Contacts of the helix formed by residues 98 - 124 (chain J) in PDB entry 6QY3
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 LYS 98 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96J ALA 3.8 2.0 + - - +
97J TRP* 1.3 76.9 - - - +
99J GLU* 1.3 65.1 + - - +
100J ASN* 4.1 10.3 - - + +
101J VAL* 3.2 14.6 + - + +
102J LYS* 3.0 23.5 + - - +
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Residues in contact with GLU 99 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97J TRP 4.3 0.2 + - - -
98J LYS* 1.3 73.3 - - - +
100J ASN* 1.3 57.8 + - - +
102J LYS* 3.9 6.9 - - - +
103J CYS* 2.9 32.1 + - - +
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Residues in contact with ASN 100 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98J LYS* 3.2 6.3 - - + +
99J GLU* 1.3 78.0 - - - +
101J VAL* 1.3 57.4 - - - +
103J CYS* 4.3 2.8 - - - +
104J GLU* 2.9 31.9 + - - +
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Residues in contact with VAL 101 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97J TRP* 6.1 1.3 - - + -
98J LYS* 3.2 20.2 + - + +
100J ASN* 1.3 75.7 - - - +
102J LYS* 1.3 60.7 + - - +
104J GLU* 3.9 4.6 - - - +
105J VAL* 2.9 32.6 + - - +
277J LEU* 5.1 11.7 - - - +
280J LEU* 4.9 21.1 - - + -
281J GLY 5.5 1.6 - - - +
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Residues in contact with LYS 102 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97J TRP* 6.0 4.0 - - + -
98J LYS 3.0 16.0 + - - +
99J GLU* 3.9 7.4 - - - +
101J VAL* 1.3 78.7 - - - +
103J CYS* 1.3 57.3 + - - +
105J VAL* 4.1 1.7 - - - +
106J TRP* 2.9 24.8 + - - +
202J GLY 5.2 1.6 - - - +
203J LEU* 3.0 40.0 - - + +
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Residues in contact with CYS 103 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99J GLU 2.9 19.2 + - - +
100J ASN* 4.3 3.1 - - - +
102J LYS* 1.3 78.0 - - - +
104J GLU* 1.3 56.2 + - - +
106J TRP* 4.1 2.6 - - - +
107J THR* 2.9 30.7 + - - -
142J ARG* 5.4 13.3 - - + +
143J PHE* 5.4 6.3 - - - +
203J LEU 3.8 5.1 + - - -
204J LYS* 5.9 2.2 - - - +
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Residues in contact with GLU 104 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100J ASN 2.9 22.1 + - - +
101J VAL* 3.9 4.9 - - - +
102J LYS 3.2 0.2 - - - -
103J CYS* 1.3 74.6 - - - +
105J VAL* 1.3 60.8 + - - +
107J THR* 3.3 5.3 + - - -
108J ALA* 2.9 29.6 + - - +
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Residues in contact with VAL 105 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101J VAL 2.9 18.5 + - - +
102J LYS* 4.2 2.2 - - - +
104J GLU* 1.3 76.7 - - - +
106J TRP* 1.3 58.2 + - - +
108J ALA* 3.4 6.4 + - - +
109J ILE* 2.9 28.9 + - - +
203J LEU* 5.8 2.5 - - + -
276J ALA* 6.3 2.9 - - + -
277J LEU* 6.1 6.5 - - + -
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Residues in contact with TRP 106 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102J LYS 2.9 20.1 + - - +
103J CYS* 4.1 3.6 - - - +
105J VAL* 1.3 79.2 - - - +
107J THR* 1.3 56.2 + - - +
109J ILE* 3.3 7.1 + - - +
110J ILE* 2.9 30.4 + - - +
203J LEU* 3.6 26.3 - - + +
204J LYS* 4.5 11.0 - - + +
217J ASP* 5.8 6.5 - - + -
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Residues in contact with THR 107 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103J CYS 2.9 21.5 + - - -
104J GLU* 3.3 5.6 + - - -
