Contacts of the helix formed by residues 90 - 115 (chain F) in PDB entry 4GTU
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 GLU 90 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E HIS* 5.4 6.5 - - + +
78E TYR* 3.2 19.8 + - + +
81E ARG* 2.9 46.4 + - - +
82E LYS* 4.3 14.8 + - - +
89F THR* 1.3 71.5 - - - +
91F GLU* 1.3 61.1 + - + +
93F LYS* 3.5 23.2 + - + +
94F ILE* 3.0 34.4 + - + +
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Residues in contact with GLU 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E HIS* 5.7 10.8 - - + +
89F THR* 2.9 12.8 + - - +
90F GLU* 1.3 80.5 - - + +
92F GLU* 1.3 61.9 + - + +
94F ILE* 3.9 7.1 + - - +
95F ARG* 2.8 29.2 + - - +
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Residues in contact with GLU 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87F GLY* 4.3 2.7 - - - -
88F GLU* 3.2 37.7 - - - +
89F THR* 2.6 29.3 + - - +
91F GLU* 1.3 72.5 - - + +
93F LYS* 1.3 62.8 + - - +
95F ARG* 3.5 7.7 + - - -
96F VAL* 3.1 27.9 + - - +
148F VAL* 3.4 26.7 - - + +
149F GLY* 5.1 0.2 - - - -
150F ASP* 4.9 2.9 + - - +
151F LYS* 3.3 33.0 + - + +
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Residues in contact with LYS 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81E ARG* 3.8 33.7 - - - +
87F GLY* 4.1 19.3 - - - -
88F GLU 3.4 25.0 + - - -
89F THR 2.8 8.9 + - - +
90F GLU* 3.5 30.9 + - - +
92F GLU* 1.3 73.4 - - - +
94F ILE* 1.3 66.6 + - - +
96F VAL* 2.9 10.9 + - - +
97F ASP* 2.9 26.4 + - - +
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Residues in contact with ILE 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E HIS* 4.1 22.2 - - + -
68E LYS 5.2 1.1 - - - +
69E ILE* 3.5 27.1 - - + -
78E TYR* 3.4 27.8 - - + -
81E ARG* 3.8 20.9 - - - +
90F GLU* 3.0 21.8 + - + +
91F GLU* 4.2 5.8 - - - +
93F LYS* 1.3 74.0 - - - +
95F ARG* 1.3 65.7 + - + +
97F ASP* 3.0 4.1 + - + +
98F ILE* 2.9 44.2 + - + +
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Residues in contact with ARG 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55E ASP* 5.0 2.6 + - - -
91F GLU* 2.8 23.3 + - - +
92F GLU* 3.7 9.4 - - - +
93F LYS 3.2 0.2 - - - -
94F ILE* 1.3 74.1 - - + +
96F VAL* 1.3 59.0 + - - +
98F ILE* 4.0 0.8 - - - +
99F LEU* 2.8 37.0 + - - +
140F PHE* 3.4 60.9 + - + +
144F ARG* 3.7 30.6 - - - +
147F PHE 2.8 25.8 + - - +
148F VAL* 3.9 28.0 - - + +
155F VAL* 5.7 0.7 - - - -
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Residues in contact with VAL 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86F CYS* 4.5 4.5 - - + -
87F GLY* 4.1 20.4 - - - +
92F GLU 3.1 15.7 + - - +
93F LYS* 2.9 13.6 + - - +
95F ARG* 1.3 76.1 - - - +
97F ASP* 1.3 58.1 + - - +
100F GLU* 2.8 40.7 + - - +
148F VAL* 3.8 15.5 - - + -
153F THR* 4.5 4.9 - - + -
154F PHE* 3.6 32.5 - - + -
155F VAL* 3.8 16.3 - - + +
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Residues in contact with ASP 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74E ALA* 3.5 25.8 - - + +
77E CYS* 3.2 30.5 - - - +
81E ARG* 3.0 26.5 + - - -
93F LYS* 2.9 18.9 + - - +
94F ILE* 3.5 8.1 - - + +
96F VAL* 1.3 79.6 - - - +
98F ILE* 1.3 64.2 + - - +
100F GLU* 3.2 25.0 - - - +
101F ASN* 3.2 13.5 + - - +
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Residues in contact with ILE 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55E ASP* 3.8 19.5 - - + +
56E PHE* 3.4 35.0 - - + -
68E LYS 3.8 4.0 - - - +
69E ILE* 4.1 0.7 - - + -
70E THR* 3.4 40.6 - - - +
71E GLN* 4.7 1.2 - - - +
74E ALA* 3.9 15.5 - - + -
94F ILE* 2.9 39.8 + - + +
95F ARG* 4.0 2.2 - - - +
97F ASP* 1.3 74.9 - - - +
99F LEU* 1.3 65.5 + - - +
101F ASN* 4.1 1.7 - - - +
