Contacts of the helix formed by residues 88 - 119 (chain L) in PDB entry 6AH0
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 PRO 88 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86L ALA* 3.2 5.7 - - - +
87L ALA* 1.3 78.6 - - - +
89L GLU* 1.3 65.7 + - - +
90L TYR 3.1 3.7 + - - -
91L ARG* 3.3 12.2 + - - -
92L VAL 3.8 5.0 + - - -
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Residues in contact with GLU 89 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87L ALA 3.3 4.4 + - - -
88L PRO* 1.3 71.5 - - - +
90L TYR* 1.3 63.4 + - - +
92L VAL* 3.0 14.5 + - - +
93L ILE* 3.1 10.2 + - - -
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Residues in contact with TYR 90 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88L PRO 3.1 1.6 - - - -
89L GLU* 1.3 77.4 - - - +
91L ARG* 1.3 56.1 + - - +
93L ILE* 3.2 2.8 + - - +
94L VAL* 2.8 27.9 + - - -
233L GLY* 6.2 0.3 - - - -
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Residues in contact with ARG 91 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88L PRO 3.3 7.8 + - - -
89L GLU 3.2 1.0 - - - -
90L TYR* 1.3 76.1 - - - +
92L VAL* 1.3 63.1 + - - +
94L VAL* 3.9 1.7 - - - +
95L ASP* 3.1 19.2 + - - -
233L GLY* 6.6 0.2 - - - -
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Residues in contact with VAL 92 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88L PRO 3.8 4.6 + - - -
89L GLU* 3.0 10.5 + - - +
91L ARG* 1.3 75.5 - - - +
93L ILE* 1.3 56.4 + - - +
95L ASP* 3.2 2.8 + - - -
96L ALA* 2.9 25.6 + - - -
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Residues in contact with ILE 93 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89L GLU 3.1 11.6 + - - -
90L TYR* 3.2 2.9 + - - +
92L VAL* 1.3 71.1 - - - +
94L VAL* 1.3 61.5 + - - +
96L ALA* 4.3 1.8 - - - +
97L ASN* 2.8 28.9 + - - -
208L VAL* 5.7 10.3 - - - +
229L ALA* 6.0 2.0 - - - -
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Residues in contact with VAL 94 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90L TYR 2.8 18.9 + - - -
91L ARG* 3.9 2.5 - - - +
93L ILE* 1.3 72.9 - - - +
95L ASP* 1.3 56.5 + - - +
97L ASN* 3.2 2.0 + - - +
98L ASN* 3.0 22.9 + - - -
229L ALA* 4.7 19.4 - - - +
233L GLY* 5.7 6.3 - - - -
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Residues in contact with ASP 95 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91L ARG 3.1 14.4 + - - -
92L VAL* 3.7 2.2 - - - +
94L VAL* 1.3 73.5 - - - +
96L ALA* 1.3 65.7 + - - +
98L ASN* 3.3 2.6 + - - +
99L LEU* 3.1 19.1 + - - -
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Residues in contact with ALA 96 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92L VAL 2.9 14.9 + - - -
93L ILE* 3.7 3.6 - - - +
95L ASP* 1.3 77.6 - - - +
97L ASN* 1.3 61.1 + - - +
99L LEU* 3.3 9.8 + - - +
100L THR* 3.4 8.8 + - - -
204L ILE* 5.9 5.3 - - - -
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Residues in contact with ASN 97 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93L ILE 2.8 20.7 + - - -
94L VAL 3.7 2.5 - - - -
95L ASP 3.2 0.2 - - - -
96L ALA* 1.3 74.1 - - - +
98L ASN* 1.3 59.8 + - - +
100L THR* 3.3 11.0 + - - +
101L VAL* 3.6 6.2 + - - -
208L VAL* 6.2 3.0 - - - +
226L SER* 6.4 2.0 - - - +
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Residues in contact with ASN 98 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94L VAL 3.0 13.0 + - - -
95L ASP* 3.3 4.2 + - - +
96L ALA 3.2 0.6 - - - -
97L ASN* 1.3 74.0 - - - +
