Contacts of the helix formed by residues 134 - 157 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103J PHE* 3.7 1.1 - - - -
132J LEU* 3.3 4.1 - - - +
133J LYS* 1.3 79.4 - - - +
135J LYS* 1.3 62.8 + - - +
136J ALA 3.7 1.0 + - - -
137J LEU* 3.5 32.5 + - - +
138J SER* 3.0 26.3 + - - -
130K GLU* 3.1 33.2 + - - -
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Residues in contact with LYS 135 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96J VAL* 4.1 16.6 - - + +
103J PHE* 3.5 49.6 - - + -
134J SER* 1.3 70.2 + - - +
136J ALA* 1.3 68.7 + - - +
138J SER* 2.9 4.9 + - - -
139J LEU* 2.9 29.1 + - + +
95K PHE* 3.4 38.6 - - + +
97K ASP* 2.8 35.2 + - - -
130K GLU* 5.2 0.6 + - - -
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Residues in contact with ALA 136 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134J SER* 3.4 7.8 + - - +
135J LYS* 1.3 79.4 - - - +
137J LEU* 1.3 59.2 + - + +
139J LEU* 3.1 1.2 + - - -
140J GLU* 2.9 29.2 + - - +
95K PHE* 3.4 26.2 - - + -
105K VAL 4.5 1.1 - - - +
126K TYR* 3.7 12.3 - - + -
128K VAL* 3.3 38.1 - - + -
130K GLU* 4.4 5.1 + - - +
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Residues in contact with LEU 137 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132J LEU* 3.8 27.0 - - + +
134J SER* 3.5 27.0 + - - +
135J LYS 3.3 0.4 - - - -
136J ALA* 1.3 83.5 - - + +
138J SER* 1.3 61.6 + - - +
140J GLU* 3.9 19.4 - - - +
141J LYS* 3.1 24.6 + - - +
58K GLY* 5.9 6.1 - - - +
128K VAL* 4.7 9.2 - - + -
130K GLU* 3.8 13.9 - - - +
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Residues in contact with SER 138 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103J PHE* 3.6 17.7 + - - +
105J VAL* 4.0 19.0 - - - +
129J SER* 3.1 33.8 + - - -
132J LEU* 3.2 15.6 + - - +
134J SER 3.0 17.2 + - - -
135J LYS 2.9 9.7 + - - -
137J LEU* 1.3 74.7 - - - +
139J LEU* 1.3 63.9 + - - +
141J LYS 3.5 0.7 + - - -
142J ALA* 3.1 19.6 + - - +
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Residues in contact with LEU 139 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93J VAL* 4.3 15.7 - - + -
96J VAL* 3.8 29.6 - - + -
105J VAL* 3.8 16.4 - - + -
107J VAL* 5.0 0.2 - - + -
135J LYS* 2.9 16.3 + - + +
136J ALA 3.7 2.7 - - - +
138J SER* 1.3 73.6 - - - +
140J GLU* 1.3 68.5 + - - +
142J ALA* 3.1 3.5 + - - -
143J ARG* 2.8 33.9 + - + +
94K ASP* 3.3 35.0 - - + +
95K PHE* 3.7 19.7 - - + -
126K TYR* 3.3 18.2 - - + +
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Residues in contact with GLU 140 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136J ALA 2.9 16.9 + - - +
137J LEU* 3.9 21.1 - - - +
139J LEU* 1.3 75.6 - - - +
141J LYS* 1.3 63.8 + - - +
143J ARG* 4.8 0.2 - - - -
144J LYS* 3.0 67.4 + - + +
126K TYR* 3.6 39.6 - - + +
128K VAL* 4.9 7.3 - - - +
149K ASP* 5.2 0.3 - - - -
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Residues in contact with LYS 141 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128J VAL* 2.8 30.6 + - - +
129J SER* 3.9 14.0 - - - +
132J LEU* 5.1 6.5 - - + -
137J LEU 3.1 17.4 + - - +
138J SER* 3.7 4.3 - - - +
139J LEU 3.1 0.2 - - - -
140J GLU* 1.3 81.1 - - - +
142J ALA* 1.3 57.3 + - - +
144J LYS* 4.1 2.3 - - - +
145J GLU* 3.0 63.9 + - - +
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Residues in contact with ALA 142 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105J VAL* 3.8 13.0 - - + +
107J VAL* 3.7 23.6 - - + -
127J GLY* 3.3 25.4 - - - +
128J VAL* 4.1 8.7 - - - +
138J SER 3.1 13.2 + - - +
139J LEU 3.1 2.6 + - - +
141J LYS* 1.3 77.4 - - - +
143J ARG* 1.3 61.2 + - - +
146J ALA* 2.9 32.9 + - - +
