Contacts of the helix formed by residues 90 - 119 (chain L) in PDB entry 6O81
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 90 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88L ARG 3.7 2.5 + - - -
89L VAL* 1.3 77.5 - - - +
91L PRO* 1.3 72.8 - - - +
92L GLU* 3.3 15.5 + - - +
93L GLU* 3.3 13.6 + - - +
94L ALA* 2.8 28.7 + - - +
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Residues in contact with PRO 91 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C SER* 6.0 1.3 - - - +
134C ILE* 4.7 10.5 - - + -
135C GLU* 5.3 11.9 - - + -
138C ASN* 4.2 22.4 - - - +
89L VAL 4.6 1.6 - - - +
90L SER* 1.3 91.3 - - - +
92L GLU* 1.3 55.3 + - - +
94L ALA* 3.3 8.3 + - + +
95L ILE* 2.9 28.8 + - - +
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Residues in contact with GLU 92 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90L SER* 3.3 10.0 + - - +
91L PRO* 1.3 76.8 - - - +
93L GLU* 1.3 58.3 + - - +
95L ILE* 3.3 6.5 + - - +
96L LYS* 2.9 36.3 + - + +
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Residues in contact with GLU 93 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18L VAL* 4.5 13.4 - - + +
89L VAL* 4.0 14.4 - - + -
90L SER* 3.3 20.7 + - - +
92L GLU* 1.3 77.0 - - - +
94L ALA* 1.3 58.5 + - - +
96L LYS* 3.7 12.9 - - - +
97L CYS* 2.9 29.6 + - - +
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Residues in contact with ALA 94 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20L MET* 4.8 0.5 - - - +
69L CYS* 4.3 21.0 - - + +
89L VAL* 4.0 10.2 - - + +
90L SER 2.8 17.9 + - - +
91L PRO* 3.6 9.6 - - + +
92L GLU 3.2 0.2 - - - -
93L GLU* 1.3 73.7 - - - +
95L ILE* 1.3 59.7 + - - +
97L CYS* 3.4 2.1 + - - +
98L GLU* 2.9 29.1 + - - +
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Residues in contact with ILE 95 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91L PRO 2.9 17.1 + - - +
92L GLU* 3.3 6.0 + - - +
94L ALA* 1.3 72.6 - - - +
96L LYS* 1.3 59.7 + - - +
98L GLU* 3.3 6.5 + - - +
99L ASP* 3.0 30.0 + - - +
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Residues in contact with LYS 96 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92L GLU* 2.9 25.1 + - + +
93L GLU* 3.7 10.8 - - - +
95L ILE* 1.3 77.7 - - + +
97L CYS* 1.3 56.9 + - - +
99L ASP* 3.4 5.3 + - - +
100L LYS* 2.9 30.2 + - - +
146L TYR* 4.7 22.0 - - + -
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Residues in contact with CYS 97 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18L VAL* 3.7 35.0 - - + +
19L VAL 5.4 1.3 - - - -
20L MET* 3.7 6.9 - - + +
69L CYS* 4.1 9.2 - - + -
93L GLU 2.9 18.1 + - - +
94L ALA 3.8 3.8 - - - +
96L LYS* 1.3 74.0 - - - +
98L GLU* 1.3 60.7 + - - +
100L LYS* 3.8 8.3 - - - +
101L PHE* 2.9 31.4 + - - +
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Residues in contact with GLU 98 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20L MET* 3.8 14.7 - - + +
94L ALA 2.9 18.3 + - - +
95L ILE* 3.7 8.1 - - - +
96L LYS 3.3 0.2 - - - -
97L CYS* 1.3 77.4 - - - +
99L ASP* 1.3 56.9 + - - +
101L PHE* 3.4 4.9 + - - +
102L THR* 2.9 29.1 + - - -
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Residues in contact with ASP 99 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95L ILE 3.0 17.1 + - - +
96L LYS* 3.9 5.6 - - - +
98L GLU* 1.3 75.9 - - - +
100L LYS* 1.3 57.4 + - - +
102L THR* 3.3 6.0 + - - -
103L LYS* 3.0 49.0 + - + +
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Residues in contact with LYS 100 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8L TYR* 3.2 32.4 - - + -
18L VAL 5.0 8.2 + - - +
37L GLU* 3.4 17.6 + - - -
96L LYS 2.9 18.4 + - - +
97L CYS* 3.9 7.4 - - - +
99L ASP* 1.3 78.1 - - - +
101L PHE* 1.3 57.4 + - - +
103L LYS* 3.4 12.1 + - - +