99L LEU* 1.3 65.6 + - - +
101L VAL* 2.8 13.8 + - - +
102L GLU* 3.1 9.0 + - - -
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Residues in contact with LEU 99 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95L ASP 3.1 13.0 + - - -
96L ALA* 3.3 4.9 + - - +
98L ASN* 1.3 72.3 - - - +
100L THR* 1.3 64.1 + - - +
102L GLU* 2.9 5.5 + - - +
103L ILE* 2.8 22.2 + - - -
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Residues in contact with THR 100 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96L ALA 3.4 8.5 + - - -
97L ASN 3.3 9.9 + - - -
98L ASN 3.1 0.8 - - - -
99L LEU* 1.3 74.4 - - - +
101L VAL* 1.3 55.3 + - - +
103L ILE* 3.5 1.9 + - - +
104L GLU* 3.0 23.0 + - - -
201L LYS* 5.9 9.0 - - - +
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Residues in contact with VAL 101 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97L ASN 3.6 4.4 + - - -
98L ASN* 2.8 15.2 + - - +
100L THR* 1.3 70.2 - - - +
102L GLU* 1.3 64.9 + - - +
104L GLU* 3.3 2.1 + - - +
105L ASN* 3.0 20.4 + - - -
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Residues in contact with GLU 102 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98L ASN 3.1 7.4 + - - -
99L LEU* 2.9 7.6 + - - +
101L VAL* 1.3 77.6 - - - +
103L ILE* 1.3 55.6 + - - +
105L ASN* 3.4 2.2 + - - +
106L GLU* 3.1 23.0 + - - -
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Residues in contact with ILE 103 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99L LEU 2.8 13.8 + - - -
100L THR* 4.0 2.7 - - - +
102L GLU* 1.3 73.7 - - - +
104L GLU* 1.3 59.1 + - - +
106L GLU* 5.2 0.9 - - - +
107L LEU* 2.9 27.0 + - - -
201L LYS* 6.6 0.4 - - - +
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Residues in contact with GLU 104 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100L THR 3.0 15.0 + - - -
101L VAL* 3.3 4.4 + - - +
103L ILE* 1.3 77.7 - - - +
105L ASN* 1.3 55.7 + - - +
107L LEU* 3.4 1.1 + - - +
108L ASN* 2.9 26.0 + - - -
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Residues in contact with ASN 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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101L VAL 3.0 14.2 + - - -
102L GLU* 3.4 3.8 + - - +
103L ILE 3.3 0.2 - - - -
104L GLU* 1.3 75.7 - - - +
106L GLU* 1.3 60.6 + - - +
108L ASN* 3.1 3.9 + - - +
109L ILE* 3.0 19.2 + - - -
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Residues in contact with GLU 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 GLU 3.1 14.9 + - - -
103L ILE* 4.0 2.0 - - - +
104L GLU 3.4 0.2 - - - -
105L ASN* 1.3 74.7 - - - +
107L LEU* 1.3 57.4 + - - +
109L ILE* 3.2 2.9 + - - +
110L ILE* 2.8 26.9 + - - -
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Residues in contact with LEU 107 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103L ILE 2.9 17.2 + - - -
104L GLU* 3.7 1.8 - - - +
106L GLU* 1.3 74.7 - - - +
108L ASN* 1.3 63.0 - - - +
110L ILE* 3.9 1.1 - - - +
111L HIS* 3.0 19.9 + - - -
194L ALA* 6.4 2.2 - - - +
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Residues in contact with ASN 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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104L GLU 2.9 15.1 + - - -
105L ASN* 3.1 4.9 + - - +
107L LEU* 1.3 75.5 - - - +
109L ILE* 1.3 62.8 + - - +
111L HIS* 3.2 3.7 + - - +
112L LYS* 3.1 18.9 + - - -
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Residues in contact with ILE 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 ASN 3.0 12.5 + - - -
