Contacts of the helix formed by residues 98 - 124 (chain m) in PDB entry 6QXT
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 m).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96m ALA 3.8 1.1 + - - +
97m TRP* 1.3 76.8 - - - +
99m GLU* 1.3 61.2 + - - +
100m ASN* 4.1 10.1 - - + +
101m VAL* 3.2 16.5 + - + +
102m LYS* 3.0 27.5 + - - +
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Residues in contact with GLU 99 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97m TRP 4.3 0.6 + - - -
98m LYS* 1.3 73.7 - - - +
100m ASN* 1.3 57.2 + - - +
102m LYS* 3.9 6.7 - - - +
103m CYS* 2.9 32.9 + - - +
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Residues in contact with ASN 100 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98m LYS* 3.2 6.4 - - + +
99m GLU* 1.3 79.9 - - - +
101m VAL* 1.3 57.3 + - - +
103m CYS* 4.3 2.6 - - - +
104m GLU* 2.9 31.4 + - - +
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Residues in contact with VAL 101 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97m TRP* 6.0 1.6 - - + -
98m LYS* 3.2 20.2 + - + +
100m ASN* 1.3 75.8 - - - +
102m LYS* 1.3 60.5 + - - +
104m GLU* 3.9 4.0 - - - +
105m VAL* 2.9 32.9 + - - +
277m LEU* 5.1 12.1 - - + +
280m LEU* 4.9 21.8 - - + -
281m GLY 5.6 1.3 - - - +
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Residues in contact with LYS 102 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97m TRP* 6.0 4.0 - - + -
98m LYS 3.0 16.1 + - - +
99m GLU* 3.9 7.6 - - - +
101m VAL* 1.3 77.9 - - - +
103m CYS* 1.3 56.8 + - - +
105m VAL* 4.1 1.3 - - - -
106m TRP* 2.9 25.3 + - - +
202m GLY 5.2 1.1 - - - +
203m LEU* 3.0 40.0 - - + +
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Residues in contact with CYS 103 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99m GLU 2.9 18.8 + - - +
100m ASN* 4.3 3.4 - - - +
102m LYS* 1.3 77.1 - - - +
104m GLU* 1.3 58.1 + - - +
106m TRP* 4.2 2.6 - - - +
107m THR* 2.9 30.8 + - - -
142m ARG* 5.4 13.7 - - + +
143m PHE* 5.4 5.6 - - - +
203m LEU 3.8 5.4 + - - +
204m LYS* 5.9 2.7 - - - +
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Residues in contact with GLU 104 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100m ASN 2.9 20.7 + - - +
101m VAL* 3.9 5.2 - - - +
103m CYS* 1.3 75.8 - - - +
105m VAL* 1.3 60.8 + - - +
107m THR* 3.3 4.6 + - - -
108m ALA* 2.9 30.0 + - - +
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Residues in contact with VAL 105 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101m VAL 2.9 19.2 + - - +
102m LYS* 4.2 2.5 - - - +
104m GLU* 1.3 75.4 - - - +
106m TRP* 1.3 57.3 + - - +
108m ALA* 3.4 6.1 + - - +
109m ILE* 2.9 29.3 + - - +
203m LEU* 5.8 2.9 - - + -
276m ALA* 6.3 3.4 - - + -
277m LEU* 6.1 6.7 - - + -
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Residues in contact with TRP 106 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102m LYS 2.9 20.6 + - - +
103m CYS* 4.2 3.6 - - - +
105m VAL* 1.3 77.1 - - - +
107m THR* 1.3 57.8 + - - +
109m ILE* 3.3 6.7 + - - +
110m ILE* 2.9 30.3 + - - +
203m LEU* 3.6 25.9 - - + +
204m LYS* 4.5 10.8 - - + +
217m ASP* 5.8 6.7 - - + -
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Residues in contact with THR 107 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103m CYS 2.9 21.8 + - - -
104m GLU* 3.7 5.6 - - - -
106m TRP* 1.3 76.8 - - - +
108m ALA* 1.3 57.2 + - - +
110m ILE* 3.4 6.1 + - - +
111m ALA* 2.9 28.6 + - - +
140m LEU* 5.7 3.4 - - - +
141m GLU 5.2 11.2 - - - -
142m ARG* 5.2 9.0 - - - -
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Residues in contact with ALA 108 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104m GLU 2.9 17.4 + - - +
105m VAL* 3.8 6.7 - - - +
107m THR* 1.3 77.2 - - - +
109m ILE* 1.3 57.6 + - - +
111m ALA* 3.3 8.9 + - - +
112m GLN* 2.9 26.9 + - - +
284m ILE* 4.8 18.2 - - + -
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Residues in contact with ILE 109 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105m VAL 2.9 17.1 + - - +
