Contacts of the helix formed by residues 120 - 141 (chain A) in PDB entry 3E6D
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 GLU 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A PHE 3.3 13.4 + - - +
117A ARG 5.2 0.2 - - - -
118A THR 4.1 0.8 - - - -
119A ASP* 1.3 73.1 + - - +
121A ASP* 1.3 62.7 + - - +
123A ILE* 3.2 41.3 + - + +
124A PHE* 4.0 5.8 - - + -
112B ARG* 2.6 40.3 + - - +
115B PHE* 5.5 3.1 - - + +
116B ARG* 2.8 53.9 + - - +
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Residues in contact with ASP 121 (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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119A ASP* 2.9 17.8 + - - +
120A GLU* 1.3 78.8 - - - +
122A MET* 1.3 68.0 + - + +
124A PHE* 3.0 17.5 + - - +
125A GLU* 3.2 12.7 + - + +
112B ARG* 2.8 37.0 + - - +
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Residues in contact with MET 122 (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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22A ILE* 5.8 0.7 - - - -
24A LYS* 4.0 26.0 - - + +
25A LEU* 4.9 9.2 - - + -
28A TYR* 3.6 34.1 - - + -
115A VAL* 4.0 22.7 - - + -
116A PHE* 3.9 5.8 - - + -
119A ASP* 3.0 32.4 + - - +
121A ASP* 1.3 79.8 - - + +
123A ILE* 1.3 68.2 + - - +
125A GLU* 3.1 34.2 + - + +
126A ILE* 3.0 29.3 + - + +
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Residues in contact with ILE 123 (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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116A PHE* 3.5 38.7 - - + +
120A GLU* 3.3 32.8 - - + +
122A MET* 1.3 78.6 - - - +
124A PHE* 1.3 65.8 + - + +
126A ILE* 3.4 3.6 + - - +
127A PHE* 2.9 27.2 + - + +
115B PHE* 3.8 34.3 - - + -
122B ILE* 3.4 39.7 - - + -
126B PHE* 4.0 7.0 - - + -
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Residues in contact with PHE 124 (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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120A GLU* 4.0 16.2 - - + -
121A ASP* 3.0 7.4 + - - +
123A ILE* 1.3 81.5 - - + +
125A GLU* 1.3 59.7 + - - +
127A PHE* 3.9 8.9 - + - +
128A LYS* 2.8 32.6 + - - +
86B LEU* 3.9 15.3 - - + -
87B TYR* 3.3 25.9 + - - +
108B GLU* 3.6 22.9 - - + +
111B LEU* 4.1 11.0 - - + -
112B ARG* 3.5 56.5 - - + +
115B PHE* 4.0 28.5 - + - -
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Residues in contact with GLU 125 (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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22A ILE* 3.6 21.9 - - + +
24A LYS* 4.2 15.6 - - + +
121A ASP* 3.2 8.4 + - + +
122A MET* 3.1 40.6 + - + +
124A PHE* 1.3 77.1 - - - +
126A ILE* 1.3 62.8 + - - +
128A LYS* 3.5 24.2 + - - +
129A ASN* 3.1 20.8 + - - +
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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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22A ILE* 4.1 16.2 - - + -
25A LEU* 4.6 16.4 - - + -
53A MET* 6.3 1.8 - - + -
83A LEU* 4.6 12.6 - - + -
112A LEU* 4.3 16.4 - - + -
116A PHE* 3.8 30.3 - - + -
122A MET* 3.0 12.5 + - + +
123A ILE 3.7 7.2 - - - +
125A GLU* 1.3 78.5 - - - +
127A PHE* 1.3 61.2 + - - +
129A ASN* 3.1 18.8 + - - +
130A TYR* 3.2 28.2 + - + -
126B PHE* 3.4 28.5 - - + -
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Residues in contact with PHE 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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123A ILE* 2.9 20.3 + - + +
