Contacts of the helix formed by residues 95 - 121 (chain F) in PDB entry 5X22
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 THR 95 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93F LEU 3.7 2.0 + - - -
94F LEU* 1.3 74.8 - - - +
96F LEU* 1.3 69.4 + - + +
97F GLU* 3.2 34.5 - - - +
98F GLU* 2.5 43.6 + - - -
99F GLU* 3.0 10.7 + - - +
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Residues in contact with LEU 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349D PRO* 4.4 20.2 - - + -
350D HIS* 4.1 21.1 - - + +
94F LEU 4.0 0.6 + - - -
95F THR* 1.3 76.5 - - + +
97F GLU* 1.3 60.3 + - + +
99F GLU* 3.2 20.4 + - - +
100F VAL* 2.9 50.0 + - + +
234F LYS* 4.4 28.7 - - + +
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Residues in contact with GLU 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207D PHE* 3.5 40.4 - - + -
209D ARG* 4.2 13.6 + - - +
349D PRO* 4.0 40.4 - - + +
391D ALA* 4.2 14.7 - - + +
95F THR* 3.2 34.9 + - - +
96F LEU* 1.3 77.3 + - - +
98F GLU* 1.3 58.5 + - - +
100F VAL* 3.6 2.1 + - - +
101F GLU* 2.9 30.0 + - - +
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Residues in contact with GLU 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168D THR* 5.3 6.4 - - - +
206D ARG* 4.4 12.3 + - - +
207D PHE* 3.5 28.5 - - + -
392D SER* 4.6 9.4 + - - -
93F LEU 4.3 2.3 - - - +
94F LEU* 3.4 21.0 - - + +
95F THR* 2.5 52.1 + - - +
97F GLU* 1.3 76.7 - - - +
99F GLU* 1.3 58.7 + - - +
101F GLU* 3.6 2.1 - - - +
102F LEU* 2.9 40.0 + - + +
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Residues in contact with GLU 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94F LEU* 4.0 25.7 - - + +
95F THR 3.0 10.6 + - - +
96F LEU* 3.5 22.9 - - + +
98F GLU* 1.3 76.8 - - - +
100F VAL* 1.3 65.1 + - + +
102F LEU* 3.8 2.6 - - - +
103F ALA* 3.0 25.6 + - + +
187F LEU* 4.8 6.9 - - + +
191F ASN* 5.0 2.3 - - - +
227F PHE* 5.0 6.1 - - + -
233F PHE 4.3 1.6 - - - +
234F LYS* 3.4 19.0 - - - +
235F PHE* 2.7 44.8 + - + +
6H T 3.9 17.3 - - - +
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Residues in contact with VAL 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349D PRO 4.2 16.6 - - - +
350D HIS* 4.0 40.4 - - + +
351D MET 5.7 1.3 - - - +
96F LEU* 2.9 33.6 + - + +
97F GLU 3.8 4.0 - - - +
99F GLU* 1.3 76.2 - - + +
101F GLU* 1.3 59.3 + - - +
103F ALA* 3.4 5.3 + - - +
104F ARG* 2.9 32.2 + - + +
229F TYR* 3.9 27.6 - - + +
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Residues in contact with GLU 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206D ARG* 2.6 38.7 + - - -
207D PHE* 3.1 19.6 - - + -
97F GLU 2.9 19.2 + - - +
98F GLU* 3.6 8.0 - - - +
100F VAL* 1.3 77.5 - - - +
102F LEU* 1.3 64.9 + - - +
104F ARG* 3.3 23.4 + - - +
105F LYS* 2.9 63.8 + - - +
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Residues in contact with LEU 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F LEU* 3.7 38.4 - - + -
98F GLU* 2.9 18.1 + - + +
99F GLU 3.8 3.4 - - - +
101F GLU* 1.3 85.5 - - - +
103F ALA* 1.3 63.1 + - - +
105F LYS* 3.3 7.1 + - + +
106F VAL* 2.9 29.3 + - - +
183F ALA* 3.7 34.7 - - + +
186F HIS* 4.1 20.4 - - + -
187F LEU* 4.0 26.2 - - + +
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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
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99F GLU* 3.0 18.3 + - + +
100F VAL* 3.8 1.8 - - - +
102F LEU* 1.3 75.1 - - - +
104F ARG* 1.3 58.0 - - - +
106F VAL* 3.2 8.0 + - - +
107F GLU* 2.9 29.5 + - - +