104L SER* 2.9 28.1 + - - -
144L PRO* 3.4 26.0 - - - +
145L GLY* 4.9 4.2 - - - -
146L TYR* 3.7 30.5 - - + -
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Residues in contact with PHE 101 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7L PHE* 3.8 27.4 - + - -
20L MET* 3.7 37.5 - - + -
36L LEU* 3.9 35.7 - - + -
37L GLU* 4.5 15.7 - - + +
67L ASN* 4.3 11.7 - - - -
97L CYS 2.9 19.4 + - - +
98L GLU* 3.9 4.9 - - - +
100L LYS* 1.3 73.4 - - - +
102L THR* 1.3 63.4 + - - +
104L SER* 4.5 3.8 - - - -
105L LYS* 2.9 48.2 + - + +
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Residues in contact with THR 102 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98L GLU 2.9 19.1 + - - -
99L ASP* 3.6 7.6 - - - -
101L PHE* 1.3 79.9 - - - +
103L LYS* 1.3 58.5 + - - +
105L LYS* 3.4 6.4 + - - +
106L THR* 2.9 29.1 + - - -
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Residues in contact with LYS 103 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99L ASP* 3.0 45.6 + - + +
100L LYS* 3.5 6.2 - - - +
102L THR* 1.3 77.2 - - - +
104L SER* 1.3 58.8 + - - +
106L THR* 3.3 3.8 + - - -
107L VAL* 3.0 27.5 + - - +
145L GLY 4.5 3.8 - - - +
146L TYR* 3.5 44.1 - - - +
149L TYR* 3.6 57.7 - - + +
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Residues in contact with SER 104 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7L PHE* 3.6 25.0 - - - -
8L TYR* 4.1 24.2 - - - -
37L GLU* 5.2 0.2 - - - -
100L LYS 2.9 19.0 + - - -
101L PHE* 4.0 3.8 - - - -
103L LYS* 1.3 75.9 - - - +
105L LYS* 1.3 58.0 + - - +
107L VAL* 3.4 7.4 + - - +
108L TYR* 2.9 28.4 + - - +
145L GLY* 4.8 8.2 + - - -
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Residues in contact with LYS 105 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7L PHE* 3.7 22.8 - - + -
101L PHE* 2.9 38.5 + - + +
102L THR* 3.8 6.5 - - - +
104L SER* 1.3 72.6 - - - +
106L THR* 1.3 61.3 + - - +
108L TYR* 3.4 6.1 + - + +
109L SER* 2.9 31.4 + - - -
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Residues in contact with THR 106 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102L THR 2.9 17.8 + - - -
103L LYS 3.3 5.6 + - - -
105L LYS* 1.3 76.4 - - - +
107L VAL* 1.3 57.0 + - - +
109L SER* 3.4 6.3 + - - +
110L ILE* 2.9 29.1 + - - +
149L TYR* 4.3 16.6 - - - -
182L ARG* 5.9 0.9 - - - +
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Residues in contact with VAL 107 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103L LYS 3.0 17.4 + - - +
104L SER* 3.8 7.0 - - - +
106L THR* 1.3 75.9 - - - +
108L TYR* 1.3 58.2 + - - +
110L ILE* 3.3 5.5 + - - +
111L LEU* 3.0 36.9 + - + +
130L PHE* 5.6 0.9 - - - -
134L ALA* 5.6 3.6 - - + -
145L GLY 6.2 0.2 - - - +
148L ALA* 5.2 9.0 - - + -
149L TYR* 5.1 7.1 - - + +
152L PHE* 4.2 26.0 - - + -
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Residues in contact with TYR 108 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3L LEU 5.2 3.1 - - - -
4L SER* 4.7 16.2 - - - -
5L CYS 4.4 17.9 - - - -
7L PHE* 3.4 39.3 - + + -
104L SER 2.9 18.1 + - - +
105L LYS* 3.6 10.5 - - + +
107L VAL* 1.3 77.4 - - - +
109L SER* 1.3 61.3 + - - +
111L LEU* 3.5 0.9 + - - +
112L ARG* 2.9 40.7 + - + +
126L LEU* 5.8 1.6 - - + -
130L PHE* 3.5 33.6 - + + -
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Residues in contact with SER 109 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105L LYS* 2.9 20.3 + - - -
106L THR* 3.4 7.2 + - - -
108L TYR* 1.3 77.8 - - - +
110L ILE* 1.3 61.4 + - - +
112L ARG* 3.7 6.8 - - - +
113L HIS* 2.9 29.8 + - - +
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Residues in contact with ILE 110 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106L THR 2.9 17.0 + - - +
107L VAL* 3.7 8.1 - - - +