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Residues in contact with ARG 143 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91J GLN* 2.8 61.8 + - - +
93J VAL* 3.5 26.9 - - - +
107J VAL* 4.1 12.3 - - + +
139J LEU* 2.8 29.5 + - + +
140J GLU* 4.2 2.5 - - - +
142J ALA* 1.3 73.5 - - - +
144J LYS* 1.3 65.5 + - + +
146J ALA 3.3 0.2 + - - -
147J VAL* 3.3 13.2 + - - +
92K ASN* 4.4 5.9 - - - +
94K ASP* 2.4 37.2 + - - -
108K CYS* 3.3 26.3 - - - -
110K PHE* 4.3 4.6 - - - -
124K VAL* 4.4 9.4 - - + -
126K TYR* 3.7 25.8 - - + -
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Residues in contact with LYS 144 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140J GLU* 3.0 51.4 + - + +
141J LYS* 4.1 2.7 - - - +
143J ARG* 1.3 76.6 - - + +
145J GLU* 1.3 62.6 + - + +
147J VAL* 3.2 5.4 + - - +
148J THR* 3.2 23.9 + - - -
124K VAL* 4.5 11.0 - - + +
125K GLY 4.6 0.7 - - - -
126K TYR* 4.0 10.3 - - + +
149K ASP* 2.6 36.5 + - - -
153K ARG* 3.6 43.5 + - - +
156K ARG* 6.0 0.8 - - - +
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Residues in contact with GLU 145 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126J TYR 4.7 1.7 - - - +
127J GLY* 4.0 8.0 - - - -
128J VAL* 3.8 10.6 + - - +
141J LYS* 3.0 63.1 + - - +
142J ALA 4.0 2.2 - - - +
144J LYS* 1.3 76.8 - - - +
146J ALA* 1.3 53.0 + - - +
148J THR* 3.3 5.8 + - - +
149J ASP* 2.7 39.5 + - + +
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Residues in contact with ALA 146 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91J GLN* 4.1 0.2 - - - +
107J VAL* 3.5 22.2 - - + +
109J ALA* 3.7 19.1 - - + +
125J GLY* 3.4 9.7 - - - -
126J TYR 3.6 4.7 - - - +
127J GLY* 3.4 21.2 - - - +
142J ALA 2.9 19.2 + - - +
143J ARG 3.6 5.2 - - - +
145J GLU* 1.3 75.6 - - - +
147J VAL* 1.3 58.2 + - - +
150J GLY 2.9 24.1 + - - -
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Residues in contact with VAL 147 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86J HIS* 5.2 7.2 - - + -
88J ILE* 3.8 26.9 - - + -
91J GLN* 3.7 9.4 - - - +
109J ALA* 3.9 11.7 - - + -
111J VAL* 3.7 8.3 - - + +
143J ARG 3.3 5.1 + - - +
144J LYS 3.2 7.1 + - - +
145J GLU 3.2 0.4 - - - -
146J ALA* 1.3 74.0 - - - +
148J THR* 1.3 70.6 + - - +
150J GLY* 2.9 3.6 + - - -
151J LEU* 2.8 22.0 + - + +
122K GLU 4.9 2.0 - - - +
123K ASP* 4.0 22.4 - - - +
124K VAL* 2.9 34.1 - - + -
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Residues in contact with THR 148 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68J GLY* 4.2 26.0 - - - +
144J LYS 3.2 11.7 + - - -
145J GLU* 3.8 8.7 - - - -
147J VAL* 1.3 79.0 - - - +
149J ASP* 1.3 65.2 + - - +
151J LEU* 3.1 11.4 + - + +
152J LYS* 2.9 34.4 + - + +
123K ASP* 5.4 1.0 + - - -
153K ARG* 3.7 13.7 + - - -
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Residues in contact with ASP 149 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140I GLU* 5.1 0.4 - - - -
144I LYS* 2.6 34.4 + - - -
125J GLY* 3.2 3.1 - - - -
126J TYR 2.8 29.2 + - - +
145J GLU 2.7 22.1 + - - +
146J ALA 3.6 4.0 - - - +
148J THR* 1.3 74.0 - - - +
150J GLY* 1.3 64.2 + - - +
152J LYS* 3.2 18.3 + - - +
153J ARG* 3.0 28.7 + - - +
156J ARG* 5.2 4.2 + - - -
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Residues in contact with GLY 150 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109J ALA 4.6 0.2 - - - -
111J VAL* 3.8 16.4 - - - +
123J ASP* 4.3 2.4 - - - +
124J VAL 4.0 5.4 - - - -
125J GLY* 3.2 22.6 - - - -
146J ALA 2.9 13.3 + - - -
147J VAL 2.9 4.1 + - - -
149J ASP* 1.3 76.3 - - - +
151J LEU* 1.3 62.5 + - - -
153J ARG* 3.2 3.8 + - - +
