Contacts of the helix formed by residues 95 - 124 (chain B) in PDB entry 1F45
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 95 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B PHE* 1.3 68.3 + - - +
97B MET* 3.1 12.1 - - - +
98B MET* 3.3 21.6 - - - +
99B ALA* 3.2 18.2 + - - +
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Residues in contact with PHE 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B SER* 1.3 78.1 - - - +
97B MET* 1.3 63.0 + - + +
99B ALA* 3.0 11.4 + - + -
100B LEU* 2.9 60.6 + - + +
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Residues in contact with MET 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ALA 4.1 4.1 - - - +
79B THR 3.8 9.0 - - - +
80B SER* 3.0 45.8 - - - +
81B PHE* 3.2 51.6 - - + +
82B ILE* 4.8 0.7 - - - -
95B SER 3.9 8.5 - - - +
96B PHE* 1.3 82.4 - - + +
98B MET* 1.3 61.8 + - - +
100B LEU* 3.1 13.8 + - + +
101B CYS* 2.9 23.2 + - - +
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Residues in contact with MET 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ILE* 4.3 20.8 - - + +
83B THR 4.6 3.8 - - - +
85B GLY 3.7 22.7 - - - +
86B SER* 4.9 3.1 - - - -
95B SER* 3.3 24.6 + - - +
97B MET* 1.3 78.1 - - - +
99B ALA* 1.3 65.6 + - - +
101B CYS* 3.1 8.6 + - - +
102B LEU* 3.0 41.0 + - + +
194B LEU* 3.9 33.7 - - + -
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Residues in contact with ALA 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B SER 3.2 7.5 + - - +
96B PHE* 3.0 15.8 + - + +
98B MET* 1.3 79.7 - - - +
100B LEU* 1.3 57.0 + - - +
102B LEU* 4.0 8.6 - - - +
103B SER* 2.8 31.4 + - - -
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Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ALA* 4.6 9.6 - - + +
80B SER* 4.7 13.0 - - - +
96B PHE* 2.9 52.3 + - + +
97B MET* 3.1 15.2 + - + +
99B ALA* 1.3 75.8 - - - +
101B CYS* 1.3 53.6 + - - +
103B SER* 3.3 9.5 + - - +
104B SER* 2.8 36.0 + - - -
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Residues in contact with CYS 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ALA* 3.4 20.1 + - - +
63B CYS* 2.0 53.4 - - - -
82B ILE* 3.9 15.3 - - + -
97B MET 2.9 8.5 + - - +
98B MET* 3.3 10.1 - - - +
100B LEU* 1.3 75.5 - - - +
102B LEU* 1.3 65.4 + - + +
104B SER* 3.0 6.2 + - - -
105B ILE* 2.9 35.0 + - - +
190B VAL* 4.2 8.5 - - - -
194B LEU* 5.6 1.8 - - - -
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Residues in contact with LEU 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B MET* 3.0 33.7 + - + +
99B ALA* 4.0 6.5 - - - +
101B CYS* 1.3 84.5 - - - +
103B SER* 1.3 58.7 + - - +
105B ILE* 3.1 18.8 + - + +
106B TYR* 2.8 30.2 + - - +
148B LEU* 4.2 28.9 - - + +
190B VAL* 5.5 1.3 - - + -
194B LEU* 4.9 9.6 - - + -
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Residues in contact with SER 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ALA 2.8 24.6 + - - -
100B LEU* 3.5 11.8 + - - +
102B LEU* 1.3 72.0 - - - +
104B SER* 1.3 65.4 + - - +
106B TYR* 3.1 9.1 + - - +
107B GLU* 2.9 32.3 + - - +
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Residues in contact with SER 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B SER 4.0 4.8 + - - -
59B THR* 2.7 40.0 + - - -
62B ALA* 4.3 10.3 - - - -
100B LEU 2.8 14.0 + - - -
101B CYS 3.0 9.2 + - - -
103B SER* 1.3 78.6 + - - +
105B ILE* 1.3 65.3 + - - +
107B GLU* 3.1 8.3 + - - +
108B ASP* 3.1 21.8 + - - +
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Residues in contact with ILE 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B THR* 3.6 22.4 - - + -
63B CYS* 4.1 0.7 - - - -
101B CYS* 2.9 25.9 + - - +
102B LEU* 3.5 16.8 - - + +
104B SER* 1.3 73.4 - - - +
106B TYR* 1.3 65.9 + - - +
108B ASP* 3.0 17.2 + - - +