102F GLN* 3.0 26.0 + - - +
140F PHE* 4.3 9.2 - - + -
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Residues in contact with LEU 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56E PHE* 3.6 28.3 - - + -
95F ARG 2.8 24.3 + - - +
96F VAL 4.1 0.9 - - - +
98F ILE* 1.3 72.1 - - - +
100F GLU* 1.3 65.9 + - - +
102F GLN* 2.8 2.9 + - + -
103F ALA* 2.7 36.5 + - + +
137F PHE* 3.9 18.2 - - + -
140F PHE* 4.0 12.6 - - + -
147F PHE* 4.0 23.3 - - + -
155F VAL* 3.8 39.0 - - + +
158F LEU* 5.4 0.2 - - + -
159F ALA* 4.5 9.6 - - + -
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Residues in contact with GLU 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E ASN* 5.1 0.3 + - - -
77E CYS* 6.1 0.7 - - - -
100E GLU* 4.0 14.4 - - - +
101E ASN* 4.5 2.9 + - - +
73F ASN* 3.6 32.4 + - - +
77F CYS* 4.6 9.8 - - - -
96F VAL* 2.8 29.0 + - - +
97F ASP* 3.2 15.9 - - - +
99F LEU* 1.3 74.1 - - - +
101F ASN* 1.3 76.9 + - - +
103F ALA* 3.4 4.3 + - - +
104F MET* 3.4 20.0 + - - +
154F PHE* 4.0 29.5 - - + -
155F VAL* 4.4 1.7 - - - +
158F LEU* 4.1 14.3 - - + +
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Residues in contact with ASN 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71E GLN* 3.2 36.4 - - + +
72E SER* 5.4 0.2 - - - -
73E ASN* 3.0 41.2 + - - +
74E ALA 3.5 4.3 + - - -
73F ASN* 4.6 4.0 - - - +
97F ASP* 3.2 9.1 + - - +
100F GLU* 1.3 102.2 + - - +
102F GLN* 1.3 57.2 + - - +
104F MET* 3.3 10.4 + - - +
105F ASP* 3.0 32.7 + - - +
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Residues in contact with GLN 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56E PHE* 3.5 57.0 - - + +
57E PRO 5.5 0.8 + - - -
58E ASN* 5.1 9.4 + - - +
70E THR 4.6 2.4 - - - +
71E GLN* 2.8 33.5 + - - +
98F ILE 3.0 19.5 + - - +
99F LEU* 2.8 10.8 + - + +
101F ASN* 1.3 74.1 - - - +
103F ALA* 1.3 63.0 + - - +
105F ASP* 3.2 11.6 + - - +
106F VAL* 2.8 29.8 + - + +
137F PHE* 4.2 6.7 - - + -
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Residues in contact with ALA 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99F LEU* 2.7 28.2 + - + +
100F GLU 3.7 4.5 - - - +
102F GLN* 1.3 72.0 - - - +
104F MET* 1.3 64.2 + - - +
106F VAL* 3.3 13.1 + - - +
107F SER* 3.4 15.8 + - - -
137F PHE* 4.7 7.0 - - + -
158F LEU* 4.0 32.5 - - + -
159F ALA* 4.8 1.6 - - - +
162F VAL* 3.5 19.5 - - + +
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Residues in contact with MET 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F LEU* 3.6 32.5 - - + -
72F SER* 4.0 17.7 - - - +
73F ASN* 3.7 36.6 - - - +
100F GLU 3.4 7.5 + - - +
101F ASN* 3.3 11.9 - - - +
102F GLN 3.2 0.2 - - - -
103F ALA* 1.3 78.3 - - - +
105F ASP* 1.3 58.0 + - - +
107F SER* 2.9 10.0 + - - +
108F ASN* 2.8 45.5 + - - +
158F LEU* 5.0 11.2 - - + -
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Residues in contact with ASP 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71E GLN* 4.0 20.2 + - - +
101F ASN* 3.0 19.3 + - - +
102F GLN* 3.2 16.8 + - - +
104F MET* 1.3 75.5 - - - +
106F VAL* 1.3 57.7 + - + +
108F ASN* 3.5 13.4 - - - +
109F GLN* 2.9 58.8 + - - +
112F ARG* 5.1 5.0 + - - -
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Residues in contact with VAL 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102F GLN* 2.8 21.3 - - + +
103F ALA* 3.5 6.7 - - - +
104F MET 3.2 0.4 - - - -
105F ASP* 1.3 74.1 - - + +
107F SER* 1.3 60.3 + - - +
109F GLN* 4.1 10.2 - - - +
110F LEU* 3.5 21.5 + - - +
126F TYR* 3.9 8.1 + - - +
133F MET* 5.4 12.6 - - + -
137F PHE* 3.6 31.4 - - + -
162F VAL* 3.7 13.7 - - + -
166F HIS* 3.7 26.9 - - + +
