Contacts of the helix formed by residues 125 - 150 (chain U) in PDB entry 2IY4
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 ASP 125 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136M LYS* 5.6 0.7 + - - -
9U THR* 3.4 24.0 - - - +
63U ARG* 2.8 27.6 + - - -
67U ILE* 3.8 10.2 - - - +
120U THR* 2.6 44.0 + - + +
123U GLU* 3.4 7.0 + - + +
124U GLY* 1.3 73.2 - - - +
126U ASN* 1.3 58.8 + - - +
127U VAL 3.7 0.9 + - - -
128U THR* 2.7 28.7 + - - -
129U ASN* 3.0 6.9 + - - +
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Residues in contact with ASN 126 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114M GLN* 4.4 12.1 + - - +
117M ILE* 3.6 28.5 - - + +
118M GLU* 5.7 2.0 - - - +
121M ASP* 5.9 2.9 - - - +
129M ASN* 5.1 2.6 + - - +
133M ILE* 3.7 27.9 - - + +
136M LYS* 6.2 0.7 - - + -
121U ASP* 5.4 3.8 - - - +
124U GLY* 3.3 19.8 + - - -
125U ASP* 1.3 70.6 + - - +
127U VAL* 1.3 60.8 + - + +
129U ASN* 3.3 9.6 - - - +
130U ASP* 2.9 32.4 + - - +
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Residues in contact with VAL 127 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133M ILE* 3.6 30.5 - - + +
136M LYS* 3.9 24.0 - - + +
137M ALA* 3.5 35.2 - - + +
140M ASP* 4.1 4.7 - - - +
63U ARG* 3.5 34.8 - - - +
125U ASP* 3.5 1.2 + - - -
126U ASN* 1.3 77.4 - - + +
128U THR* 1.3 59.6 + - - +
130U ASP* 3.3 2.9 + - - +
131U MET* 3.0 29.8 + - + +
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Residues in contact with THR 128 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9U THR* 3.8 10.4 - - + +
13U LEU* 3.7 38.6 - - + +
63U ARG* 2.8 24.2 + - - +
67U ILE* 4.5 0.2 - - - +
120U THR* 3.8 5.2 - - - +
125U ASP* 2.7 31.7 + - - -
127U VAL* 1.3 74.1 - - - +
129U ASN* 1.3 66.2 + - - +
131U MET* 3.4 11.8 + - + +
132U LEU* 3.0 33.2 + - + +
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Residues in contact with ASN 129 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126Q ASN* 5.3 1.9 + - - +
117U ILE* 2.9 43.2 + - - +
120U THR* 3.0 16.3 - - + +
121U ASP* 3.8 23.1 + - - +
125U ASP 3.0 11.0 + - - +
126U ASN* 3.3 15.5 - - - +
128U THR* 1.3 75.1 - - - +
130U ASP* 1.3 68.8 + - - +
132U LEU* 3.2 4.4 + - - +
133U ILE* 3.0 44.1 + - - +
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Residues in contact with ASP 130 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130M ASP* 2.9 31.1 - - - +
133M ILE* 3.3 31.1 - - + +
130Q ASP* 3.2 22.6 - - - +
126U ASN 2.9 16.8 + - - +
127U VAL 3.3 3.3 + - - +
129U ASN* 1.3 82.0 - - - +
131U MET* 1.3 61.8 + - - +
133U ILE* 3.4 7.0 + - - +
134U ALA* 3.1 24.1 + - - +
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Residues in contact with MET 131 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13U LEU* 4.1 8.7 - - + -
59U GLU* 3.9 15.9 - - - +
60U VAL* 4.0 15.3 - - + -
63U ARG* 3.9 37.5 - - + -
127U VAL* 3.0 20.2 + - + +
128U THR* 3.5 6.3 - - + +
129U ASN 3.3 0.2 - - - -
130U ASP* 1.3 76.9 - - - +