109B LEU* 3.1 14.8 + - + +
144B LEU* 5.7 0.4 - - + -
148B LEU* 4.0 19.5 - - + -
187B ILE* 3.6 39.3 - - + -
190B VAL* 3.7 31.2 - - + -
191B MET* 5.6 2.5 - - + -
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Residues in contact with TYR 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B LEU 2.8 16.3 + - - +
103B SER* 3.5 7.6 - - - +
105B ILE* 1.3 77.8 - - - +
107B GLU* 1.3 78.0 + - - +
109B LEU* 3.5 5.1 + - - +
110B LYS* 3.2 43.0 + - + +
145B MET* 3.5 51.1 - - + +
148B LEU* 3.9 34.3 - - + +
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Residues in contact with GLU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B SER* 2.9 22.7 + - - +
104B SER* 3.1 9.6 + - - +
106B TYR* 1.3 93.1 - - - +
108B ASP* 1.3 67.5 - - - +
110B LYS* 3.1 19.5 + - - +
111B MET* 3.0 46.8 + - + +
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Residues in contact with ASP 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B THR* 2.4 35.0 + - - +
104B SER* 3.1 6.3 + - - +
105B ILE* 3.0 10.5 + - - +
107B GLU* 1.3 79.8 - - - +
109B LEU* 1.3 64.3 + - + +
111B MET* 3.3 12.9 + - - +
112B TYR* 3.2 34.4 + - + -
180B PHE* 6.2 0.2 - - - -
183B ARG* 3.0 39.5 + - + +
187B ILE* 5.1 3.3 - - + +
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Residues in contact with LEU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ILE* 3.1 16.0 + - + +
106B TYR* 3.8 5.4 - - - +
107B GLU 3.2 0.2 - - - -
108B ASP* 1.3 80.0 - - - +
110B LYS* 1.3 51.7 + - - +
112B TYR* 3.1 5.4 + - - +
113B GLN* 2.7 36.9 + - - +
141B ILE* 4.0 26.1 - - + +
144B LEU* 3.6 36.3 - - + -
145B MET* 3.6 28.0 - - + -
148B LEU* 3.8 21.3 - - + -
180B PHE* 4.3 9.6 - - + -
187B ILE* 3.9 20.9 - - + -
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Residues in contact with LYS 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B TYR* 3.2 37.3 + - + +
107B GLU* 3.1 25.6 + - - +
109B LEU* 1.3 74.1 - - - +
111B MET* 1.3 69.8 + - + +
113B GLN* 3.3 9.0 + - - +
114B VAL* 3.3 28.9 + - + +
145B MET* 3.8 19.5 - - + +
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Residues in contact with MET 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B GLU* 3.0 51.2 + - + +
108B ASP* 3.5 16.2 - - - +
109B LEU 3.2 0.2 - - - -
110B LYS* 1.3 81.7 - - + +
112B TYR* 1.3 66.5 + - + +
114B VAL* 3.2 12.0 + - - +
115B GLU* 3.2 20.0 + - + +
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Residues in contact with TYR 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ASP* 3.2 27.2 + - + +
109B LEU* 3.1 7.0 + - - +
111B MET* 1.3 81.0 - - + +
113B GLN* 1.3 66.9 + - - +
114B VAL 3.1 0.2 + - - -
115B GLU* 3.2 6.9 + - + +
116B PHE* 2.8 39.2 + + + -
141B ILE* 3.8 17.0 - - + -
176B LEU* 4.3 24.7 - - + -
179B ALA* 3.4 26.3 + - + +
180B PHE* 3.7 46.0 - + + -
183B ARG* 4.6 16.1 - - + +
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Residues in contact with GLN 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B LEU 2.7 20.6 + - - +
110B LYS* 3.3 9.6 + - - +
112B TYR* 1.3 75.1 - - - +
114B VAL* 1.3 63.6 + - + +
116B PHE* 3.7 0.7 + - - -
117B LYS* 3.1 44.6 + - + +
138B LEU* 4.1 9.5 - - + +
141B ILE* 3.8 13.4 - - + +
142B ASP* 2.9 31.0 + - - +
145B MET* 3.4 30.6 - - - +
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Residues in contact with VAL 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B LYS* 3.3 12.7 + - + +
111B MET* 3.2 9.5 + - - +
112B TYR 3.1 1.0 - - - -
113B GLN* 1.3 78.8 - - + +
115B GLU* 1.3 77.3 + - - +
117B LYS* 3.2 6.6 + - - +
118B THR* 2.9 36.2 + - - +
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Residues in contact with GLU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B MET* 3.2 15.6 + - + +
112B TYR* 3.4 13.7 - - + +
114B VAL* 1.3 85.1 - - - +