154J ALA* 2.9 23.6 + - - +
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Residues in contact with LEU 151 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71J VAL* 5.6 0.7 - - + -
72J ILE* 4.6 18.8 - - + -
84J TRP* 4.0 13.9 - - + -
86J HIS* 3.7 40.2 - - + +
111J VAL* 3.7 13.4 - - + +
113J VAL* 3.6 23.6 - - + -
147J VAL* 2.8 16.9 + - + +
148J THR* 3.6 13.7 - - + +
150J GLY* 1.3 70.3 - - - +
152J LYS* 1.3 65.4 + - + +
154J ALA* 3.2 1.0 + - - +
155J LEU* 3.0 37.9 + - + +
123K ASP* 6.0 0.7 - - - +
157K SER* 5.1 0.7 - - - +
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Residues in contact with LYS 152 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55J ARG* 6.2 0.2 - - - +
65J TYR* 4.2 16.0 - - - +
66J ILE* 2.9 33.6 + - + +
68J GLY* 4.3 12.2 - - - +
71J VAL* 3.8 33.0 - - + -
148J THR* 2.9 29.8 + - + +
149J ASP* 3.6 21.4 + - - +
151J LEU* 1.3 76.3 - - + +
153J ARG* 1.3 65.0 + - + +
154J ALA 3.2 0.2 + - - -
155J LEU* 3.2 3.6 + - - +
156J ARG* 3.0 35.9 + - + +
162J LEU 4.6 1.7 - - - +
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Residues in contact with ARG 153 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144I LYS* 3.5 68.2 + - - +
147I VAL* 5.0 0.4 - - - +
148I THR* 3.8 13.1 + - - -
123J ASP* 3.1 37.8 + - + +
124J VAL 2.9 26.7 + - - +
149J ASP* 3.0 21.6 + - - +
150J GLY 3.2 3.8 + - - +
152J LYS* 1.3 77.3 - - + +
154J ALA* 1.3 62.0 + - - +
156J ARG* 3.5 54.6 - - - +
157J SER* 3.9 4.9 + - - -
167J LEU* 5.8 0.2 - - - +
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Residues in contact with ALA 154 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111J VAL 4.0 13.0 - - - +
113J VAL* 3.5 26.5 - - + -
121J HIS* 3.8 21.8 + - - +
122J GLU 5.0 0.9 - - - -
123J ASP* 3.9 10.3 - - - +
150J GLY 2.9 16.7 + - - +
151J LEU* 3.5 3.1 - - - +
152J LYS 3.1 0.2 - - - -
153J ARG* 1.3 76.0 - - - +
155J LEU* 1.3 65.7 + - - +
157J SER* 3.1 23.4 + - - -
158J PHE* 4.4 1.0 + - - -
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Residues in contact with LEU 155 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71J VAL* 3.3 39.9 - - + +
72J ILE* 5.6 0.4 - - + -
75J ALA* 4.4 7.4 - - + -
79J PHE* 4.7 3.1 - - + -
84J TRP* 4.2 17.7 - - + -
113J VAL* 3.7 24.9 - - + -
151J LEU* 3.0 39.5 + - + +
152J LYS 3.8 3.6 - - - +
154J ALA* 1.3 75.1 - - - +
156J ARG* 1.3 64.8 + - - +
158J PHE* 2.9 37.1 + - + +
162J LEU* 3.5 24.5 - - + +
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Residues in contact with ARG 156 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72I ILE* 4.7 3.1 - - + -
144I LYS* 5.9 1.2 - - - +
65J TYR* 6.4 0.2 - - - +
149J ASP* 5.2 4.8 + - - -
152J LYS* 3.0 27.5 + - + +
153J ARG* 3.5 52.6 - - - +
154J ALA 3.2 0.6 - - - -
155J LEU* 1.3 75.8 - - - +
157J SER* 1.3 64.2 + - - +
158J PHE 2.9 1.8 + - - -
159J GLY 3.1 10.9 + - - -
162J LEU 3.8 11.3 + - - +
163J GLY* 3.6 23.8 - - - +
164J ASN* 3.4 27.6 - - - +
166J ILE* 3.9 19.7 - - - +
167J LEU* 3.4 34.5 - - - +
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Residues in contact with SER 157 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72I ILE* 3.4 23.1 - - - +
76I ASN* 3.3 20.3 + - - +
84I TRP* 3.7 11.6 - - - -
86I HIS* 3.4 17.8 + - - -
151I LEU* 4.9 1.9 - - - +
121J HIS* 3.4 29.4 - - - +
123J ASP* 4.7 3.6 + - - -
153J ARG 3.9 6.3 + - - -
154J ALA* 3.1 14.0 + - - -
155J LEU 3.0 1.4 + - - -
156J ARG* 1.3 79.9 - - - +
158J PHE* 1.3 58.4 + - - +
159J GLY 3.4 0.2 - - - -
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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