132U LEU* 1.3 81.0 + - + +
134U ALA* 3.4 5.4 + - - +
135U PHE* 3.1 55.4 + - + -
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Residues in contact with LEU 132 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12U PHE* 3.6 33.2 - - + -
13U LEU* 4.1 9.0 - - + -
16U GLN* 5.8 0.7 - - + -
60U VAL* 4.6 4.7 - - + -
113U TYR* 4.0 16.3 - - + +
116U GLY 4.0 19.3 - - - +
117U ILE* 3.7 16.7 - - + +
120U THR* 4.2 2.9 - - - +
128U THR* 3.0 33.8 + - + +
129U ASN 3.7 3.6 - - - +
131U MET* 1.3 95.0 - - + +
133U ILE* 1.3 59.4 + - - +
135U PHE* 3.4 16.9 + - + +
136U LYS* 2.8 28.2 + - - +
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Residues in contact with ILE 133 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126Q ASN* 3.5 42.2 - - + +
127Q VAL* 3.7 14.7 - - + +
130Q ASP* 3.3 32.1 - - + +
117U ILE* 3.8 20.4 - - + -
129U ASN* 3.0 42.1 + - - +
130U ASP* 3.6 10.3 - - - +
131U MET 3.3 0.2 - - - -
132U LEU* 1.3 73.2 - - - +
134U ALA* 1.3 55.4 + - - +
136U LYS* 3.0 3.8 + - - +
137U ALA* 2.7 34.7 + - + +
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Residues in contact with ALA 134 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130Q ASP* 5.3 0.2 + - - -
130U ASP 3.1 12.5 + - - +
131U MET* 3.4 10.3 + - - +
133U ILE* 1.3 75.5 - - - +
135U PHE* 1.3 68.2 + - + +
137U ALA* 3.3 17.3 + - - +
138U SER* 3.3 12.6 + - - -
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Residues in contact with PHE 135 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56U GLN* 3.6 51.4 + - + +
59U GLU* 3.4 31.0 - - + -
60U VAL* 3.7 26.0 - - + -
113U TYR* 3.6 19.5 - + + -
131U MET* 3.1 35.9 + - + -
132U LEU* 3.5 17.3 - - + +
134U ALA* 1.3 79.9 - - + +
136U LYS* 1.3 60.4 + - - +
138U SER* 3.4 5.2 + - - -
139U ILE* 3.1 28.8 + - - +
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Residues in contact with LYS 136 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63Q ARG* 4.4 6.2 - - - +
125Q ASP* 5.6 0.2 + - - -
126Q ASN* 5.9 2.0 - - - +
127Q VAL* 3.9 16.6 - - + +
110U ARG* 3.9 36.0 - - + +
113U TYR* 4.3 5.1 - - + -
114U GLN* 3.4 26.2 - - + +
117U ILE* 4.0 18.8 - - + -
132U LEU 2.8 19.6 + - - +
133U ILE 3.0 4.9 + - - +
135U PHE* 1.3 70.7 - - - +
137U ALA* 1.3 60.2 + - - +
139U ILE* 4.3 7.6 - - + -
140U ASP* 2.7 66.6 + - - +
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Residues in contact with ALA 137 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63Q ARG* 5.1 1.0 + - - -
127Q VAL* 3.4 32.6 - - + +
133U ILE* 2.7 15.1 + - + +
134U ALA* 3.3 14.3 + - - +
136U LYS* 1.3 72.1 - - - +
138U SER* 1.3 60.2 + - - +
140U ASP* 3.6 3.2 + - - +
141U LYS* 3.3 20.8 + - - +
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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
----------------------------------------------------------
52U GLU* 2.4 33.5 + - - -
53U PHE* 5.4 0.2 - - - -
56U GLN* 4.8 3.5 + - - -
134U ALA 3.3 8.6 + - - -
135U PHE* 3.8 7.6 - - - -