124A PHE* 3.9 12.3 - + + +
126A ILE* 1.3 78.5 - - - +
128A LYS* 1.3 62.0 + - - +
130A TYR* 3.2 4.9 + - + +
131A LEU* 3.0 44.6 + - + +
52B MET* 3.9 31.0 - - + -
82B LEU* 5.0 0.9 - - + -
86B LEU* 3.8 20.2 - - + -
111B LEU* 4.7 7.6 - - + -
115B PHE* 6.2 2.2 - + - -
125B ILE* 3.4 36.6 - - + -
126B PHE* 4.5 13.9 - + + -
129B TYR* 3.4 37.9 - + + -
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Residues in contact with LYS 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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124A PHE 2.8 23.4 + - - +
125A GLU* 3.8 25.3 + - - +
127A PHE* 1.3 73.7 - - - +
129A ASN* 1.3 63.9 + - - +
131A LEU* 3.5 5.4 + - + +
132A THR* 2.8 38.5 + - - +
87B TYR* 3.5 43.4 - - + -
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Residues in contact with ASN 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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20A PHE* 2.9 37.4 + - - +
21A PRO 4.4 2.2 + - - -
22A ILE* 4.3 21.8 - - + +
83A LEU* 4.4 7.3 - - + +
125A GLU 3.1 13.4 + - - +
126A ILE* 3.1 14.0 + - - +
128A LYS* 1.3 82.7 - - + +
130A TYR* 1.3 81.5 + - - +
132A THR* 3.5 7.0 + - - -
133A LYS* 3.3 36.0 + - - +
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Residues in contact with TYR 130 (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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53A MET* 2.9 29.3 - - + +
83A LEU* 3.9 24.3 + - + -
84A ILE* 5.1 0.5 - - - -
85A GLY 4.6 1.2 + - - -
126A ILE* 3.2 24.3 + - + +
127A PHE* 3.2 8.9 + - + +
129A ASN* 1.3 91.7 - - - +
131A LEU* 1.3 65.2 + - - +
132A THR 3.2 0.2 - - - -
133A LYS* 3.4 19.2 + - + +
134A VAL* 3.0 29.6 + - - +
126B PHE* 5.8 1.3 - + - -
129B TYR* 4.0 27.6 - - + -
130B LEU* 3.5 27.8 - - + +
133B VAL* 3.7 27.4 - - + -
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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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127A PHE* 3.0 49.7 + - + +
128A LYS* 3.8 9.9 - - + +
129A ASN 3.4 0.2 - - - -
130A TYR* 1.3 76.4 - - - +
132A THR* 1.3 58.8 + - - +
134A VAL* 3.5 4.4 + - + +
135A ALA* 3.0 28.4 + - - +
52B MET* 4.3 6.1 - - + -
84B GLY 4.5 7.0 - - - +
85B LYS* 4.3 6.1 - - + -
86B LEU* 3.9 29.8 - - + +
87B TYR* 4.5 5.2 - - + +
89B THR* 4.5 12.0 - - + +
129B TYR* 3.5 37.0 - - + +
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Residues in contact with THR 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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20A PHE* 4.0 20.6 - - + -
128A LYS* 2.8 24.4 + - - +
129A ASN* 3.6 10.7 - - - -
131A LEU* 1.3 79.2 - - - +
133A LYS* 1.3 57.4 + - - +
135A ALA* 3.3 8.3 + - + +
136A TYR* 3.0 26.5 + - - +
88B PRO 5.5 2.4 + - - -
89B THR* 5.0 10.8 - - + +
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Residues in contact with LYS 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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19A PHE 5.3 1.1 - - - -
20A PHE* 3.7 47.3 - - + -
76A TYR* 6.2 1.8 - - - -
83A LEU 2.9 31.3 + - - +
84A ILE* 5.5 1.4 - - - +
129A ASN* 3.3 34.0 + - - +
130A TYR* 3.7 27.9 + - + +
131A LEU 3.4 0.2 - - - -
132A THR* 1.3 73.4 - - - +
134A VAL* 1.3 61.3 + - - +
136A TYR* 3.2 1.5 + - - +
137A TYR* 2.9 46.3 + - + -
133B VAL* 4.0 18.1 - - + +
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Residues in contact with VAL 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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130A TYR 3.0 16.8 + - - +