106J TRP* 1.3 78.0 - - - +
108J ALA* 1.3 56.9 + - - +
110J ILE* 3.4 6.6 + - - +
111J ALA* 2.9 28.5 + - - +
141J GLU 5.2 11.2 - - - -
142J ARG* 5.2 9.0 - - - -
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Residues in contact with ALA 108 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104J GLU 2.9 17.8 + - - +
105J VAL* 3.8 6.5 - - - +
107J THR* 1.3 75.7 - - - +
109J ILE* 1.3 57.9 + - - +
111J ALA* 3.3 9.0 + - - +
112J GLN* 2.9 27.7 + - - +
284J ILE* 4.8 18.4 - - + -
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Residues in contact with ILE 109 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105J VAL 2.9 18.1 + - - +
106J TRP* 3.7 7.4 - - - +
107J THR 3.3 0.2 - - - -
108J ALA* 1.3 74.8 - - - +
110J ILE* 1.3 59.5 + - - +
112J GLN* 3.1 9.3 + - - +
113J LYS* 2.9 27.2 + - - +
217J ASP* 4.2 19.1 - - + +
220J GLU* 5.3 3.3 - - + +
221J PRO* 4.7 7.0 - - + +
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Residues in contact with ILE 110 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106J TRP 2.9 16.1 + - - +
107J THR* 3.8 7.4 - - - +
109J ILE* 1.3 76.0 - - - +
111J ALA* 1.3 58.0 + - - +
113J LYS* 3.2 7.6 + - - +
114J ILE* 2.9 30.5 + - - +
149J GLU* 5.2 14.6 - - + -
220J GLU* 5.8 2.9 - - - -
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Residues in contact with ALA 111 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107J THR 2.9 17.2 + - - +
108J ALA* 3.5 9.6 - - - +
109J ILE 3.2 0.2 - - - -
110J ILE* 1.3 77.9 - - - +
112J GLN* 1.3 56.4 + - - +
114J ILE* 3.9 5.1 - - - +
115J LEU* 2.9 30.5 + - - +
137J TYR* 5.0 15.4 - - + +
140J LEU* 5.5 4.9 - - + -
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Residues in contact with GLN 112 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108J ALA 2.9 14.2 + - - +
109J ILE* 3.1 11.6 + - - +
111J ALA* 1.3 75.4 - - - +
113J LYS* 1.3 58.5 + - - +
115J LEU* 3.8 5.7 - - - +
116J ASN* 2.9 28.8 + - - +
221J PRO* 4.6 12.6 - - + +
286J GLU* 5.4 8.1 - - + -
287J PHE 4.7 18.5 - - - +
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Residues in contact with LYS 113 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109J ILE 2.9 12.3 + - - +
110J ILE* 3.2 11.4 + - - +
112J GLN* 1.3 74.7 - - - +
114J ILE* 1.3 59.9 + - - +
116J ASN* 3.1 5.3 + - - +
117J GLN* 2.9 26.5 + - - +
220J GLU* 3.7 29.8 - - + +
221J PRO* 3.8 13.2 - - + +
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Residues in contact with ILE 114 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110J ILE 2.9 17.2 + - - +
111J ALA* 4.1 3.8 - - - +
113J LYS* 1.3 76.0 - - - +
115J LEU* 1.3 57.4 + - - +
117J GLN* 3.2 8.6 + - - +
118J SER* 2.9 28.2 + - - -
133J ILE* 4.8 9.1 - - + +
136J LEU 5.6 0.9 - - - -
137J TYR* 4.2 23.6 - - + +
149J GLU* 6.2 2.7 - - - -
152J SER* 4.9 16.4 - - - -
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Residues in contact with LEU 115 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111J ALA 2.9 21.0 + - - +
112J GLN* 3.8 6.7 - - - +
114J ILE* 1.3 77.2 - - - +
116J ASN* 1.3 57.5 + - - +
118J SER* 3.4 7.9 + - - -
119J TYR* 2.9 27.5 + - - +
137J TYR* 4.7 8.0 - - + +
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Residues in contact with ASN 116 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112J GLN 2.9 18.7 + - - +
113J LYS 3.1 5.6 + - - +
115J LEU* 1.3 75.0 - - - +