136U LYS 3.3 0.4 - - - -
137U ALA* 1.3 77.2 - - - +
139U ILE* 1.3 65.2 + - - +
141U LYS* 3.1 10.2 + - - +
142U HIS* 2.9 32.7 + - - -
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Residues in contact with ILE 139 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53U PHE* 3.9 28.9 - - + -
56U GLN* 4.2 2.0 - - - +
106U LEU* 3.4 33.0 - - + +
109U LEU* 4.2 15.9 - - + -
110U ARG* 3.9 10.5 - - + -
113U TYR* 3.6 33.7 - - + -
135U PHE 3.1 18.9 + - - +
136U LYS* 3.3 6.9 + - - +
138U SER* 1.3 74.3 - - - +
140U ASP* 1.3 64.7 + - - +
142U HIS* 3.2 10.1 + - - +
143U ILE* 2.9 31.8 + - + +
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Residues in contact with ASP 140 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63Q ARG* 2.8 33.4 + - - +
66Q ALA* 3.8 19.8 - - + +
127Q VAL* 4.0 1.6 - - - +
110U ARG* 3.3 33.7 - - - +
136U LYS* 2.7 47.5 + - - +
137U ALA 3.7 3.4 - - - +
139U ILE* 1.3 72.5 - - - +
141U LYS* 1.3 61.2 + - - +
143U ILE* 3.4 8.2 + - - +
144U TRP* 3.2 17.2 + - - +
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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
----------------------------------------------------------
62Q GLU* 3.4 29.0 + - + +
66Q ALA* 4.6 5.4 - - + +
43S HIS* 5.4 2.8 + - - -
137U ALA 3.3 11.2 + - - +
138U SER* 3.1 12.4 + - - +
140U ASP* 1.3 76.7 - - - +
142U HIS* 1.3 65.9 + - + +
144U TRP* 3.2 23.8 + - + -
145U MET* 3.1 49.9 + - - +
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Residues in contact with HIS 142 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45U LYS* 4.5 13.3 + - - -
49U LEU* 3.6 25.6 - - + +
52U GLU* 2.8 29.0 + - - -
53U PHE* 4.0 22.8 - + - -
106U LEU* 3.9 17.7 - - + -
138U SER* 2.9 31.3 + - - -
139U ILE* 3.5 7.2 - - - +
141U LYS* 1.3 79.1 - - + +
143U ILE* 1.3 57.3 - - - +
145U MET* 4.5 8.6 - - - +
146U PHE* 2.8 46.8 + - + +
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Residues in contact with ILE 143 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66Q ALA 6.0 0.4 - - - +
103U VAL* 4.3 11.9 - - + -
106U LEU* 3.7 42.8 - - + +
107U GLU* 4.0 8.1 - - + +
110U ARG* 3.9 34.1 - - - +
139U ILE* 2.9 27.6 + - + +
140U ASP* 3.6 7.6 - - - +
141U LYS 3.2 0.2 - - - -
142U HIS* 1.3 74.0 - - - +
144U TRP* 1.3 67.4 + - - +
147U LYS* 2.9 33.8 + - + +
154U PRO* 3.5 26.5 - - + +
155U LEU* 5.5 1.6 - - + -
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Residues in contact with TRP 144 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62Q GLU* 3.4 53.6 - - + -
65Q LEU* 3.7 35.1 - - + +
66Q ALA* 4.1 9.6 - - - -
31S HIS 4.5 2.2 - - - -
32S TRP* 4.2 10.7 + - - -
34S MET 5.4 0.4 + - - -
39S PHE* 3.9 17.5 - + - -
43S HIS* 3.5 21.5 - + - -
140U ASP 3.2 13.9 + - - +
141U LYS* 3.2 33.4 + - + +
143U ILE* 1.3 77.0 - - - +
145U MET* 1.3 69.9 + - + +
147U LYS* 3.7 1.9 - - - +
148U ALA* 2.9 33.3 + - + +
152U LYS 4.9 0.5 - - - +
154U PRO* 3.8 34.2 - - + +
