Contacts of the helix formed by residues 134 - 156 (chain K) in PDB entry 1KN0
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 SER 134 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A GLU* 3.2 34.0 + - - -
103K PHE* 3.7 1.1 - - - -
132K LEU* 3.3 3.6 - - - +
133K LYS* 1.3 79.3 - - - +
135K LYS* 1.3 64.0 + - - +
136K ALA 3.7 0.7 + - - -
137K LEU* 3.4 33.0 + - - +
138K SER* 3.2 24.4 + - - -
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Residues in contact with LYS 135 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A PHE* 3.5 38.0 - - + +
97A ASP* 2.9 34.3 + - - -
130A GLU* 5.2 0.8 + - - -
96K VAL* 4.1 17.9 - - + -
103K PHE* 3.4 46.3 - - + -
105K VAL* 6.1 0.2 - - + -
133K LYS 3.7 0.4 + - - -
134K SER* 1.3 69.6 + - - +
136K ALA* 1.3 66.7 + - - +
138K SER* 3.0 4.0 + - - -
139K LEU* 3.0 29.9 + - + +
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Residues in contact with ALA 136 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A PHE* 3.3 26.6 - - + -
105A VAL 4.5 2.5 - - - +
126A TYR* 3.5 12.1 - - + -
128A VAL* 3.6 35.2 - - + -
130A GLU* 4.3 5.8 + - - +
134K SER* 3.7 6.9 + - - +
135K LYS* 1.3 79.9 - - - +
137K LEU* 1.3 58.4 + - + +
139K LEU* 3.3 0.5 + - - +
140K GLU* 2.9 29.5 + - - +
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Residues in contact with LEU 137 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLY* 6.0 4.5 - - - +
128A VAL* 4.7 9.2 - - + -
130A GLU* 3.8 13.2 - - - +
132K LEU* 3.8 25.6 - - + +
134K SER* 3.4 27.1 + - - +
135K LYS 3.3 0.2 - - - -
136K ALA* 1.3 84.4 - - + +
138K SER* 1.3 61.3 - - - +
140K GLU* 3.9 18.7 - - - +
141K LYS* 3.1 24.6 + - - +
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Residues in contact with SER 138 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103K PHE* 3.6 19.4 + - - +
105K VAL* 4.0 20.0 - - - -
129K SER* 3.1 33.1 + - - -
132K LEU* 3.4 13.4 - - - +
134K SER 3.2 14.8 + - - -
135K LYS* 3.0 9.7 + - - -
137K LEU* 1.3 74.5 - - - +
139K LEU* 1.3 60.0 + - - +
141K LYS 3.4 0.7 + - - -
142K ALA* 3.0 26.3 + - - +
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Residues in contact with LEU 139 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ASP* 3.4 26.0 - - + +
95A PHE* 3.7 19.3 - - + -
126A TYR* 3.4 26.0 - - + +
93K VAL* 4.3 17.9 - - + -
96K VAL* 3.8 19.5 - - + -
105K VAL* 3.7 25.8 - - + -
107K VAL* 5.0 0.2 - - + -
135K LYS* 3.0 15.9 + - + +
136K ALA 3.8 2.0 - - - +
138K SER* 1.3 74.0 - - - +
140K GLU* 1.3 68.5 + - - +
142K ALA* 2.9 3.6 + - - -
143K ARG* 2.8 34.4 + - + +
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Residues in contact with GLU 140 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A TYR* 3.5 39.0 - - + +
128A VAL* 4.8 5.7 - - - +
149A ASP* 4.4 1.2 - - - +
136K ALA 2.9 17.5 + - - +
137K LEU* 3.9 23.1 - - - +
139K LEU* 1.3 76.6 - - - +
141K LYS* 1.3 63.5 + - - +
143K ARG* 4.8 0.2 - - - -
144K LYS* 3.1 65.0 + - + +
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Residues in contact with LYS 141 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128K VAL* 2.9 30.8 + - - +
129K SER* 3.9 13.4 - - - +
132K LEU* 5.1 5.4 - - + -
137K LEU 3.1 16.5 + - - +
138K SER 3.6 3.6 - - - +
139K LEU 3.1 0.8 - - - -
140K GLU* 1.3 81.5 - - - +
142K ALA* 1.3 57.1 + - - +
144K LYS* 4.1 2.1 - - - +
145K GLU* 2.9 64.0 + - - +
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Residues in contact with ALA 142 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105K VAL* 3.6 27.8 - - + +