117J GLN* 1.3 60.7 + - - +
119J TYR* 3.3 7.5 + - - +
120J TYR* 2.9 28.2 + - - +
221J PRO 4.1 18.6 - - - +
224J PRO* 4.4 11.8 - - + +
287J PHE 4.8 10.1 - - - +
288J ARG* 5.6 1.3 - - - +
289J ILE* 5.3 14.0 - - + +
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Residues in contact with GLN 117 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113J LYS 2.9 12.9 + - - +
114J ILE* 3.5 11.4 - - - +
116J ASN* 1.3 75.4 - - - +
118J SER* 1.3 59.8 + - - +
120J TYR* 3.2 7.5 + - - +
121J LEU* 2.9 29.9 + - - +
133J ILE* 5.2 8.1 - - + -
152J SER* 5.7 5.2 - - - +
156J TYR* 5.2 14.8 - - + -
224J PRO* 4.9 7.7 - - + +
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Residues in contact with SER 118 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114J ILE 2.9 15.8 + - - -
115J LEU* 3.4 8.3 + - - -
116J ASN 3.3 0.2 - - - -
117J GLN* 1.3 75.8 - - - +
119J TYR* 1.3 58.0 + - - +
121J LEU* 4.6 0.2 - - - -
122J GLY* 2.9 23.4 + - - -
130J SER* 3.5 34.6 - - - +
133J ILE* 4.4 4.6 - - - +
134J MET* 4.3 18.2 - - - -
137J TYR* 6.1 0.2 - - - -
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Residues in contact with TYR 119 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115J LEU 2.9 16.8 + - - +
116J ASN* 3.6 8.7 - - - +
117J GLN 3.2 0.2 - - - -
118J SER* 1.3 76.1 - - - +
120J TYR* 1.3 59.6 + - - +
122J GLY* 3.8 1.2 - - - -
123J GLU* 2.9 28.6 + - - +
288J ARG* 6.2 2.5 - - + -
289J ILE* 5.1 17.0 - - + +
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Residues in contact with TYR 120 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116J ASN 2.9 15.9 + - - +
117J GLN* 3.2 8.3 + - - +
119J TYR* 1.3 75.4 - - - +
121J LEU* 1.3 60.8 + - - +
123J GLU* 3.3 7.5 + - - +
124J CYS* 2.9 26.9 + - - +
224J PRO* 4.6 15.3 - - + +
228J ARG* 6.4 1.8 - - + -
289J ILE* 5.7 5.1 - - + +
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Residues in contact with LEU 121 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117J GLN 2.9 15.1 + - - +
118J SER* 4.6 0.2 - - - -
120J TYR* 1.3 75.0 - - - +
122J GLY* 1.3 57.9 + - - +
124J CYS* 3.2 8.9 + - - +
125J SER 3.0 7.3 + - - -
126J PHE* 3.0 34.8 + - + +
129J LYS* 4.7 5.2 - - + -
130J SER* 3.6 29.8 - - - +
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Residues in contact with GLY 122 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118J SER 2.9 18.9 + - - -
119J TYR* 3.8 2.2 - - - -
120J TYR 3.2 0.2 - - - -
121J LEU* 1.3 74.8 - - - +
123J GLU* 1.3 62.3 + - - +
125J SER* 3.1 14.0 + - - -
126J PHE 4.7 2.2 - - - -
130J SER* 3.8 7.8 - - - -
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Residues in contact with GLU 123 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119J TYR 2.9 17.6 + - - +
120J TYR* 3.7 7.0 - - - +
122J GLY* 1.3 75.8 - - - +
124J CYS* 1.3 58.2 + - - +
125J SER* 3.2 2.7 + - - -
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Residues in contact with CYS 124 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120J TYR 2.9 17.3 + - - +
121J LEU* 3.6 10.1 - - - +
122J GLY 3.2 0.4 - - - -
123J GLU* 1.3 74.1 - - - +
125J SER* 1.3 70.8 + - - +
126J PHE* 3.4 5.4 + - + +
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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) + - + + + + + -
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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