Contacts of the helix formed by residues 122 - 146 (chain B) in PDB entry 1K0N
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 ASN 122 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B ASN* 3.0 28.5 + - - +
121B SER* 1.3 78.4 + - - +
123B PRO* 1.3 76.9 - - - +
124B ALA* 3.3 19.0 + - - +
125B LEU* 2.6 61.0 + - + +
126B ASN 3.1 1.4 + - - -
240B LEU* 4.4 0.4 - - - -
241B LYS* 4.6 0.4 - - - -
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Residues in contact with PRO 123 (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 SER 3.2 4.0 - - - +
122B ASN* 1.3 90.7 - - - +
124B ALA* 1.3 57.5 + - - +
125B LEU 2.9 5.9 + - - -
126B ASN* 3.0 16.6 + - - +
127B ASP* 4.4 4.3 + - - -
240B LEU* 4.2 23.1 - - + -
241B LYS* 3.1 37.2 - - - +
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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
----------------------------------------------------------
122B ASN* 3.2 18.2 + - - +
123B PRO* 1.3 78.7 - - - +
125B LEU* 1.3 63.1 + - + +
127B ASP* 5.3 1.1 + - - +
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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
----------------------------------------------------------
120B ASN* 3.7 21.1 - - - +
122B ASN* 2.6 33.7 + - + +
124B ALA* 1.3 85.4 - - + +
126B ASN* 1.3 64.9 + - - +
127B ASP 3.5 2.1 + - - -
128B ASN* 3.7 9.3 + - + +
129B LEU* 3.6 23.1 + - + +
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Residues in contact with ASN 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B TYR* 3.1 34.9 + - - -
120B ASN* 3.8 6.9 - - - +
122B ASN 3.1 3.6 + - - -
123B PRO 3.0 13.9 + - - +
125B LEU* 1.3 76.9 - - - +
127B ASP* 1.3 67.7 + - - +
129B LEU* 2.9 8.2 + - - +
130B GLU* 2.7 46.5 + - - +
195B ARG* 3.8 13.3 - - - +
240B LEU* 3.8 34.1 - - + +
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Residues in contact with ASP 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B PRO 4.4 4.1 + - - -
124B ALA 5.3 1.0 + - - +
125B LEU 3.5 0.8 - - - -
126B ASN* 1.3 94.9 - - - +
128B ASN* 1.3 53.3 + - - +
130B GLU* 3.7 10.1 - - - +
131B LYS* 2.7 56.3 + - + +
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Residues in contact with ASN 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B LEU* 3.7 10.4 + - + +
126B ASN 3.3 0.6 - - - -
127B ASP* 1.3 75.7 - - - +
129B LEU* 1.3 70.4 + - + +
131B LYS* 3.5 10.2 + - - +
132B GLY* 3.2 17.2 + - - -
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Residues in contact with LEU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B LYS* 4.6 3.2 - - - +
116B ALA* 3.7 30.7 - - + +
117B TYR* 3.9 20.1 - - + +
120B ASN* 3.5 36.8 - - + +
125B LEU* 3.6 19.2 + - + +
126B ASN* 2.9 6.5 + - - +
128B ASN* 1.3 81.7 - - + +
130B GLU* 1.3 66.3 + - - +
132B GLY* 3.3 2.6 + - - -
133B LEU* 3.1 20.8 + - - +
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Residues in contact with GLU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B TYR* 3.7 28.2 + - + -
126B ASN* 2.7 36.8 + - - +
127B ASP* 3.7 9.8 - - - +
129B LEU* 1.3 70.0 - - - +
131B LYS* 1.3 62.4 + - + +
133B LEU* 3.3 5.1 + - + +
134B LEU* 2.9 46.3 + - + +
197B PHE* 4.0 27.7 - - + -
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Residues in contact with LYS 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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127B ASP* 2.7 43.1 + - - +
128B ASN* 3.8 9.4 - - - +
129B LEU 3.2 0.2 - - - -
130B GLU* 1.3 78.3 - - + +
132B GLY* 1.3 51.8 + - - +
134B LEU* 3.2 10.6 + - + +
