Contacts of the helix formed by residues 134 - 157 (chain U) in PDB entry 5XS0
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 U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103U PHE* 4.0 0.7 - - - -
132U LEU* 3.4 0.5 - - - +
133U LYS* 1.3 71.9 - - - +
135U LYS* 1.3 63.5 + - - +
136U ALA* 3.6 4.0 + - - +
137U LEU* 3.2 39.7 + - - +
138U SER* 2.9 27.4 + - - -
130V GLU* 4.0 18.7 + - - -
8X C 2.7 21.5 + - - -
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Residues in contact with LYS 135 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96U VAL* 4.2 16.2 - - + -
103U PHE* 3.6 50.3 - - + -
133U LYS 3.6 1.2 + - - -
134U SER* 1.3 71.4 - - - +
136U ALA* 1.3 58.0 + - - +
138U SER* 3.2 4.6 + - - -
139U LEU* 2.9 37.6 + - + +
95V PHE* 3.5 37.9 - - + +
97V ASP* 3.0 34.6 + - - -
130V GLU* 5.7 0.4 + - - -
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Residues in contact with ALA 136 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134U SER* 3.3 6.6 + - - +
135U LYS* 1.3 80.4 - - - +
137U LEU* 1.3 58.1 + - + +
139U LEU 3.4 0.2 + - - -
140U GLU* 2.9 26.6 + - - +
95V PHE* 3.5 26.9 - - + -
105V VAL 4.8 0.7 - - - +
106V GLY* 4.7 1.6 - - - -
126V TYR* 3.4 13.8 - - + -
128V VAL* 3.6 37.9 - - + -
130V GLU* 4.8 5.8 + - + +
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Residues in contact with LEU 137 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132U LEU* 4.7 12.1 - - + +
134U SER* 3.2 22.7 + - - +
136U ALA* 1.3 81.8 - - + +
138U SER* 1.3 60.8 + - - +
140U GLU* 3.8 17.9 - - - +
141U LYS* 2.9 32.1 + - - +
128V VAL* 4.8 8.3 - - + -
130V GLU* 4.7 9.2 - - - +
8X C 3.4 46.7 - - + +
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Residues in contact with SER 138 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103U PHE* 3.9 12.6 + - - +
105U VAL* 4.0 20.4 - - - -
129U SER* 3.3 28.2 + - - -
132U LEU* 3.4 16.6 - - - +
134U SER 2.9 21.3 + - - -
135U LYS* 3.5 7.2 - - - -
137U LEU* 1.3 77.5 - - - +
139U LEU* 1.3 57.3 + - - +
142U ALA* 2.9 31.8 + - - +
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Residues in contact with LEU 139 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93U VAL* 4.5 9.2 - - + -
96U VAL* 4.0 25.4 - - + -
105U VAL* 4.0 13.0 - - + -
107U VAL* 4.9 1.3 - - + -
135U LYS* 2.9 21.9 + - + +
136U ALA 3.8 0.2 - - - +
138U SER* 1.3 75.6 - - - +
140U GLU* 1.3 64.5 + - - +
142U ALA* 3.9 2.4 - - - +
143U ARG* 2.9 41.6 + - + +
94V ASP* 3.6 19.7 - - + +
95V PHE* 3.6 28.0 - - + -
126V TYR* 3.3 27.4 - - + +
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Residues in contact with GLU 140 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136U ALA 2.9 16.2 + - - +
137U LEU* 3.8 21.1 - - - +
139U LEU* 1.3 74.6 - - - +
141U LYS* 1.3 66.0 + - - +
143U ARG* 4.0 0.8 - - - -
144U LYS* 2.7 65.5 + - + +
126V TYR* 3.6 34.3 - - + +
128V VAL* 4.5 8.5 - - - +
149V ASP* 4.5 0.5 - - - +
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Residues in contact with LYS 141 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128U VAL 3.3 22.8 + - - +
129U SER* 3.9 17.2 - - - +
130U GLU 5.3 0.8 - - - +
132U LEU* 4.7 11.5 - - + +
137U LEU 2.9 18.5 + - - +
138U SER 3.8 2.9 - - - +
140U GLU* 1.3 77.6 - - - +
142U ALA* 1.3 57.3 + - - +
144U LYS* 4.2 2.8 - - - +
145U GLU* 2.9 63.5 + - + +
7X C 5.2 8.5 + - - -
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Residues in contact with ALA 142 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105U VAL* 3.8 16.4 - - + +
107U VAL* 3.7 23.3 - - + +
127U GLY* 3.4 26.5 - - - +
128U VAL 4.3 6.3 - - - +
138U SER 2.9 17.4 + - - +