107K VAL* 3.7 9.1 - - + +
127K GLY* 3.2 33.4 - - - +
128K VAL* 4.1 4.7 - - - +
138K SER 3.0 16.6 + - - +
139K LEU 2.9 2.8 + - - +
141K LYS* 1.3 74.7 - - - +
143K ARG* 1.3 64.8 + - - +
146K ALA* 3.0 23.6 + - - +
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Residues in contact with ARG 143 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ASN* 4.4 6.3 - - - +
94A ASP* 2.4 45.0 + - - -
108A CYS* 3.4 24.5 - - - -
110A PHE* 4.2 6.5 - - - -
124A VAL* 4.4 9.0 - - + -
126A TYR* 3.8 14.1 - - + -
91K GLN* 2.6 63.6 + - - +
93K VAL* 3.5 27.5 - - - +
107K VAL* 4.2 12.1 - - + +
139K LEU* 2.8 30.1 + - + +
140K GLU* 4.2 3.1 - - - +
142K ALA* 1.3 73.0 - - - +
144K LYS* 1.3 63.5 + - + +
146K ALA* 3.5 0.3 + - - +
147K VAL* 3.3 15.1 + - - +
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Residues in contact with LYS 144 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A VAL* 4.4 12.1 - - + +
125A GLY 4.6 0.2 - - - -
126A TYR* 4.0 10.3 - - + +
149A ASP* 2.6 36.9 + - - -
153A ARG* 3.5 45.2 + - - +
156A ARG* 6.0 0.6 - - - +
140K GLU* 3.1 50.8 + - + +
141K LYS* 4.2 2.2 - - - +
143K ARG* 1.3 77.0 - - + +
145K GLU* 1.3 63.3 + - - +
147K VAL* 3.3 2.8 + - - +
148K THR* 3.1 25.4 + - - -
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Residues in contact with GLU 145 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126K TYR 4.1 4.2 - - - +
127K GLY* 3.9 10.0 - - - -
128K VAL* 3.6 12.0 + - - +
141K LYS* 2.9 63.4 + - - +
144K LYS* 1.3 76.7 - - - +
146K ALA* 1.3 53.6 + - - +
148K THR* 3.2 6.2 + - - -
149K ASP* 2.7 36.5 + - + +
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Residues in contact with ALA 146 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107K VAL* 3.5 20.0 - - + +
109K ALA* 3.7 21.8 - - + +
125K GLY* 3.3 8.8 - - - -
126K TYR* 3.4 14.6 - - - +
127K GLY* 3.4 14.2 - - - +
142K ALA 3.0 19.8 + - - +
143K ARG 3.7 4.9 - - - +
144K LYS 3.4 0.2 - - - -
145K GLU* 1.3 74.3 - - - +
147K VAL* 1.3 58.3 + - - +
150K GLY* 2.9 23.4 + - - -
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Residues in contact with VAL 147 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A GLU 4.7 2.9 - - - +
123A ASP* 3.8 24.0 - - - +
124A VAL* 3.0 30.7 - - + -
86K HIS* 5.1 6.5 - - + -
88K ILE* 3.8 29.2 - - + -
91K GLN* 3.5 15.3 - - - +
109K ALA* 4.0 12.3 - - + -
111K VAL* 3.7 7.8 - - + +
143K ARG 3.3 1.8 + - - +
144K LYS 3.7 6.5 - - - +
145K GLU 3.2 1.0 - - - -
146K ALA* 1.3 74.3 - - - +
148K THR* 1.3 62.4 + - - +
150K GLY* 3.0 2.8 + - - -
151K LEU* 2.8 27.0 + - + +
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Residues in contact with THR 148 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A ASP* 5.4 1.4 + - - -
153A ARG* 3.8 13.2 + - - -
68K GLY* 4.1 27.1 - - - +
144K LYS 3.1 11.7 + - - -
145K GLU* 3.8 7.6 - - - -
147K VAL* 1.3 78.0 - - - +
149K ASP* 1.3 64.8 + - - +
151K LEU* 3.1 12.1 + - + +
152K LYS* 2.9 35.6 + - + +
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Residues in contact with ASP 149 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140J GLU* 5.2 0.2 - - - -
144J LYS* 2.6 35.2 + - - -
125K GLY* 3.3 2.6 - - - -
126K TYR 2.9 31.1 + - - +
145K GLU* 2.7 21.4 + - + +
146K ALA 3.8 0.2 - - - +
148K THR* 1.3 73.1 - - - +
150K GLY* 1.3 58.5 + - - +
152K LYS* 3.3 17.6 + - - +
153K ARG* 2.9 36.2 + - - +
156K ARG* 5.0 4.9 + - - -