135B LYS* 2.7 58.8 + - + +
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Residues in contact with GLY 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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113B LYS* 4.0 22.7 - - - +
128B ASN 3.2 11.3 + - - -
129B LEU* 3.3 3.6 + - - -
130B GLU 3.2 0.4 - - - -
131B LYS* 1.3 77.7 - - - +
133B LEU* 1.3 58.1 + - - +
135B LYS* 3.9 8.8 - - - +
136B ALA* 3.0 28.9 + - - +
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Residues in contact with LEU 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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110B ILE* 3.9 35.7 - - + +
113B LYS* 3.9 13.5 - - + +
114B PHE* 3.9 17.3 - - + +
117B TYR* 3.6 35.7 - - + -
129B LEU 3.1 12.1 + - - +
130B GLU* 3.5 8.5 - - - +
131B LYS 3.2 0.2 - - - -
132B GLY* 1.3 75.9 - - - +
134B LEU* 1.3 56.9 + - - +
136B ALA* 3.2 4.7 + - - +
137B LEU* 3.0 37.5 + - + +
187B VAL* 4.7 3.8 - - + -
191B CYS* 4.3 12.8 - - - -
197B PHE* 4.4 15.9 - - + -
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Residues in contact with LEU 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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130B GLU* 2.9 45.6 + - + +
131B LYS* 3.7 9.0 - - + +
133B LEU* 1.3 73.2 - - - +
135B LYS* 1.3 55.9 + - + +
137B LEU* 3.1 6.9 + - + +
138B LYS* 2.7 37.7 + - - +
197B PHE* 3.6 24.2 - - + -
200B PRO* 3.6 33.2 - - + -
203B PHE* 4.0 9.8 - - + -
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Residues in contact with LYS 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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131B LYS* 2.7 43.5 + - - +
132B GLY* 3.9 7.4 - - - +
134B LEU* 1.3 72.7 - - + +
136B ALA* 1.3 62.8 + - - +
138B LYS* 3.0 50.3 - - + +
139B VAL* 3.1 12.9 + - + +
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Residues in contact with ALA 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B GLY* 5.1 0.9 - - - -
109B ASP* 3.7 28.1 - - - +
110B ILE* 3.9 23.4 - - + +
113B LYS* 4.3 11.4 - - + -
132B GLY 3.0 19.2 + - - +
133B LEU* 3.4 5.8 - - - +
134B LEU 3.2 0.2 - - - -
135B LYS* 1.3 73.9 - - - +
137B LEU* 1.3 64.1 + - - +
139B VAL* 3.2 8.1 + - - +
140B LEU* 3.2 19.9 + - - +
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Residues in contact with LEU 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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110B ILE* 3.9 26.9 - - + -
133B LEU* 3.0 36.2 + - + +
134B LEU* 3.6 11.4 - - + +
136B ALA* 1.3 76.7 - - - +
138B LYS* 1.3 58.4 + - - +
140B LEU* 3.2 3.5 + - + +
141B ASP* 2.8 29.6 + - - +
184B LEU* 4.3 10.5 - - + -
187B VAL* 5.6 4.0 - - + -
197B PHE* 4.5 15.9 - - + -
199B ILE* 4.2 38.4 - - + -
200B PRO* 4.8 0.4 - - + -
203B PHE* 3.7 13.5 - - + -
206B VAL* 3.9 14.2 - - + +
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Residues in contact with LYS 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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134B LEU 2.7 13.4 + - - +
135B LYS* 3.0 49.9 - - + +
136B ALA 3.2 0.2 - - - -
137B LEU* 1.3 78.8 - - - +
139B VAL* 1.3 65.5 + - + +
141B ASP* 3.4 2.9 + - - +
142B ASN* 3.0 39.6 + - - +
203B PHE* 3.6 27.6 - - + -
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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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106B ALA* 6.4 0.7 - - - -
107B GLY 5.8 4.5 - - - +
109B ASP* 6.0 2.7 - - - +
135B LYS* 3.1 15.5 + - + +
136B ALA* 3.6 9.2 - - - +
137B LEU 3.2 0.2 - - - -