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Residues in contact with MET 145 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39S PHE* 3.6 33.9 - - + -
40S PHE* 3.7 31.9 - - + -
43S HIS* 3.8 20.4 - - + +
45U LYS* 4.4 12.6 - - - +
141U LYS* 3.1 48.6 + - - +
142U HIS* 3.8 10.8 - - - +
143U ILE 3.3 0.2 - - - -
144U TRP* 1.3 91.6 - - + +
146U PHE* 1.3 57.1 + - + +
148U ALA* 3.2 3.8 + - - +
149U PHE* 2.8 26.7 + - - +
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Residues in contact with PHE 146 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40S PHE* 3.5 33.4 - + - -
42U LEU* 5.1 1.3 - - + -
45U LYS* 3.8 15.5 - - + -
46U MET* 3.8 23.6 - - + -
49U LEU* 3.9 25.6 - - + -
99U MET* 3.7 35.6 - - + +
102U LEU* 4.0 13.9 - - + -
103U VAL* 4.1 19.1 - - + -
106U LEU* 4.2 0.4 - - + -
142U HIS* 2.8 44.9 + - + +
145U MET* 1.3 71.3 - - - +
147U LYS* 1.3 64.0 + - - +
149U PHE* 3.5 6.1 + - + +
150U LEU* 3.3 28.1 + - - +
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Residues in contact with LYS 147 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100U GLU* 5.3 3.4 + - - -
103U VAL* 4.1 23.4 - - + +
107U GLU* 3.3 27.8 + - - -
143U ILE* 2.9 26.4 + - + +
144U TRP 3.7 2.9 - - - +
146U PHE* 1.3 75.4 - - - +
148U ALA* 1.3 58.3 + - - +
150U LEU* 2.9 22.3 + - + +
151U GLY 3.2 0.2 + - - -
152U LYS* 2.9 46.0 + - + +
153U ALA 3.5 23.3 - - - +
154U PRO* 3.5 19.1 - - + +
156U GLU 2.8 25.5 + - - +
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Residues in contact with ALA 148 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34S MET 3.9 9.4 - - - +
35S ARG* 3.4 10.7 - - + +
36S GLY 2.7 30.2 + - - -
39S PHE* 3.7 27.4 - - + -
144U TRP* 2.9 25.3 + - + +
145U MET 3.2 6.0 + - - +
147U LYS* 1.3 73.2 - - - +
149U PHE* 1.3 59.1 + - - +
151U GLY 3.0 6.8 + - - +
152U LYS 3.5 8.4 + - - +
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Residues in contact with PHE 149 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36S GLY* 3.2 27.2 - - - -
37S HIS* 3.2 59.1 + + + -
39S PHE* 4.0 3.9 - - + +
40S PHE* 3.9 30.1 - + + -
38U ASN* 4.1 5.8 - - - -
42U LEU* 3.5 28.5 - - + -
95U MET* 4.0 10.5 - - + -
96U ASP* 3.5 20.2 - - - -
99U MET* 3.6 27.8 - - + -
145U MET 2.8 13.6 + - - +
146U PHE* 3.5 9.0 - + - +
148U ALA* 1.3 74.5 - - - +
150U LEU* 1.3 65.5 + - + +
151U GLY 3.4 1.9 + - - -
----------------------------------------------------------
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Residues in contact with LEU 150 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37S HIS* 5.3 0.9 - - - -
96U ASP* 3.6 53.9 - - + +
99U MET* 3.9 25.6 - - + +
100U GLU* 4.1 23.1 - - - +
103U VAL* 4.3 11.9 - - + -
146U PHE 3.3 17.0 + - - +
147U LYS* 2.9 16.3 + - + +
149U PHE* 1.3 79.6 - - + +
151U GLY* 1.3 60.5 + - - +
152U LYS* 3.3 20.6 + - + +
----------------------------------------------------------
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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