Contacts of the helix formed by residues 126 - 149 (chain A) in PDB entry 1TK0
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 126 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A SER* 5.1 4.0 + - - +
99A HIS* 4.1 24.2 - - + +
102A LEU* 4.1 15.9 - - + +
103A LYS 5.1 2.4 + - - -
125A LEU* 1.3 71.4 - - - +
127A ALA* 1.3 60.0 + - - +
128A TRP* 3.0 28.7 + - - +
129A GLY* 2.7 30.8 + - - -
130A TYR* 2.9 26.2 + - - +
181A LEU* 3.9 15.0 - - + +
184A LYS* 2.7 34.9 + - - +
995A SO4 4.1 11.4 - - - +
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Residues in contact with ALA 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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125A LEU 3.3 5.4 + - - +
126A GLU* 1.3 74.5 + - - +
128A TRP* 1.3 72.5 + - + +
130A TYR* 3.2 8.3 + - - +
131A ARG* 3.0 28.2 + - + +
184A LYS* 4.9 2.8 - - - +
995A SO4 4.9 1.4 + - - -
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Residues in contact with TRP 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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126A GLU* 3.0 23.9 + - - +
127A ALA* 1.3 78.7 - - + +
129A GLY* 1.3 57.9 + - - +
131A ARG* 3.2 13.9 + - + +
132A LEU* 3.0 32.8 + - - +
177A VAL* 3.6 37.1 - - + +
180A ALA* 3.9 24.0 + - + +
181A LEU* 3.8 31.4 - - + -
184A LYS* 4.1 16.0 - - + +
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Residues in contact with GLY 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A HIS* 4.7 12.3 + - - -
92A LEU* 6.4 0.2 - - - -
95A SER* 5.8 1.3 - - - -
104A ASP* 6.5 0.9 - - - -
105A THR* 5.5 0.5 + - - -
107A MET* 5.6 0.2 - - - +
126A GLU* 2.7 23.4 + - - -
128A TRP* 1.3 69.6 - - - +
130A TYR* 1.3 66.3 + - - +
132A LEU* 3.5 11.3 + - - +
133A GLY* 2.9 20.3 + - - -
181A LEU* 4.5 2.9 - - - +
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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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105A THR* 4.8 6.2 + - + -
112A SER* 3.5 35.0 + - - -
125A LEU* 3.8 27.6 - - + +
126A GLU 2.9 16.2 + - - +
127A ALA* 3.2 12.1 + - - +
129A GLY* 1.3 77.5 - - - +
131A ARG* 1.3 85.9 + - + +
133A GLY* 3.1 4.1 + - - -
134A GLU* 3.0 58.4 + - + +
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Residues in contact with ARG 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 ALA 3.0 15.7 + - - +
128A TRP* 3.3 21.8 - - + +
130A TYR* 1.3 98.6 - - + +
132A LEU* 1.3 63.2 + - - +
134A GLU* 3.0 14.3 + - - +
135A MET* 3.1 30.7 + - + +
138A GLU* 2.7 34.4 + - - -
177A VAL* 4.5 13.7 - - + -
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Residues in contact with LEU 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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59A HIS* 3.5 48.0 - - + +
107A MET* 4.2 11.9 - - + +
128A TRP 3.0 19.9 + - - +
129A GLY 3.8 3.1 - - - +
131A ARG* 1.3 77.5 - - - +
133A GLY* 1.3 62.3 + - - +
134A GLU 3.3 0.3 + - - -
135A MET* 3.4 19.2 + - + +
136A LYS* 5.0 0.5 + - - +
174A ASP* 3.5 43.5 - - + +
177A VAL* 3.6 20.2 - - + -
178A THR* 3.7 13.2 - - - +
181A LEU* 4.1 12.1 - - + -
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Residues in contact with GLY 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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105A THR* 4.2 7.2 - - - -
107A MET* 3.6 28.7 - - - +
108A GLY* 3.5 21.7 + - - -
129A GLY 2.9 16.0 + - - -
130A TYR 3.1 4.5 + - - -
132A LEU* 1.3 78.3 - - - +