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Residues in contact with GLY 150 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109K ALA 4.4 0.4 - - - -
111K VAL* 3.8 16.7 - - - +
123K ASP* 4.4 3.3 - - - +
124K VAL 4.0 4.3 - - - -
125K GLY* 3.3 22.4 - - - -
146K ALA 2.9 14.4 + - - -
147K VAL 3.0 3.8 + - - -
149K ASP* 1.3 76.7 - - - +
151K LEU* 1.3 61.7 + - - +
153K ARG* 3.3 2.9 + - - +
154K ALA* 2.9 23.9 + - - +
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Residues in contact with LEU 151 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ASP* 6.0 0.4 - - - +
157A SER* 5.1 0.2 - - - +
71K VAL* 5.7 0.4 - - + -
72K ILE* 4.6 20.0 - - + -
84K TRP* 3.8 21.8 - - + -
86K HIS* 3.7 33.9 - - + +
111K VAL* 3.7 12.8 - - + +
113K VAL* 3.7 22.7 - - + -
147K VAL* 2.8 16.3 + - + +
148K THR* 3.5 13.0 - - + +
150K GLY* 1.3 72.8 - - - +
152K LYS* 1.3 64.9 + - + +
154K ALA* 3.2 2.2 + - - +
155K LEU* 3.0 39.2 + - + +
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Residues in contact with LYS 152 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55K ARG* 6.2 0.2 - - - +
65K TYR* 4.2 16.0 - - - +
66K ILE* 2.8 33.9 + - + +
67K GLU* 4.7 0.2 - - - +
68K GLY* 4.3 11.9 - - - +
71K VAL* 3.7 35.4 - - + -
148K THR* 2.9 30.9 + - + +
149K ASP* 3.7 19.2 + - - +
151K LEU* 1.3 77.3 - - + +
153K ARG* 1.3 66.0 + - + +
154K ALA 3.2 0.2 + - - -
155K LEU* 3.3 2.1 + - - +
156K ARG* 3.1 36.7 + - + +
162K LEU 4.8 1.4 - - - +
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Residues in contact with ARG 153 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144J LYS* 3.6 54.3 + - - +
147J VAL* 4.9 0.8 - - - +
148J THR* 3.7 13.9 + - - -
123K ASP* 2.9 41.4 + - - +
124K VAL 2.9 25.9 + - - +
149K ASP* 2.9 32.8 + - - +
150K GLY 3.8 2.7 - - - +
152K LYS* 1.3 77.8 - - - +
154K ALA* 1.3 62.2 + - - +
156K ARG* 3.4 52.7 - - - +
157K SER* 4.0 4.2 + - - -
167K LEU* 6.0 0.2 - - - +
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Residues in contact with ALA 154 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111K VAL 4.0 13.0 - - - +
113K VAL* 3.4 26.5 - - + -
121K HIS* 3.8 22.1 + - - +
122K GLU 4.9 0.7 - - - -
123K ASP* 3.8 11.4 - - - +
150K GLY 2.9 17.0 + - - +
151K LEU* 3.6 1.8 - - - +
153K ARG* 1.3 75.6 - - - +
155K LEU* 1.3 65.7 + - - +
157K SER* 3.0 24.1 + - - -
158K PHE* 4.4 0.5 + - - -
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Residues in contact with LEU 155 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71K VAL* 3.3 41.5 - - + +
72K ILE* 6.1 0.2 - - + -
75K ALA* 4.3 8.3 - - + -
79K PHE* 4.8 2.7 - - + -
84K TRP* 4.1 18.4 - - + -
113K VAL* 3.8 24.2 - - + -
151K LEU* 3.0 40.5 + - + +
152K LYS 3.8 3.1 - - - +
154K ALA* 1.3 75.5 - - - +
156K ARG* 1.3 63.7 + - - +
157K SER 2.9 0.2 - - - -
158K PHE* 2.8 37.3 + - + +
162K LEU* 3.6 24.5 - - + +
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Residues in contact with ARG 156 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72J ILE* 4.7 4.7 - - + -
144J LYS* 6.0 0.8 - - - +
65K TYR* 6.4 0.2 - - - +
149K ASP* 5.0 5.7 + - - -
152K LYS* 3.1 25.3 + - + +
153K ARG* 3.4 51.7 - - - +
154K ALA 3.1 0.6 - - - -
155K LEU* 1.3 75.7 - - - +
157K SER* 1.3 61.0 + - - +
158K PHE 3.1 1.6 + - - -
159K GLY 3.3 10.2 + - - -
162K LEU 3.9 11.6 + - - +
163K GLY* 3.7 25.8 - - - +
164K ASN* 3.4 26.8 - - - +
166K ILE* 3.9 19.7 - - - +
167K LEU* 3.4 35.7 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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