187F LEU* 4.5 10.9 - - + +
227F PHE* 3.9 26.3 - - + +
229F TYR* 3.7 27.3 - - + +
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Residues in contact with ARG 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352D ASN* 3.6 49.1 - - - +
100F VAL* 2.9 19.7 + - - +
101F GLU* 3.5 33.6 + - - +
103F ALA* 1.3 76.7 - - - +
105F LYS* 1.3 74.3 + - - +
107F GLU* 3.3 1.0 + - - +
108F GLU* 2.9 71.6 + - + +
229F TYR* 3.6 39.6 - - + +
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Residues in contact with LYS 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101F GLU* 2.9 52.8 + - + +
102F LEU* 3.6 3.4 - - + +
104F ARG* 1.3 94.2 - - - +
106F VAL* 1.3 56.3 + - - +
108F GLU* 3.9 6.7 - - - +
109F GLY* 2.9 22.5 + - - -
176F ILE* 4.5 1.9 - - - +
179F GLU* 3.1 42.9 + - + +
180F GLY* 3.3 13.6 + - - -
183F ALA* 3.6 26.5 - - + -
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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
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102F LEU 2.9 20.7 + - - +
103F ALA* 3.2 11.2 + - - +
105F LYS* 1.3 74.1 - - - +
107F GLU* 1.3 68.1 + - - +
109F GLY* 3.0 2.9 + - - -
110F MET* 2.9 37.2 + - + +
180F GLY* 3.7 8.9 - - - +
183F ALA 4.0 1.1 - - - -
184F ARG* 3.6 45.1 - - + +
187F LEU* 4.7 8.5 - - + -
224F VAL* 4.4 19.1 - - + +
225F GLU* 5.5 1.8 - - - +
227F PHE 6.2 0.2 - - - +
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Residues in contact with GLU 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F ALA 2.9 15.6 + - - +
104F ARG 3.8 3.4 - - - +
106F VAL* 1.3 78.0 - - - +
108F GLU* 1.3 61.4 + - + +
110F MET* 3.1 12.3 + - + +
111F GLU* 3.0 46.6 + - + +
227F PHE 4.0 7.6 - - - +
228F GLU* 3.7 33.6 - - - +
229F TYR* 3.3 16.1 - - + -
230F LYS* 3.2 31.2 + - - +
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Residues in contact with GLU 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352D ASN* 5.5 0.5 + - - -
104F ARG* 2.9 58.3 + - + +
105F LYS* 4.1 4.7 - - - +
107F GLU* 1.3 76.4 - - + +
109F GLY* 1.3 56.6 + - - +
111F GLU* 3.6 19.6 - - - +
112F ALA* 2.9 28.6 + - - +
176F ILE* 3.5 19.5 - - + +
229F TYR* 4.5 5.7 + - + +
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Residues in contact with GLY 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105F LYS 2.9 17.2 + - - -
106F VAL 3.0 5.3 + - - -
108F GLU* 1.3 75.1 - - - +
110F MET* 1.3 59.9 + - - +
112F ALA* 3.1 4.2 + - - +
113F ILE* 2.9 33.9 + - - +
176F ILE* 3.9 17.2 - - - +
177F ALA* 4.0 8.7 - - - +
180F GLY* 4.3 4.7 - - - -
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Residues in contact with MET 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106F VAL* 2.9 29.7 + - + +
107F GLU* 3.1 11.6 + - - +
109F GLY* 1.3 72.5 - - - +
111F GLU* 1.3 66.8 + - + +
113F ILE* 3.0 16.3 + - + +
114F LYS* 2.9 26.9 + - + +
128F ARG* 6.2 3.4 - - - -
225F GLU* 4.1 27.1 - - + +
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Residues in contact with GLU 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107F GLU* 3.0 38.7 + - + +
108F GLU* 3.6 22.2 - - - +
109F GLY 3.3 0.2 - - - -
110F MET* 1.3 75.6 - - + +
112F ALA* 1.3 58.0 + - - +
114F LYS* 3.3 10.3 + - - +
115F LYS* 2.9 31.8 + - + +
230F LYS* 5.2 3.3 + - - -
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Residues in contact with ALA 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108F GLU 2.9 18.6 + - - +
109F GLY 3.1 6.3 + - - +
111F GLU* 1.3 75.5 - - - +
113F ILE* 1.3 58.0 + - - +
115F LYS* 3.3 9.0 + - - +