138B LYS* 1.3 90.8 - - + +
140B LEU* 1.3 65.5 + - - +
142B ASN* 3.5 10.4 + - - +
143B TYR* 3.2 21.2 + - + +
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Residues in contact with LEU 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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106B ALA* 4.2 15.9 - - + -
107B GLY* 4.2 8.9 - - - +
110B ILE* 3.5 26.5 - - + -
136B ALA 3.2 9.1 + - - +
137B LEU* 3.2 8.2 + - + +
139B VAL* 1.3 76.6 - - - +
141B ASP* 1.3 67.5 + - - +
143B TYR* 3.0 7.9 + - + +
144B LEU* 3.0 42.6 + - + +
168B LEU* 4.0 23.8 - - + -
180B LEU* 4.1 9.6 - - + -
184B LEU* 3.7 26.7 - - + -
206B VAL* 4.3 10.3 - - + -
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Residues in contact with ASP 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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137B LEU 2.8 13.3 + - - +
138B LYS 3.4 10.1 - - - +
139B VAL 3.3 0.2 - - - -
140B LEU* 1.3 76.2 - - - +
142B ASN* 1.3 67.7 + - - +
144B LEU* 2.9 15.8 + - - +
145B THR* 2.9 29.0 + - - +
202B ALA 4.4 2.9 - - - +
203B PHE* 2.9 52.7 - - + -
204B ARG 4.2 1.4 + - - -
205B GLY 3.0 12.2 + - - -
206B VAL* 3.1 16.8 + - + +
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Residues in contact with ASN 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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138B LYS* 3.0 33.9 + - - +
139B VAL* 3.9 10.0 - - - +
140B LEU 3.3 0.4 - - - -
141B ASP* 1.3 79.3 - - - +
143B TYR* 1.3 61.8 + - - +
145B THR* 3.0 14.1 + - - -
146B SER* 2.6 29.5 + - - +
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Residues in contact with TYR 143 (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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100B ASN* 4.0 10.4 + - - +
102B GLU* 3.6 24.6 + - + +
103B SER* 3.1 35.6 + - - -
106B ALA* 3.6 27.8 - - + -
139B VAL* 3.2 12.9 + - + +
140B LEU* 3.0 12.7 + - - +
142B ASN* 1.3 78.9 - - - +
144B LEU* 1.3 54.5 + - - +
146B SER* 3.4 14.0 - - - +
165B ARG* 2.7 30.2 + - - -
168B LEU* 3.6 31.2 + - + -
169B ASP* 5.6 0.2 - - - -
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Residues in contact with LEU 144 (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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140B LEU* 3.0 41.7 + - + +
141B ASP 2.9 5.6 + - - +
143B TYR* 1.3 79.4 - - - +
145B THR* 1.3 58.7 + - - +
146B SER 3.5 0.2 - - - -
165B ARG* 3.2 31.6 + - - +
166B LYS 6.2 0.2 - - - -
167B PHE* 4.2 12.6 - - - +
168B LEU* 4.2 19.5 - - + -
205B GLY* 3.9 17.3 - - - +
206B VAL* 3.9 25.6 - - + +
208B ARG* 5.9 0.5 + - - -
209B TYR* 4.1 29.2 - - + -
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Residues in contact with THR 145 (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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141B ASP* 3.1 32.9 + - - +
142B ASN* 3.0 21.0 + - - -
144B LEU* 1.3 77.7 - - - +
146B SER* 1.3 62.7 + - - +
147B PRO* 3.7 6.9 - - - +
204B ARG* 5.6 2.7 - - + +
205B GLY* 4.1 15.5 - - - +
208B ARG* 5.8 2.0 - - - +
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Residues in contact with SER 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ASN* 2.6 26.0 + - - +
143B TYR* 3.4 10.1 - - - +
145B THR* 1.3 80.7 + - - +
147B PRO* 1.3 78.8 - - - +
165B ARG* 3.2 13.4 + - - -
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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
------------------------------------------------------------
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