139U LEU 3.9 1.8 - - - +
140U GLU 3.3 0.2 - - - -
141U LYS* 1.3 77.3 - - - +
143U ARG* 1.3 57.8 + - - +
146U ALA* 2.9 31.4 + - - +
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Residues in contact with ARG 143 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91U GLN* 2.7 54.4 + - - +
93U VAL* 3.4 30.1 - - + +
107U VAL* 4.0 12.3 - - + -
139U LEU* 2.9 25.4 + - - +
140U GLU* 4.0 3.1 - - - +
142U ALA* 1.3 75.4 - - - +
144U LYS* 1.3 63.7 + - + +
146U ALA 3.2 1.4 + - - -
147U VAL* 3.0 22.2 + - - +
92V ASN* 4.6 7.5 - - - +
94V ASP* 2.7 37.4 + - - -
108V CYS* 3.5 38.0 - - - +
110V PHE* 4.2 6.5 - - - -
124V VAL* 4.4 10.3 - - + -
126V TYR* 4.1 5.6 - - + -
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Residues in contact with LYS 144 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140U GLU* 2.7 56.0 + - + +
141U LYS* 4.2 2.9 - - - +
143U ARG* 1.3 76.3 - - + +
145U GLU* 1.3 59.2 + - + +
147U VAL* 3.3 2.8 + - - -
148U THR* 2.9 33.4 + - - -
124V VAL* 4.1 9.9 - - + +
125V GLY* 4.5 0.2 - - - -
126V TYR* 4.0 10.5 - - + +
149V ASP* 2.7 33.6 + - - -
153V ARG* 3.5 45.2 + - - +
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Residues in contact with GLU 145 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126U TYR 3.9 3.1 - - - +
127U GLY* 4.0 6.6 - - - -
128U VAL* 3.6 20.6 + - - +
141U LYS* 2.9 54.0 + - + +
142U ALA 3.9 2.2 - - - +
144U LYS* 1.3 75.2 - - + +
146U ALA* 1.3 59.3 + - - +
148U THR* 4.0 4.9 - - - +
149U ASP* 2.8 34.1 + - - +
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Residues in contact with ALA 146 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91U GLN* 4.0 0.2 - - - +
107U VAL* 3.3 32.5 - - + +
109U ALA* 3.7 20.7 - - + +
125U GLY* 3.5 9.0 - - - -
126U TYR 3.5 13.2 - - - -
127U GLY* 3.6 1.1 - - - +
142U ALA 2.9 20.2 + - - +
143U ARG 3.5 4.7 - - - +
145U GLU* 1.3 75.9 - - - +
147U VAL* 1.3 58.1 + - - +
150U GLY* 2.9 24.8 + - - -
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Residues in contact with VAL 147 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86U HIS* 5.3 3.1 - - + +
88U ILE* 3.8 22.7 - - + -
91U GLN* 3.5 16.8 - - - +
109U ALA* 3.9 11.0 - - + -
111U VAL* 3.6 7.8 - - + +
143U ARG 3.0 10.9 + - - +
144U LYS* 3.8 5.4 - - - +
146U ALA* 1.3 77.3 - - - +
148U THR* 1.3 59.4 + - - +
150U GLY 3.2 1.0 + - - -
151U LEU* 2.9 27.8 + - + +
122V GLU 4.8 0.2 - - - +
123V ASP* 3.2 29.4 - - - +
124V VAL* 3.4 29.8 - - + -
153V ARG* 4.8 4.0 - - - +
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Residues in contact with THR 148 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68U GLY* 4.4 22.9 - - - -
72U ILE* 6.6 0.2 - - + -
144U LYS 2.9 19.0 + - - -
145U GLU* 4.0 5.4 - - - -
147U VAL* 1.3 77.5 - - - +
149U ASP* 1.3 58.1 + - - +
151U LEU* 3.2 10.9 + - + +
152U LYS* 2.9 37.9 + - + +
123V ASP* 5.7 0.2 + - - -
153V ARG* 3.9 14.2 + - - -
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Residues in contact with ASP 149 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144T LYS* 2.6 37.0 + - - -
55U ARG* 5.8 2.1 + - - -
125U GLY* 4.0 0.4 - - - -
126U TYR 3.3 19.6 + - - +
145U GLU 2.8 18.6 + - - +
146U ALA 3.8 1.3 - - - +
148U THR* 1.3 76.8 - - - +
150U GLY* 1.3 58.8 + - - +
152U LYS* 3.3 19.1 + - - +
153U ARG* 2.9 39.5 + - - +
156U ARG* 4.8 3.6 + - - -
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Residues in contact with GLY 150 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111U VAL* 3.8 16.3 - - - +
123U ASP* 4.5 3.4 - - - +
124U VAL 4.0 3.8 - - - -
125U GLY* 3.4 24.6 - - - -
146U ALA 2.9 13.2 + - - -