106L GLU* 3.2 4.2 + - - +
108L ASN* 1.3 76.1 - - - +
110L ILE* 1.3 61.4 + - - +
112L LYS* 3.3 2.8 + - - +
113L PHE* 3.0 19.6 + - - -
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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 GLU 2.8 19.7 + - - -
107L LEU* 4.0 2.2 - - - +
109L ILE* 1.3 72.1 - - - +
111L HIS* 1.3 51.9 + - - +
113L PHE* 3.3 2.3 + - - +
114L ILE* 2.7 33.8 + - - -
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Residues in contact with HIS 111 (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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107L LEU 3.0 15.4 + - - -
108L ASN 3.2 4.0 + - - -
110L ILE* 1.3 76.3 - - - +
112L LYS* 1.3 51.8 + - - +
114L ILE* 3.2 1.6 + - - +
115L ARG* 2.8 33.4 + - - -
132L ALA* 6.1 5.6 - - - +
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Residues in contact with LYS 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 ASN 3.1 12.8 + - - -
109L ILE* 3.7 3.4 - - - +
111L HIS* 1.3 73.3 - - - +
113L PHE* 1.3 63.7 + - - +
115L ARG* 3.4 1.3 + - - +
116L ASP* 3.0 19.9 + - - -
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Residues in contact with PHE 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 ILE 3.0 13.8 + - - -
110L ILE* 3.6 4.0 - - - +
112L LYS* 1.3 75.5 - - - +
114L ILE* 1.3 56.1 + - - +
116L ASP* 3.1 3.7 + - - +
117L LYS* 2.9 26.7 + - - -
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Residues in contact with ILE 114 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110L ILE 2.7 18.8 + - - -
111L HIS* 3.7 1.6 - - - +
113L PHE* 1.3 69.1 - - - +
115L ARG* 1.3 64.8 + - - +
117L LYS* 4.1 1.2 - - - +
118L TYR* 3.1 20.8 + - - -
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Residues in contact with ARG 115 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111L HIS 2.8 15.3 + - - -
112L LYS* 3.8 2.0 - - - +
114L ILE* 1.3 77.7 - - - +
116L ASP* 1.3 55.0 + - - +
118L TYR 3.8 0.7 - - - -
119L SER* 3.0 27.7 + - - -
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Residues in contact with ASP 116 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112L LYS 3.0 14.5 + - - -
113L PHE* 3.6 3.1 - - - +
115L ARG* 1.3 76.6 - - - +
117L LYS* 1.3 62.4 + - - +
119L SER* 3.3 11.7 + - - +
120L LYS 4.5 1.2 + - - -
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Residues in contact with LYS 117 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113L PHE 2.9 14.3 + - - -
114L ILE* 4.1 1.6 - - - +
116L ASP* 1.3 77.5 - - - +
118L TYR* 1.3 58.5 + - - +
119L SER 3.2 0.9 + - - -
120L LYS* 3.8 7.4 + - - -
121L ARG 4.9 0.7 + - - -
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Residues in contact with TYR 118 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114L ILE 3.1 17.0 + - - -
115L ARG 3.8 1.1 - - - -
117L LYS* 1.3 71.9 - - - +
119L SER* 1.3 63.9 + - - +
120L LYS 3.0 4.9 + - - -
121L ARG* 3.1 13.2 + - - +
122L PHE 3.1 15.3 + - - +
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Residues in contact with SER 119 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115L ARG 3.0 16.2 + - - -
116L ASP 3.3 6.5 + - - -
117L LYS 3.2 2.2 - - - -
118L TYR* 1.3 77.9 - - - +
120L LYS* 1.3 58.7 + - - +
122L PHE 4.7 0.9 - - - -
123L PRO* 3.1 33.7 - - - +
176L GLY* 5.5 0.3 - - - -
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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