Contacts of the helix formed by residues 113 - 139 (chain I) in PDB entry 1F33
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 ASN 113 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55I ARG* 3.4 7.9 - - - +
56I GLY* 5.1 4.9 - - - -
57I ALA 5.6 0.9 + - - -
112I HIS* 1.3 81.5 - - - +
114I VAL* 1.3 67.5 + - - +
115I GLN* 2.8 46.7 - - - +
116I ASP* 3.1 34.6 + - - +
117I HIS* 3.2 12.0 + - - -
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Residues in contact with VAL 114 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54I MET* 4.4 12.8 - - + -
55I ARG 2.9 37.9 + - - +
56I GLY* 3.8 5.8 - - - +
57I ALA 3.4 27.8 - - - +
58I ASN* 4.4 1.3 - - + +
59I PHE* 4.2 11.0 - - - -
62I VAL* 4.2 24.0 - - + -
112I HIS 4.2 1.1 - - - -
113I ASN* 1.3 72.7 - - - +
115I GLN* 1.3 63.6 + - + +
117I HIS* 3.2 4.5 + - - +
118I LEU* 2.8 46.0 + - + +
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Residues in contact with GLN 115 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57H ALA* 5.8 0.4 - - - +
57I ALA* 5.2 4.0 + - + +
58I ASN* 5.9 3.4 - - - +
113I ASN* 2.8 21.6 - - - +
114I VAL* 1.3 77.9 - - + +
116I ASP* 1.3 62.7 + - - +
118I LEU* 3.3 12.0 + - - +
119I LYS* 3.0 43.5 + - - +
165I ASN 3.2 21.6 + - - -
166I ILE* 3.3 13.2 - - - +
167I GLU* 2.8 54.7 + - + +
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Residues in contact with ASP 116 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111I ILE* 4.2 27.7 - - + +
112I HIS 4.8 0.5 + - - -
113I ASN* 3.1 33.7 + - - +
115I GLN* 1.3 79.7 - - - +
117I HIS* 1.3 63.1 + - - +
119I LYS* 3.2 15.8 + - - +
120I GLU* 3.0 26.4 + - + +
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Residues in contact with HIS 117 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49I GLN* 4.6 2.0 - - - -
50I ALA* 3.5 20.2 - - + -
53I ASN* 3.4 17.6 + - + -
54I MET* 3.6 27.4 - - + -
107I TYR* 2.6 36.9 + + - +
108I PRO 4.9 1.6 - - - -
111I ILE* 3.3 41.2 + - + +
112I HIS* 3.4 23.8 - - - -
113I ASN 3.2 9.3 + - - -
114I VAL 3.6 6.5 - - - +
116I ASP* 1.3 78.2 - - - +
118I LEU* 1.3 53.8 + - - +
120I GLU 3.1 0.7 + - - -
121I LEU* 2.7 41.5 + - - +
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Residues in contact with LEU 118 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54I MET* 5.0 1.3 - - + -
58I ASN* 5.8 0.4 - - - +
62I VAL* 3.8 28.0 - - + -
65I MET* 5.1 4.0 - - + -
66I LEU* 5.5 0.2 - - + -
114I VAL* 2.8 34.4 + - + +
115I GLN* 3.5 15.3 - - - +
117I HIS* 1.3 77.3 - - - +
119I LYS* 1.3 56.6 + - - +
121I LEU* 4.4 9.9 - - + -
122I ALA* 2.8 26.2 + - - +
162I ILE* 3.3 39.8 - - + +
165I ASN* 3.7 34.1 - - + +
166I ILE* 3.9 10.5 - - + +
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Residues in contact with LYS 119 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G ARG* 4.4 8.2 + - - +
115I GLN* 3.0 35.3 + - - +
116I ASP* 3.6 12.8 + - - +
118I LEU* 1.3 74.0 - - - +
120I GLU* 1.3 67.5 + - + +
122I ALA* 3.3 3.7 + - - +
123I ASP* 3.1 29.3 + - - +
166I ILE* 4.0 37.5 - - + -
167I GLU 5.7 0.9 - - - -
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Residues in contact with GLU 120 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107I TYR* 3.5 23.6 - - + +
108I PRO* 3.9 10.6 - - + +
111I ILE* 3.7 20.8 - - + +
116I ASP* 3.0 19.8 + - + +
119I LYS* 1.3 78.9 - - - +
121I LEU* 1.3 62.3 + - - +
123I ASP* 3.4 13.3 + - - +
124I ARG* 2.9 53.8 + - - +
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Residues in contact with LEU 121 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46I ILE* 3.9 27.1 - - + +
47I THR* 4.2 9.0 - - - -
50I ALA* 3.6 33.7 - - + -
54I MET* 4.7 1.3 - - + -
66I LEU* 3.7 32.5 - - + -
107I TYR* 4.0 3.1 - - + +
117I HIS 2.7 30.4 + - - +
118I LEU* 3.7 11.7 - - + +
120I GLU* 1.3 70.3 - - - +
122I ALA* 1.3 66.8 + - - +
124I ARG* 3.1 4.5 + - - -
125I TYR* 2.7 39.7 + - + -