134A GLU* 1.3 62.5 + - - +
135A MET 3.7 0.3 + - - -
136A LYS* 4.7 5.7 + - - +
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Residues in contact with GLU 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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105A THR* 4.0 17.8 + - - +
108A GLY* 4.7 5.0 - - - -
110A LEU 5.1 1.2 - - - +
112A SER* 4.6 5.3 + - - -
130A TYR* 3.0 59.2 + - + +
131A ARG* 3.0 8.5 + - - +
133A GLY* 1.3 79.8 - - - +
135A MET* 1.3 60.3 + - - +
136A LYS 3.4 2.7 - - - -
137A GLY* 3.5 6.3 + - - +
138A GLU* 2.8 41.1 + - + +
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Residues in contact with MET 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 ARG* 3.1 33.6 + - - +
132A LEU* 3.4 18.0 + - + +
134A GLU* 1.3 76.9 - - - +
136A LYS* 1.3 59.9 + - + +
138A GLU* 2.9 44.5 - - + +
139A TYR* 2.7 32.4 + - - +
170A TYR* 3.9 23.7 - - + +
173A GLN* 5.2 8.3 - - - -
174A ASP* 2.9 35.4 - - - +
177A VAL* 6.1 3.6 - - - -
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Residues in contact with LYS 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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11A LEU* 3.6 2.4 - - - +
107A MET* 5.1 4.9 - - + +
132A LEU 5.0 0.4 + - - +
133A GLY 4.7 5.2 + - - +
134A GLU 3.4 0.6 - - - -
135A MET* 1.3 77.1 - - + +
137A GLY* 1.3 65.1 + - - +
139A TYR* 3.0 6.7 + - - +
140A LYS* 2.9 23.2 + - - +
159A GLU* 5.3 0.2 - - - +
160A TRP* 3.9 28.3 + - + +
901A 1PE 2.8 120.6 + - - +
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Residues in contact with GLY 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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133A GLY 5.5 0.4 + - - -
134A GLU* 3.5 8.4 + - - +
136A LYS* 1.3 78.8 - - - +
138A GLU* 1.3 61.0 + - - +
140A LYS* 3.3 13.4 + - - +
141A ASP* 3.1 29.3 + - - +
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Residues in contact with GLU 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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131A ARG* 2.7 32.5 + - - -
134A GLU* 2.8 24.6 + - + +
135A MET* 2.9 30.3 - - + +
137A GLY* 1.3 77.1 - - - +
139A TYR* 1.3 56.9 + - - +
141A ASP* 3.3 12.3 + - - +
142A ASP* 2.4 34.4 + - - +
170A TYR* 3.5 14.8 + - - +
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Residues in contact with TYR 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 MET 2.7 22.2 + - - +
136A LYS* 3.4 3.4 - - - +
138A GLU* 1.3 70.9 - - - +
140A LYS* 1.3 67.5 + - - +
142A ASP* 3.2 2.6 + - - +
143A PHE* 3.0 25.7 + + - +
159A GLU* 2.7 49.0 + - + -
160A TRP* 3.5 34.8 - + + -
164A ASN* 3.1 20.4 + - - -
166A GLU* 3.5 29.4 - - + -
167A MET* 3.6 18.3 - - + +
170A TYR* 3.6 39.9 + + + -
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Residues in contact with LYS 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 LYS 2.9 13.6 + - - +
137A GLY* 3.4 14.8 - - - +
139A TYR* 1.3 81.4 - - - +
141A ASP* 1.3 58.5 + - - +
143A PHE* 3.3 6.5 + - - +
144A LYS* 2.9 57.9 + - + +
154A TYR* 3.5 23.3 + - + +
156A ASP 5.3 2.0 + - - -
159A GLU* 3.4 29.4 - - - +
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Residues in contact with ASP 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 GLY 3.1 21.5 + - - +
138A GLU* 3.4 15.4 - - + +
139A TYR 3.2 0.2 - - - -
140A LYS* 1.3 79.7 - - - +
142A ASP* 1.3 65.6 + - - +
144A LYS* 3.2 10.1 + - - +
145A ARG* 2.9 37.1 + - - +