116F LEU* 2.9 34.4 + - - +
173F TYR* 3.4 34.4 - - + +
176F ILE* 3.7 16.6 - - + -
177F ALA 4.1 1.6 - - - +
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Residues in contact with ILE 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109F GLY 2.9 19.2 + - - +
110F MET* 3.0 16.5 + - + +
112F ALA* 1.3 75.4 - - - +
114F LYS* 1.3 62.2 + - + +
116F LEU* 3.3 7.9 + - - +
117F SER* 2.9 27.2 + - - -
124F PRO* 3.6 30.1 - - + +
127F ILE* 4.3 11.0 - - + +
128F ARG* 3.7 41.5 - - + +
131F VAL* 5.0 5.6 - - + -
177F ALA* 3.8 18.8 - - + +
181F GLU* 4.8 8.1 - - + +
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Residues in contact with LYS 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F MET 2.9 16.4 + - - +
111F GLU* 3.4 12.1 - - - +
113F ILE* 1.3 75.8 - - + +
115F LYS* 1.3 58.5 + - + +
117F SER* 3.2 7.7 + - - -
118F GLU* 2.9 40.2 + - - +
124F PRO* 4.8 24.0 - - + +
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Residues in contact with LYS 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111F GLU* 2.9 16.3 + - + +
112F ALA* 3.3 13.0 - - - +
113F ILE 3.2 0.2 - - - -
114F LYS* 1.3 77.8 - - + +
116F LEU* 1.3 56.8 - - - +
118F GLU* 3.0 29.6 + - + +
119F ILE* 2.9 35.2 + - + +
173F TYR* 3.4 46.2 + - + -
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Residues in contact with LEU 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112F ALA 2.9 20.3 + - - +
113F ILE* 3.3 4.2 + - - +
115F LYS* 1.3 75.8 - - - +
117F SER* 1.3 57.0 + - - +
119F ILE* 3.7 11.2 - - + -
120F THR* 2.9 34.3 + - - -
127F ILE* 3.7 28.5 - - + +
131F VAL* 5.4 0.9 - - + -
163F LEU* 4.5 10.8 - - + -
166F LEU* 4.4 15.3 - - + -
170F HIS 3.7 23.8 - - - +
173F TYR* 3.7 14.8 - - + +
174F LEU* 3.8 34.3 - - + +
177F ALA* 4.8 5.8 - - + -
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Residues in contact with SER 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113F ILE 2.9 13.4 + - - -
114F LYS* 3.3 13.5 - - - -
116F LEU* 1.3 77.4 - - - +
118F GLU* 1.3 62.2 + - - +
121F GLY* 3.1 23.8 + - - +
122F LEU 3.2 17.3 + - - -
124F PRO* 3.3 30.4 - - - +
127F ILE* 3.8 8.9 - - - +
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Residues in contact with GLU 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F LYS* 2.9 27.2 + - - +
115F LYS* 3.0 31.4 + - + +
117F SER* 1.3 76.9 - - - +
119F ILE* 1.3 64.5 + - + +
121F GLY* 4.7 1.6 + - - -
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Residues in contact with ILE 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115F LYS* 2.9 21.4 + - + +
116F LEU* 3.8 13.2 - - + +
117F SER 3.2 0.2 - - - -
118F GLU* 1.3 81.8 - - + +
120F THR* 1.3 68.4 + - - +
121F GLY* 3.6 0.3 + - - -
166F LEU* 3.9 21.3 - - + -
170F HIS* 3.5 57.7 - - + +
173F TYR* 4.0 22.0 - - + -
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Residues in contact with THR 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F LEU 2.9 17.0 + - - -
119F ILE* 1.3 76.3 - - - +
121F GLY* 1.3 59.1 + - - +
122F LEU* 3.7 34.2 - - + +
127F ILE* 4.8 0.9 - - - -
162F LYS* 4.8 20.4 - - + +
163F LEU* 3.7 14.2 - - + +
166F LEU* 3.6 26.7 - - + +
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Residues in contact with GLY 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117F SER 3.1 16.4 + - - -
118F GLU 5.2 1.3 - - - -
119F ILE 3.4 1.7 - - - -
120F THR* 1.3 80.3 - - - +
122F LEU* 1.3 67.9 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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