162I ILE* 4.1 12.1 - - + -
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Residues in contact with ALA 122 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G ARG* 3.5 31.1 - - - +
118I LEU 2.8 19.1 + - - +
119I LYS* 3.5 7.4 - - - +
121I LEU* 1.3 75.8 - - - +
123I ASP* 1.3 55.5 + - - +
125I TYR* 3.5 1.3 + - - -
126I ALA* 2.8 32.2 + - - +
159I LEU* 3.5 9.7 - - - +
162I ILE* 3.8 14.7 - - + +
163I GLU* 4.3 6.5 - - + -
166I ILE* 4.2 4.7 - - + -
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Residues in contact with ASP 123 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G ARG* 2.8 30.6 + - - +
119I LYS* 3.1 13.8 + - - +
120I GLU* 3.6 16.1 - - - +
121I LEU 3.1 0.8 - - - -
122I ALA* 1.3 76.1 - - - +
124I ARG* 1.3 69.4 + - - +
126I ALA* 3.3 4.3 + - - +
127I ILE* 3.1 29.7 + - + +
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Residues in contact with ARG 124 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43I LEU* 3.8 18.2 - - + -
46I ILE* 4.1 13.4 - - + +
104I LEU* 3.8 18.5 - - + +
105I LYS* 2.9 49.8 + - - +
106I SER 3.6 6.5 + - - -
107I TYR* 2.9 36.1 - - - +
108I PRO* 3.5 15.8 - - - +
120I GLU* 2.9 43.1 + - - +
121I LEU* 3.1 6.4 + - - +
123I ASP* 1.3 78.8 - - - +
125I TYR* 1.3 66.6 + - - +
127I ILE* 3.2 9.2 + - - +
128I VAL* 3.1 26.5 + - - +
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Residues in contact with TYR 125 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43I LEU* 3.5 34.5 - - + -
47I THR* 2.6 32.8 + - + +
66I LEU* 5.4 0.2 - - + -
69I PHE* 3.6 17.3 - + - +
73I LEU* 3.5 11.9 - - + +
121I LEU* 2.7 41.2 + - + +
122I ALA 3.8 3.1 - - - +
124I ARG* 1.3 73.3 - - - +
126I ALA* 1.3 52.3 + - - +
128I VAL* 3.3 1.0 + - - +
129I ALA* 2.6 40.0 + - - +
155I LEU* 4.2 10.0 - - + +
158I PHE* 3.7 35.0 - + + -
159I LEU* 4.1 14.1 - - + -
162I ILE* 3.5 27.1 - - + -
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Residues in contact with ALA 126 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G ARG* 3.5 31.9 - - + -
122I ALA 2.8 19.7 + - - +
123I ASP* 3.4 5.6 - - - +
125I TYR* 1.3 76.5 - - - +
127I ILE* 1.3 57.7 + - + +
129I ALA* 4.2 0.2 - - - -
130I ASN* 2.8 45.0 + - - +
159I LEU* 3.9 15.2 - - + +
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Residues in contact with ILE 127 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39I GLN* 4.3 11.0 - - - +
103I PRO* 4.5 17.5 - - + +
104I LEU* 3.9 23.8 - - + -
105I LYS* 5.5 2.9 - - + +
123I ASP* 3.1 19.4 + - + +
124I ARG* 3.2 12.8 + - - +
126I ALA* 1.3 76.7 - - + +
128I VAL* 1.3 62.4 + - - +
130I ASN* 4.2 3.9 - - - +
131I ASP* 3.0 27.5 + - + +
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Residues in contact with VAL 128 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39I GLN* 3.4 34.9 - - + +
40I PHE* 3.7 28.3 - - + -
43I LEU* 4.0 16.8 - - + -
104I LEU* 3.9 18.2 - - + -
124I ARG 3.1 13.9 + - - +
125I TYR 3.8 4.9 - - - +
127I ILE* 1.3 72.6 - - - +
129I ALA* 1.3 60.6 + - - +
131I ASP* 3.7 0.3 - - - +
132I VAL* 2.9 33.4 + - - +
155I LEU* 3.5 21.3 - - + -
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Residues in contact with ALA 129 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125I TYR 2.6 24.0 + - - +
126I ALA* 3.7 5.6 - - - +
128I VAL* 1.3 72.0 - - - +
130I ASN* 1.3 63.3 + - - +
132I VAL* 3.2 10.3 - - - +
133I ARG* 3.0 30.6 + - - +
155I LEU* 3.8 20.3 - - + +
156I ASP* 3.7 18.1 - - - +
159I LEU* 4.4 12.8 - - + -
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Residues in contact with ASN 130 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G ARG 3.1 19.8 + - - -
19G ASN* 3.5 4.4 - - - -
20G ASP* 2.8 36.8 + - - +
126I ALA* 2.8 33.5 + - - +
127I ILE* 4.2 2.8 - - - +
129I ALA* 1.3 74.3 - - - +
131I ASP* 1.3 62.4 + - - +
133I ARG* 2.5 35.9 + - - +
134I LYS* 3.3 32.9 + - - +