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Residues in contact with SER 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F LEU* 4.6 21.2 - - - +
103F ALA 3.4 10.7 + - - -
104F MET* 2.9 12.9 + - - +
106F VAL* 1.3 76.0 - - - +
108F ASN* 1.3 61.8 + - - +
110F LEU* 3.5 4.0 + - - +
111F ALA* 2.8 32.8 + - - +
161F ASP* 6.0 1.0 - - - -
162F VAL* 3.5 19.7 - - - +
165F LEU* 5.7 6.6 - - - +
166F HIS* 5.8 0.7 - - - -
208F TYR* 4.8 1.4 + - - -
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Residues in contact with ASN 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108E ASN* 5.9 2.6 - - - -
12F LEU* 5.9 4.6 - - - +
104F MET* 2.8 31.8 + - - +
105F ASP* 3.5 15.5 + - - +
107F SER* 1.3 75.7 - - - +
109F GLN* 1.3 63.5 + - - +
111F ALA* 2.9 9.4 + - - +
112F ARG* 2.9 53.7 + - - +
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Residues in contact with GLN 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105F ASP* 2.9 46.7 + - - +
106F VAL* 4.1 11.5 - - - +
108F ASN* 1.3 76.6 - - - +
110F LEU* 1.3 61.3 + - - +
112F ARG* 3.5 25.9 + - - +
113F VAL* 3.3 25.8 + - - +
126F TYR* 4.8 12.4 - - + -
133F MET* 4.0 23.3 - - - +
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Residues in contact with LEU 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106F VAL 3.5 15.0 + - - +
107F SER* 3.5 5.0 + - - +
108F ASN 3.2 0.6 - - - -
109F GLN* 1.3 75.4 - - - +
111F ALA* 1.3 67.7 + - - +
113F VAL* 3.0 7.2 + - + -
114F CYS* 2.8 22.1 + - - +
126F TYR* 3.3 33.3 + - + +
165F LEU* 3.3 33.4 - - + -
166F HIS* 3.9 22.9 - - + +
169F PHE* 3.8 35.9 - - + -
208F TYR* 3.2 9.9 - - - +
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Residues in contact with ALA 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F LEU* 5.9 7.0 - - + -
107F SER 2.8 20.1 + - - +
108F ASN* 2.9 8.9 + - - +
110F LEU* 1.3 75.6 - - - +
112F ARG* 1.3 63.0 + - + +
114F CYS* 2.9 4.2 + - - -
115F TYR* 2.8 39.9 + - + -
208F TYR* 3.4 25.1 + - + -
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Residues in contact with ARG 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108E ASN* 5.3 11.9 - - - +
112E ARG* 4.5 29.7 - - - +
105F ASP* 5.1 5.1 + - - -
108F ASN* 2.9 42.7 + - - +
109F GLN* 3.6 37.9 - - - +
111F ALA* 1.3 75.7 - - + +
113F VAL* 1.3 57.7 + - + +
115F TYR* 2.9 9.3 + - - +
116F SER* 2.8 31.6 + - - -
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Residues in contact with VAL 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109F GLN 3.3 15.0 - - - +
110F LEU* 3.0 15.7 + - + +
112F ARG* 1.3 78.6 - - + +
114F CYS* 1.3 60.8 + - - +
115F TYR 3.1 1.1 + - - -
116F SER* 3.6 16.2 + - - +
119F PHE* 3.7 19.6 - - + -
122F LEU* 4.5 15.5 - - + +
123F LYS* 4.1 35.2 - - + +
126F TYR* 4.4 27.8 - - + -
169F PHE* 5.1 1.6 - - + -
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Residues in contact with CYS 114 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110F LEU* 2.8 13.0 + - - +
111F ALA 2.9 8.0 + - - +
113F VAL* 1.3 76.9 - - - +
115F TYR* 1.3 59.7 + - - +
119F PHE* 4.9 1.3 - - - -
169F PHE* 3.6 20.4 - - - -
208F TYR* 3.7 32.1 - - + -
212F ALA* 3.7 5.7 - - - -
213F VAL* 2.9 36.0 + - - +
214F TRP* 3.4 41.7 - - + +
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Residues in contact with TYR 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111F ALA* 2.8 31.4 + - + +
112F ARG* 2.9 8.0 + - - +
114F CYS* 1.3 83.8 - - - +
116F SER* 1.3 61.3 + - - +
117F PRO* 3.6 7.1 - - - +
208F TYR* 4.0 20.9 - + - -
209F THR* 3.1 31.8 + - - +
211F VAL* 3.6 32.2 - - + +
212F ALA* 3.9 17.5 - - + -
213F VAL* 4.5 5.8 - - - +
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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