
32A TRP* 5.4 5.2 - - + +
40A LEU* 5.5 9.9 - - + -
116A VAL* 6.6 0.2 - - + -
117A GLY 3.3 17.9 + - - +
118A VAL* 3.0 1.3 - - - -
119A ILE* 1.3 83.5 - - + +
121A THR* 1.3 74.1 + - + +
123A VAL* 3.1 6.7 + - - +
124A ALA* 2.6 36.4 + - - +
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Residues in contact with THR 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 5.3 11.0 - - + -
42A ALA* 6.2 1.1 - - + -
118A VAL* 3.1 31.2 + - + +
120A VAL* 1.3 88.5 - - + +
122A ILE* 1.3 57.4 + - - +
124A ALA* 3.4 9.9 - - - +
125A LEU* 3.1 32.7 + - - +
160A MET* 3.8 26.9 - - + +
161A ASN 5.1 0.8 - - - -
162A GLY* 4.3 13.6 + - - -
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Residues in contact with ILE 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A VAL* 3.1 27.2 + - + +
119A ILE* 3.6 24.2 - - + +
121A THR* 1.3 80.2 - - - +
123A VAL* 1.3 71.0 + - + +
125A LEU* 3.4 11.0 + - + +
126A ILE* 3.0 22.9 + - - +
162A GLY* 5.3 12.1 - - - +
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Residues in contact with VAL 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LYS* 5.8 1.1 - - + -
30A ALA* 4.8 18.8 - - + +
119A ILE* 3.2 19.5 - - + +
120A VAL* 3.1 5.6 + - - +
122A ILE* 1.3 78.6 - - + +
124A ALA* 1.3 66.8 + - - +
126A ILE* 2.9 24.8 + - + +
127A CYS* 3.0 32.1 + - - -
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Residues in contact with ALA 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LYS* 3.6 35.6 - - - +
120A VAL 2.6 21.6 + - - +
121A THR* 3.4 14.6 - - - +
123A VAL* 1.3 71.9 - - - +
125A LEU* 1.3 62.1 + - - +
127A CYS* 3.9 3.6 - - - -
128A THR* 2.6 33.2 + - - +
157A ASP 6.0 0.4 - - - -
160A MET* 3.9 14.8 - - + -
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Residues in contact with LEU 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A THR* 3.1 20.8 + - - +
122A ILE* 3.5 12.3 - - + +
123A VAL 3.3 0.2 - - - -
124A ALA* 1.3 74.3 - - - +
126A ILE* 1.3 55.7 + - - +
128A THR* 3.0 5.5 + - - -
129A ILE* 2.6 61.6 + - + +
157A ASP 5.7 1.1 - - - -
158A VAL* 4.3 12.6 - - - +
160A MET* 3.3 46.8 - - + +
162A GLY* 4.8 8.3 - - - +
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Residues in contact with ILE 126 (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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122A ILE 3.0 7.9 + - - +
123A VAL* 2.9 35.3 + - + +
125A LEU* 1.3 79.1 - - - +
127A CYS* 1.3 60.6 + - + +
129A ILE* 3.8 7.7 - - + +
130A ILE* 2.8 34.6 + - + +
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Residues in contact with CYS 127 (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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23A LEU* 3.8 22.2 - - + +
26A ILE* 5.6 11.7 - - + -
27A LYS* 4.3 20.6 - - - -
123A VAL* 3.0 43.9 + - - -
124A ALA* 3.9 6.5 - - - -
126A ILE* 1.3 78.2 - - + +
128A THR* 1.3 63.7 + - - +
130A ILE* 3.5 12.5 - - + +
131A LEU* 3.2 22.9 + - - +
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Residues in contact with THR 128 (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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27A LYS* 4.8 12.0 + - - +
124A ALA* 2.6 25.8 + - - +
125A LEU* 3.0 3.4 + - - -
127A CYS* 1.3 77.3 - - - +
129A ILE* 1.3 64.7 + - - +
131A LEU* 3.1 6.8 + - + +
132A VAL* 2.9 24.3 + - - +
154A TYR* 3.6 41.7 - - + +
157A ASP* 4.0 18.0 + - + +
158A VAL* 3.7 12.1 - - + +
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Residues in contact with ILE 129 (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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125A LEU* 2.6 49.9 + - + +
126A ILE* 3.8 8.3 - - + +
128A THR* 1.3 74.3 - - - +
130A ILE* 1.3 68.7 + - + +
132A VAL* 3.6 2.9 + - - +
133A SER* 3.3 25.1 + - - +
158A VAL* 3.8 31.6 - - + +
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Residues in contact with ILE 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 5.6 6.5 - - + -
126A ILE* 2.8 29.2 - - + +
127A CYS* 3.5 14.1 - - + +
128A THR 3.2 0.2 - - - -
129A ILE* 1.3 82.4 - - + +
131A LEU* 1.3 66.0 + - - +
133A SER* 3.5 4.4 + - - -
134A PHE* 3.3 17.9 + - + +
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Residues in contact with LEU 131 (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 THR 4.9 0.2 - - - +
20A ALA* 3.3 44.2 - - + +
21A SER* 4.0 6.5 - - - +
23A LEU* 4.6 9.9 - - + -
24A LEU* 5.2 3.1 - - + -
127A CYS 3.2 9.7 + - - +
128A THR* 3.1 11.5 + - - +
130A ILE* 1.3 79.1 - - - +
132A VAL* 1.3 52.8 + - + +
134A PHE* 2.7 30.1 + - + +
135A GLN* 2.8 38.3 + - + +
154A TYR* 3.7 46.2 - - + -
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Residues in contact with VAL 132 (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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128A THR 2.9 22.3 + - - +