116B PHE* 1.3 65.1 + - - +
118B THR* 3.2 5.0 + - - +
119B MET* 3.0 28.6 + - - +
172B LYS* 3.3 26.7 + - - -
176B LEU* 3.8 31.7 - - + +
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Residues in contact with PHE 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B TYR* 2.8 40.5 + + - +
115B GLU* 1.3 74.6 - - - +
117B LYS* 1.3 57.1 + - - +
119B MET* 3.3 4.5 + - + +
120B ASN* 2.9 31.5 + - - +
134B ASP* 3.9 27.3 - - + +
137B MET* 3.9 21.8 - - + -
138B LEU* 4.0 23.9 - - + +
141B ILE* 3.5 28.0 - - + -
173B LEU* 5.0 4.9 - - + -
176B LEU* 3.5 29.6 - - + -
177B LEU* 3.9 22.4 - - + -
180B PHE* 4.0 15.0 - + + -
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Residues in contact with LYS 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B GLN* 3.1 39.4 + - + +
114B VAL* 3.2 6.7 + - - +
116B PHE* 1.3 71.6 - - - +
118B THR* 1.3 66.5 + - - +
120B ASN* 3.8 6.7 - - - +
121B ALA* 3.0 23.2 + - - +
138B LEU* 4.4 16.6 - - + -
142B ASP* 4.9 6.3 - - - -
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Residues in contact with THR 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B VAL* 2.9 26.9 + - - +
115B GLU* 3.6 6.7 - - - -
117B LYS* 1.3 74.9 - - - +
119B MET* 1.3 63.3 + - - +
121B ALA* 3.1 9.3 + - - +
122B LYS* 3.0 50.7 + - + +
172B LYS* 4.7 4.5 - - - +
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Residues in contact with MET 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B GLU 3.0 18.8 + - - +
116B PHE* 3.5 10.3 - - + +
118B THR* 1.3 76.7 - - - +
120B ASN* 1.3 54.8 + - - +
122B LYS* 3.0 11.2 + - + +
123B LEU* 2.7 65.7 + - + +
134B ASP* 6.4 0.4 - - + -
169B THR* 3.9 15.5 - - + +
172B LYS* 4.0 34.5 - - - +
173B LEU* 3.7 39.7 - - + -
176B LEU* 4.6 11.0 - - + -
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Residues in contact with ASN 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B PHE 2.9 18.0 + - - +
117B LYS* 3.8 7.2 + - - +
119B MET* 1.3 77.4 - - - +
121B ALA* 1.3 63.4 + - - +
123B LEU* 4.0 6.0 - - - +
124B LEU* 3.2 26.3 + - - +
130B GLN* 3.2 29.9 - - - +
134B ASP* 3.9 8.8 - - - +
135B GLN* 4.0 10.1 - - - +
138B LEU* 5.4 9.5 - - + +
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Residues in contact with ALA 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LYS 3.0 15.3 + - - +
118B THR* 3.3 10.5 - - - +
119B MET 3.0 0.2 - - - -
120B ASN* 1.3 77.9 - - - +
122B LYS* 1.3 71.7 + - + +
124B LEU* 3.3 14.3 + - - +
125B MET* 3.8 9.2 - - - +
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Residues in contact with LYS 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B THR* 3.0 33.1 + - + +
119B MET* 3.0 14.2 + - + +
121B ALA* 1.3 84.4 - - - +
123B LEU* 1.3 55.0 + - - +
124B LEU 2.7 10.9 + - - -
125B MET* 3.3 20.3 + - - +
169B THR* 3.3 31.4 - - + +
172B LYS* 3.3 37.4 - - - +
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Residues in contact with LEU 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B MET* 2.7 31.4 + - + +
120B ASN* 4.0 5.8 - - - +
122B LYS* 1.3 71.0 - - - +
124B LEU* 1.3 60.5 + - - +
125B MET 3.0 3.9 + - - -
126B ASP* 3.1 24.4 + - + +
129B ARG 3.7 7.8 - - - +
130B GLN* 3.7 34.1 - - + +
131B ILE* 5.2 1.3 - - + -
134B ASP* 5.0 1.1 - - - +
169B THR* 3.0 38.6 - - + +
170B LYS* 4.9 11.9 - - + -
173B LEU* 3.4 35.0 - - + -
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Residues in contact with LEU 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B ASN* 3.2 19.1 + - - +
121B ALA* 3.5 14.4 - - - +
122B LYS 2.7 7.7 + - - -
123B LEU* 1.3 72.6 - - - +
125B MET* 1.3 69.9 + - + +
126B ASP 3.2 1.6 + - - +
129B ARG* 2.9 51.8 + - + +
130B GLN* 5.0 6.5 - - + +
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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