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Residues in contact with ASP 131 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35I ARG* 2.9 40.4 + - - -
36I GLN* 3.7 2.5 - - - +
39I GLN* 3.0 26.7 + - - +
127I ILE* 3.0 21.6 + - + +
128I VAL 3.7 2.5 - - - +
130I ASN* 1.3 76.1 - - - +
132I VAL* 1.3 66.1 + - - +
134I LYS* 3.0 11.2 + - - +
135I ALA* 3.0 17.3 + - - +
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Residues in contact with VAL 132 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36I GLN* 3.7 28.9 + - - +
40I PHE* 4.3 19.1 - - + -
128I VAL 2.9 19.3 + - - +
129I ALA* 3.2 17.0 - - - +
131I ASP* 1.3 73.6 - - - +
133I ARG* 1.3 66.8 + - - +
135I ALA* 3.1 10.8 + - - +
136I ILE* 3.3 12.6 + - - +
148I LEU* 3.9 36.6 - - + +
151I ALA* 4.7 0.7 - - + -
152I SER* 3.9 20.9 - - - +
155I LEU* 4.8 2.9 - - + -
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Residues in contact with ARG 133 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G ASN* 3.0 23.0 + - - +
20G ASP* 3.2 13.5 + - - -
21G VAL* 3.3 18.3 - - - +
83G ARG* 4.0 9.6 - - - +
141G ASP* 4.3 7.0 - - - +
142G ASP* 4.4 8.1 - - + +
143G ASP* 3.9 9.9 - - - +
129I ALA* 3.0 14.3 + - - +
130I ASN* 2.5 34.2 + - - +
131I ASP 3.2 0.2 - - - -
132I VAL* 1.3 82.6 - - - +
134I LYS* 1.3 63.1 + - + +
136I ILE* 3.4 24.5 - - + +
137I GLY 4.4 0.2 + - - -
152I SER* 3.6 14.1 - - - +
156I ASP* 2.6 44.2 + - - -
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Residues in contact with LYS 134 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G ASP* 2.5 42.4 + - - -
130I ASN* 3.3 22.4 + - - +
131I ASP* 3.0 10.5 + - - +
133I ARG* 1.3 77.6 - - + +
135I ALA* 1.3 65.5 + - - +
136I ILE 3.0 3.7 + - - -
137I GLY* 3.1 12.0 + - - -
138I GLU* 3.3 14.2 + - - +
----------------------------------------------------------
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Residues in contact with ALA 135 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32I LEU* 3.9 19.6 - - + +
35I ARG* 4.3 3.6 - - - +
36I GLN* 3.6 23.3 - - - +
131I ASP 3.0 8.9 + - - +
132I VAL* 3.1 10.5 + - - +
134I LYS* 1.3 77.0 - - - +
136I ILE* 1.3 56.8 + - - +
138I GLU* 3.4 13.5 + - - +
139I ALA* 2.8 31.9 + - - +
148I LEU* 3.7 12.2 - - + +
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Residues in contact with ILE 136 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142G ASP* 3.8 27.6 - - + +
143G ASP* 3.4 25.8 - - - +
132I VAL 3.5 8.7 - - - +
133I ARG* 3.4 20.0 - - + +
134I LYS 3.0 0.6 - - - -
135I ALA* 1.3 77.9 - - - +
137I GLY* 1.3 62.7 + - - +
139I ALA* 3.2 21.0 + - - +
145I ALA* 4.0 14.1 - - + +
148I LEU* 3.9 21.1 - - + -
149I THR* 3.4 30.7 - - - +
152I SER* 3.7 11.0 - - - +
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Residues in contact with GLY 137 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142G ASP* 4.3 10.2 + - - -
133I ARG 4.4 0.4 + - - -
134I LYS 3.1 7.4 + - - -
136I ILE* 1.3 81.8 - - - +
138I GLU* 1.3 59.4 + - - +
139I ALA 3.4 5.1 + - - +
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Residues in contact with GLU 138 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32I LEU* 3.6 28.3 - - + +
35I ARG* 3.8 13.5 + - - -
134I LYS* 3.3 12.8 + - - +
135I ALA* 3.1 13.1 + - - +
137I GLY* 1.3 76.6 - - - +
139I ALA* 1.3 61.1 + - - +
140I LYS* 3.5 12.0 + - - +
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Residues in contact with ALA 139 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32I LEU* 4.0 11.2 - - + -
135I ALA 2.8 11.3 + - - +
136I ILE 3.2 18.1 + - - +
137I GLY 4.1 4.4 - - - +
138I GLU* 1.3 76.8 - - - +
140I LYS* 1.3 63.6 + - - +
141I ASP 4.4 0.7 - - - +
144I THR* 4.4 6.3 - - + -
145I ALA* 3.9 30.9 - - + +
148I LEU* 4.1 10.3 - - + -
----------------------------------------------------------
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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