129A ILE* 4.0 4.7 - - - +
131A LEU* 1.3 72.8 - - - +
133A SER* 1.3 58.8 + - - +
135A GLN* 3.5 11.0 - - - +
136A ARG* 2.7 35.2 + - + +
151A MET* 4.1 4.4 - - + +
154A TYR* 3.6 43.5 - - + +
155A GLN* 3.8 25.1 - - + +
158A VAL* 4.0 13.5 - - + -
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Residues in contact with SER 133 (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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129A ILE* 3.3 20.0 + - - +
130A ILE* 3.9 4.7 - - - -
131A LEU 3.0 1.4 - - - -
132A VAL* 1.3 77.7 - - - +
134A PHE* 1.3 59.1 + - - +
135A GLN 3.2 0.2 - - - -
136A ARG* 3.6 7.6 - - - +
137A TRP* 2.8 29.5 + - - +
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Residues in contact with PHE 134 (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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13A ALA 5.0 2.0 - - - -
16A ALA* 4.1 19.5 - - + -
17A THR* 3.7 19.7 - - - -
20A ALA* 3.5 33.7 - - + -
130A ILE* 3.3 11.7 + - + +
131A LEU* 2.7 15.9 + - + +
133A SER* 1.3 73.2 - - - +
135A GLN* 1.3 61.1 + - - +
137A TRP* 3.0 44.9 + + + +
138A VAL* 3.0 24.8 + - + +
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Residues in contact with GLN 135 (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 THR* 3.6 17.0 + - - +
21A SER* 5.0 1.0 - - - -
131A LEU* 2.8 29.5 + - + +
132A VAL* 3.5 19.5 - - - +
134A PHE* 1.3 77.4 - - + +
136A ARG* 1.3 57.2 + - - +
138A VAL* 3.1 11.5 + - - +
139A VAL* 2.9 34.0 + - + +
147A VAL* 4.3 4.5 - - + +
150A ASP* 3.5 13.3 - - - +
151A MET* 3.2 45.9 + - + +
154A TYR* 3.5 29.6 - - - +
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Residues in contact with ARG 136 (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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132A VAL* 2.7 26.5 + - + +
133A SER* 3.2 8.3 + - - +
135A GLN* 1.3 73.1 - - - +
137A TRP* 1.3 62.6 + - - +
139A VAL* 3.5 4.7 + - + +
140A ARG* 3.0 44.8 + - - +
151A MET* 3.6 24.1 - - + +
155A GLN* 3.9 20.8 + - - +
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Residues in contact with TRP 137 (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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9A VAL* 6.0 6.3 - - + -
13A ALA* 5.7 5.8 - - + -
133A SER 2.8 16.9 + - - +
134A PHE* 3.0 41.5 + + + +
136A ARG* 1.3 74.7 - - - +
138A VAL* 1.3 66.5 + - + +
140A ARG* 3.4 16.8 + - + +
141A ARG* 2.9 79.0 + - + +
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Residues in contact with VAL 138 (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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13A ALA* 3.3 45.8 - - + +
14A ILE* 4.0 3.1 - - - +
17A THR* 3.8 28.3 - - + -
134A PHE* 3.0 28.7 + - + +
135A GLN* 3.4 7.6 - - - +
137A TRP* 1.3 78.8 - - + +
139A VAL* 1.3 56.9 + - - +
141A ARG* 4.2 4.9 - - + -
142A THR* 2.7 48.5 + - + +
147A VAL* 4.7 5.6 - - + -
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Residues in contact with VAL 139 (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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135A GLN 2.9 24.3 + - - +
136A ARG* 3.7 8.1 - - + +
138A VAL* 1.3 71.5 - - - +
140A ARG* 1.3 62.4 + - - +
142A THR 3.1 14.9 - - - +
143A GLN* 3.1 27.7 - - - +
144A SER 5.0 2.5 - - - +
147A VAL* 3.6 22.9 - - + +
148A ARG* 4.0 31.9 - - + +
151A MET* 3.8 24.5 - - + -
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Residues in contact with ARG 140 (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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136A ARG* 3.0 38.5 + - - +
137A TRP* 3.6 16.9 - - + +
139A VAL* 1.3 79.6 - - - +
141A ARG* 1.3 64.1 + - + +
142A THR* 3.5 0.5 + - - -
143A GLN* 4.4 7.3 - - - +
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Residues in contact with ARG 141 (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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8A LEU* 4.6 26.9 - - - +
9A VAL* 5.1 7.5 + - - +
13A ALA* 5.6 3.4 - - + -
137A TRP* 2.9 72.6 + - + +
138A VAL* 3.7 6.7 - - + +
140A ARG* 1.3 78.8 - - + +
142A THR* 1.3 65.5 + - + +
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Residues in contact with THR 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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11A ARG* 3.1 44.4 + - + -
13A ALA* 4.3 9.0 - - + -
14A ILE* 3.5 19.4 - - + +
138A VAL* 2.7 50.5 + - + +
139A VAL* 3.1 8.5 - - - +
141A ARG* 1.3 80.3 - - + +
143A GLN* 1.3 52.6 + - - +
144A SER* 2.5 18.6 + - - -
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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