108L TYR 3.3 0.2 - - - -
109L SER* 1.3 76.8 - - - +
111L LEU* 1.3 62.6 + - + +
113L HIS* 3.3 7.0 + - - +
114L VAL* 2.9 27.1 + - - +
152L PHE* 5.7 4.7 - - + -
178L ASN* 4.1 16.7 - - + +
179L ILE* 5.4 4.3 - - + +
182L ARG* 4.9 17.7 - - + -
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Residues in contact with LEU 111 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107L VAL 3.0 25.9 + - - +
108L TYR 4.1 2.5 - - - +
110L ILE* 1.3 78.1 - - + +
112L ARG* 1.3 60.6 + - - +
114L VAL* 3.6 8.6 - - + +
115L ALA* 2.9 29.3 + - - +
126L LEU* 5.8 0.6 - - - +
129L LEU* 4.0 6.5 - - + +
130L PHE* 3.7 54.3 - - + +
133L THR* 3.8 19.3 - - - -
134L ALA* 4.5 7.6 - - + -
152L PHE* 3.6 33.2 - - + -
175L LEU* 6.4 2.5 - - + -
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Residues in contact with ARG 112 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108L TYR* 2.9 34.7 + - + +
109L SER* 3.7 7.6 - - - +
110L ILE 3.3 0.2 - - - -
111L LEU* 1.3 74.6 - - - +
113L HIS* 1.3 60.4 + - - +
115L ALA* 3.4 5.5 + - - +
116L GLU* 2.9 29.3 + - - +
126L LEU* 5.6 5.4 - - + -
130L PHE* 5.4 2.4 - - + -
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Residues in contact with HIS 113 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109L SER 2.9 17.8 + - - +
110L ILE* 3.3 6.5 + - - +
112L ARG* 1.3 74.8 - - - +
114L VAL* 1.3 58.2 + - - +
116L GLU* 3.4 6.5 + - - +
117L VAL* 2.9 29.5 + - - +
178L ASN* 4.9 9.2 - - + -
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Residues in contact with VAL 114 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110L ILE 2.9 17.6 + - - +
111L LEU* 3.6 11.0 - - + +
112L ARG 3.3 0.2 - - - -
113L HIS* 1.3 77.5 - - - +
115L ALA* 1.3 56.7 + - - +
117L VAL* 3.4 7.2 + - - +
118L LEU* 2.9 27.9 + - - +
129L LEU* 5.4 3.4 - - + -
171L GLU 5.5 1.1 - - - +
174L VAL* 4.6 9.1 - - + +
175L LEU* 4.4 29.4 - - + +
178L ASN* 4.7 5.1 - - + +
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Residues in contact with ALA 115 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3L LEU* 6.0 2.0 - - + -
111L LEU 2.9 17.6 + - - +
112L ARG 3.9 3.6 - - - +
114L VAL* 1.3 75.2 - - - +
116L GLU* 1.3 59.7 + - - +
118L LEU* 4.2 6.3 - - - +
119L GLU 2.8 22.2 + - - -
120L TYR* 3.0 19.1 + - + +
126L LEU* 3.7 30.5 - - + -
129L LEU* 4.1 20.4 - - + +
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Residues in contact with GLU 116 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3L LEU* 6.4 1.8 - - + -
112L ARG 2.9 18.5 + - - +
113L HIS* 3.7 7.9 - - - +
114L VAL 3.3 0.2 - - - -
115L ALA* 1.3 75.9 - - - +
117L VAL* 1.3 63.0 + - - +
119L GLU* 3.4 13.4 + - - +
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Residues in contact with VAL 117 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113L HIS 2.9 17.9 + - - +
114L VAL* 3.7 6.7 - - - +
116L GLU* 1.3 77.5 - - - +
118L LEU* 1.3 59.4 + - - +
119L GLU* 3.5 2.1 + - - +
174L VAL* 4.7 14.4 - - + -
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Residues in contact with LEU 118 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114L VAL 2.9 17.7 + - - +
115L ALA* 3.9 7.4 - - - +
116L GLU 3.3 0.2 - - - -
117L VAL* 1.3 73.9 - - - +
119L GLU* 1.3 68.8 + - - +
120L TYR* 3.4 7.7 + - + +
129L LEU* 5.0 8.1 - - + -
171L GLU* 5.6 12.3 - - + -
174L VAL* 5.7 2.7 - - + +
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Residues in contact with GLU 119 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115L ALA 2.8 9.2 + - - -
116L GLU* 3.4 10.0 + - - +
117L VAL 3.3 5.2 - - - +
118L LEU* 1.3 80.2 - - - +
120L TYR* 1.3 57.3 + - - +
121L THR* 3.2 9.3 + - - -
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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