147U VAL 3.2 4.0 + - - -
149U ASP* 1.3 76.3 - - - +
151U LEU* 1.3 57.6 + - - +
153U ARG* 3.4 1.3 + - - +
154U ALA* 2.9 31.2 + - - +
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Residues in contact with LEU 151 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71U VAL* 5.7 1.8 - - + -
72U ILE* 4.2 28.5 - - + -
84U TRP* 3.8 19.3 - - + -
86U HIS* 3.7 34.3 - - + +
111U VAL* 3.8 10.4 - - + +
113U VAL* 3.7 24.2 - - + -
147U VAL* 2.9 14.4 + - + +
148U THR* 3.5 13.9 - - + +
150U GLY* 1.3 77.2 - - - +
152U LYS* 1.3 63.6 + - + +
154U ALA* 3.3 1.1 + - - +
155U LEU* 2.9 30.2 + - + +
123V ASP* 5.5 2.9 - - - +
157V SER* 5.1 1.6 - - - +
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Residues in contact with LYS 152 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55U ARG* 5.3 5.9 - - - +
65U TYR* 4.2 17.6 - - - +
66U ILE* 3.2 29.4 + - + +
68U GLY* 4.3 12.9 - - - +
71U VAL* 3.9 31.4 - - + +
148U THR* 2.9 29.5 + - + +
149U ASP* 3.3 22.7 + - - +
151U LEU* 1.3 77.8 - - + +
153U ARG* 1.3 57.9 + - + +
155U LEU* 3.3 2.4 + - - +
156U ARG* 2.9 36.6 + - - +
162U LEU 4.8 1.7 - - - +
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Residues in contact with ARG 153 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144T LYS* 3.4 64.6 + - - +
148T THR* 4.0 11.7 + - - -
123U ASP* 3.0 38.4 + - + +
124U VAL 2.7 25.6 + - - +
149U ASP* 2.9 27.5 + - - +
150U GLY 4.0 2.7 - - - +
152U LYS* 1.3 76.2 - - + +
154U ALA* 1.3 62.6 + - - +
156U ARG* 3.2 59.5 + - - +
157U SER* 3.8 5.5 + - - -
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Residues in contact with ALA 154 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111U VAL 3.8 14.6 - - - +
113U VAL* 3.7 17.9 - - + -
121U HIS* 3.6 39.9 - - - +
122U GLU 4.9 0.2 - - - -
123U ASP* 3.7 11.4 - - - +
150U GLY 2.9 19.6 + - - +
151U LEU* 3.8 1.6 - - - +
153U ARG* 1.3 77.0 - - - +
155U LEU* 1.3 62.5 + - - +
157U SER* 3.4 10.7 + - - -
158U PHE* 4.4 2.1 - - - -
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Residues in contact with LEU 155 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71U VAL* 3.7 29.4 - - + +
72U ILE 5.3 0.4 - - - +
75U ALA* 3.9 16.8 - - + -
79U PHE* 4.9 3.1 - - + -
84U TRP* 3.9 26.5 - - + -
113U VAL* 3.7 27.4 - - + -
151U LEU* 2.9 30.8 + - + +
152U LYS 3.9 3.1 - - - +
154U ALA* 1.3 72.5 - - - +
156U ARG* 1.3 65.6 + - - +
157U SER 3.1 4.0 + - - -
158U PHE* 3.2 27.9 + - + -
162U LEU* 3.4 30.9 - - + +
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Residues in contact with ARG 156 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72T ILE* 5.2 4.0 - - + -
144T LYS* 5.9 0.2 - - - +
149U ASP* 4.8 3.8 + - - -
152U LYS* 2.9 19.9 + - + +
153U ARG* 3.2 60.0 - - - +
154U ALA 3.3 0.6 - - - -
155U LEU* 1.3 77.0 - - - +
157U SER* 1.3 57.5 + - - +
158U PHE 3.0 6.3 + - - -
159U GLY 3.3 17.3 + - - +
162U LEU 3.9 8.9 + - - +
163U GLY* 3.4 32.3 - - - +
164U ASN* 3.5 15.0 - - + +
166U ILE* 4.7 5.7 - - - +
167U LEU* 3.6 40.6 - - + +
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Residues in contact with SER 157 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72T ILE* 3.5 29.2 - - - +
76T ASN* 3.2 19.9 + - - +
84T TRP* 3.8 4.9 - - - -
86T HIS* 3.7 15.9 + - - -
151T LEU* 4.9 1.4 - - - +
121U HIS* 3.6 38.2 + - - -
123U ASP* 4.4 4.2 + - - -
153U ARG 3.8 10.7 + - - -
154U ALA* 3.4 4.7 + - - -
155U LEU 3.1 2.0 + - - -
156U ARG* 1.3 75.9 - - - +
158U PHE* 1.3 56.3 + - - +
159U 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
------------------------------------------------------------
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