131A LEU 4.0 4.0 - - - +
133A LYS* 1.3 74.2 - - - +
135A ALA* 1.3 65.3 + - - +
137A TYR* 4.6 3.6 - - - +
138A ALA* 3.2 25.1 + - + +
75B TYR* 4.9 13.0 - - + +
129B TYR* 3.7 30.7 - - + -
132B LYS* 4.1 16.6 - - + -
133B VAL* 3.5 23.6 - - + +
136B TYR* 4.4 19.1 - - + -
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Residues in contact with ALA 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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131A LEU 3.0 18.8 + - - +
132A THR* 3.5 7.0 - - + +
134A VAL* 1.3 75.9 - - - +
136A TYR* 1.3 67.9 + - - +
138A ALA* 4.3 1.2 - - - +
139A ARG* 3.2 14.1 + - - +
89B THR* 3.8 30.3 - - + +
91B ASN* 3.2 31.0 + - + +
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Residues in contact with TYR 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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18A ASN* 4.6 20.1 + - + +
20A PHE* 3.5 30.1 - + + -
132A THR 3.0 13.9 + - - +
133A LYS 3.4 7.6 - - - +
135A ALA* 1.3 80.2 - - - +
137A TYR* 1.3 85.5 + + - +
139A ARG* 3.3 9.4 + - - +
140A GLN* 2.9 58.6 + - + +
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Residues in contact with TYR 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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20A PHE* 4.3 13.0 - + - -
75A LEU 6.0 0.9 - - - -
76A TYR* 3.4 31.7 - + + +
133A LYS* 2.9 39.1 + - + +
134A VAL* 4.6 1.8 - - - +
136A TYR* 1.3 98.1 - + - +
138A ALA* 1.3 61.0 + - - +
140A GLN* 3.2 6.6 + - + +
141A VAL* 2.9 35.4 + - - +
133B VAL* 4.1 27.4 - - + -
136B TYR* 3.3 26.7 - - + -
137B ALA* 4.2 25.1 - - + -
140B VAL* 4.7 17.9 - - + -
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Residues in contact with ALA 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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134A VAL* 3.2 20.0 + - + +
135A ALA* 4.3 2.0 - - - +
137A TYR* 1.3 77.5 - - - +
139A ARG* 1.3 62.9 + - - +
141A VAL* 3.4 18.2 + - - +
74B LEU* 3.3 35.0 - - + +
75B TYR* 4.1 17.5 - - + -
91B ASN* 5.6 0.4 - - - +
136B TYR* 4.1 22.8 - - + -
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Residues in contact with ARG 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 ALA 3.2 18.8 + - - +
136A TYR* 3.4 8.5 - - - +
137A TYR 3.2 0.6 - - - -
138A ALA* 1.3 81.2 - - - +
140A GLN* 1.3 68.2 + - - +
141A VAL 4.5 1.2 - - - -
64B ILE* 4.2 14.4 - - + +
66B PHE* 4.3 41.3 - - + +
67B GLU* 5.5 2.8 - - - +
74B LEU* 4.2 4.9 - - - +
89B THR 5.8 0.6 + - - -
90B GLY 4.1 14.8 + - - -
91B ASN* 3.4 28.5 + - - +
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Residues in contact with GLN 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 TYR* 2.9 65.0 + - + +
137A TYR* 3.2 8.7 + - + +
139A ARG* 1.3 85.2 - - - +
141A VAL* 1.3 63.3 + - - +
140B VAL* 4.6 14.5 - - + +
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Residues in contact with VAL 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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137A TYR 2.9 17.1 + - - +
138A ALA 3.4 15.0 + - - +
139A ARG 4.5 1.3 - - - -
140A GLN* 1.3 80.5 - - - +
72B LYS* 5.1 9.0 + - - +
74B LEU 6.1 0.7 - - - -
136B TYR* 4.1 33.2 - - + +
139B GLN* 4.4 15.7 - - + -
140B VAL* 3.7 25.4 - - + -
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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