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Residues in contact with ASP 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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138A GLU* 2.4 27.4 - - - +
139A TYR 3.2 6.3 + - - +
141A ASP* 1.3 75.9 - - - +
143A PHE* 1.3 59.8 + - - +
145A ARG* 3.1 26.9 + - - +
146A MET* 2.9 36.1 + - + +
166A GLU* 3.8 14.4 - - + +
170A TYR* 2.7 29.2 + - + -
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Residues in contact with PHE 143 (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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139A TYR* 3.0 25.7 + - + +
140A LYS 3.6 7.4 - - - +
142A ASP* 1.3 80.7 - - - +
144A LYS* 1.3 62.9 + - - +
146A MET* 3.3 5.1 + - + +
147A LEU* 3.1 54.1 + - + +
154A TYR* 4.5 5.8 - + - -
158A MET* 3.7 32.8 - - + -
159A GLU* 3.9 27.8 - - + -
164A ASN* 3.7 20.2 - - - -
166A GLU* 3.5 24.6 + - - +
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Residues in contact with LYS 144 (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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140A LYS* 2.9 52.7 + - + +
141A ASP* 3.7 9.2 - - - +
143A PHE* 1.3 73.5 - - - +
145A ARG* 1.3 62.5 + - - +
147A LEU* 3.4 4.1 + - - +
148A GLU* 3.1 46.0 + - - +
154A TYR* 3.4 48.2 - - + -
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Residues in contact with ARG 145 (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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141A ASP* 2.9 24.3 + - - +
142A ASP* 3.5 35.0 + - - +
144A LYS* 1.3 74.4 - - - +
146A MET* 1.3 70.6 + - + +
148A GLU* 3.5 5.1 + - - +
149A GLU* 3.0 45.3 + - - +
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Residues in contact with MET 146 (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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142A ASP* 2.9 21.4 + - + +
143A PHE* 3.3 6.0 + - + +
145A ARG* 1.3 81.7 - - + +
147A LEU* 1.3 63.5 + - + +
149A GLU* 3.2 21.5 - - - +
150A GLN* 3.1 24.1 - - + +
166A GLU* 3.6 34.1 - - - +
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Residues in contact with LEU 147 (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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143A PHE* 3.1 36.5 + - + +
144A LYS* 3.7 7.4 - - - +
145A ARG 3.2 0.2 - - - -
146A MET* 1.3 75.2 - - + +
148A GLU* 1.3 56.8 + - + +
149A GLU 2.8 4.3 - - - -
150A GLN* 2.5 29.8 + - + +
151A GLY 3.0 9.0 + - - -
152A GLU* 3.4 39.0 + - + +
153A GLU 3.8 14.4 - - - +
154A TYR* 4.3 9.0 - - + +
158A MET* 3.6 37.5 - - + -
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Residues in contact with GLU 148 (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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144A LYS* 3.1 38.4 + - - +
145A ARG* 3.8 4.7 - - - +
147A LEU* 1.3 74.6 - - + +
149A GLU* 1.3 58.1 + - - +
150A GLN 3.2 0.2 - - - -
151A GLY* 3.8 10.0 + - - +
152A GLU 3.8 13.5 - - - +
153A GLU* 5.5 0.9 - - - -
154A TYR* 4.8 11.9 - - + +
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Residues in contact with GLU 149 (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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145A ARG* 3.0 39.6 + - - +
146A MET* 3.2 19.7 - - - +
147A LEU 2.8 0.2 - - - -
148A GLU* 1.3 78.8 - - - +
150A GLN* 1.3 69.9 + - + +
151A GLY 3.5 0.4 - - - -
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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