106m TRP* 3.7 7.6 - - - +
107m THR 3.3 0.2 - - - -
108m ALA* 1.3 76.4 - - - +
110m ILE* 1.3 60.5 + - - +
112m GLN* 3.1 9.9 + - - +
113m LYS* 2.9 27.2 + - - +
217m ASP 4.3 18.2 - - - +
218m ILE* 6.1 0.4 - - - -
220m GLU* 5.6 4.0 - - + -
221m PRO* 4.7 7.2 - - + +
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Residues in contact with ILE 110 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106m TRP 2.9 16.8 + - - +
107m THR* 3.8 6.3 - - - +
109m ILE* 1.3 76.5 - - - +
111m ALA* 1.3 57.9 + - - +
113m LYS* 3.2 7.2 + - - +
114m ILE* 2.9 30.7 + - - +
149m GLU* 5.2 14.8 - - + -
220m GLU* 5.7 3.1 - - - -
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Residues in contact with ALA 111 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107m THR 2.9 18.5 + - - +
108m ALA* 3.5 9.0 - - - +
110m ILE* 1.3 77.2 - - - +
112m GLN* 1.3 56.0 + - - +
114m ILE* 4.2 3.9 - - - +
115m LEU* 2.9 31.1 + - - +
137m TYR* 5.0 14.1 - - + +
140m LEU* 5.5 9.0 - - + -
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Residues in contact with GLN 112 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108m ALA 2.9 14.2 + - - +
109m ILE* 3.1 11.9 + - - +
111m ALA* 1.3 75.9 - - - +
113m LYS* 1.3 59.5 + - - +
115m LEU* 3.8 5.1 - - - +
116m ASN* 2.9 28.4 + - - +
221m PRO* 4.5 13.0 - - + +
285m PRO 5.5 3.1 - - - +
286m GLU* 5.4 8.1 - - + -
287m PHE 4.7 18.4 - - - +
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Residues in contact with LYS 113 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109m ILE 2.9 12.7 + - - +
110m ILE* 3.2 10.5 + - - +
112m GLN* 1.3 75.4 - - - +
114m ILE* 1.3 61.0 + - - +
116m ASN* 3.1 5.2 + - - +
117m GLN* 2.9 27.1 + - - +
220m GLU* 3.7 29.4 - - + +
221m PRO* 3.8 12.9 - - + +
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Residues in contact with ILE 114 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110m ILE 2.9 16.9 + - - +
111m ALA* 4.2 3.8 - - - +
113m LYS* 1.3 75.8 - - - +
115m LEU* 1.3 58.6 + - - +
117m GLN* 3.2 8.6 + - - +
118m SER* 2.9 27.9 + - - -
133m ILE* 4.8 8.9 - - + +
136m LEU* 5.6 0.9 - - + -
137m TYR* 4.2 23.1 - - + +
148m ARG 6.0 0.2 - - - +
149m GLU* 6.2 2.2 - - - -
152m SER* 4.9 16.8 - - - -
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Residues in contact with LEU 115 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111m ALA 2.9 20.4 + - - +
112m GLN* 3.8 7.4 - - - +
114m ILE* 1.3 79.1 - - - +
116m ASN* 1.3 55.7 + - - +
118m SER* 3.4 7.7 + - - -
119m TYR* 2.9 27.0 + - - +
137m TYR* 4.7 7.3 - - + +
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Residues in contact with ASN 116 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112m GLN 2.9 18.5 + - - +
113m LYS 3.5 4.9 - - - +
115m LEU* 1.3 72.8 - - - +
117m GLN* 1.3 61.1 + - - +
119m TYR* 3.3 7.7 + - - +
120m TYR* 2.9 27.5 + - - +
221m PRO* 4.1 18.6 - - + +
224m PRO* 4.4 12.1 - - + +
287m PHE 4.8 10.1 - - - +
288m ARG* 5.6 1.3 - - - +
289m ILE* 5.3 14.1 - - + +
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Residues in contact with GLN 117 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113m LYS 2.9 12.7 + - - +
114m ILE* 3.2 11.6 + - - +
116m ASN* 1.3 74.9 - - - +
118m SER* 1.3 59.9 + - - +
120m TYR* 3.2 7.8 + - - +
121m LEU* 2.9 29.1 + - - +
133m ILE* 5.2 8.3 - - + -
152m SER* 5.7 5.4 - - - +
156m TYR* 5.2 14.1 - - + -
224m PRO* 4.8 7.5 - - + +
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Residues in contact with SER 118 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114m ILE 2.9 16.5 + - - -
115m LEU* 3.7 8.1 - - - -
116m ASN 3.3 0.2 - - - -
117m GLN* 1.3 75.5 - - - +
119m TYR* 1.3 58.5 + - - +
122m GLY* 2.9 22.9 + - - -
130m SER* 3.5 34.4 - - - +
133m ILE* 4.4 4.6 - - - +
134m MET* 4.2 18.8 - - - -
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Residues in contact with TYR 119 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115m LEU 2.9 17.3 + - - +
116m ASN* 3.6 9.4 - - - +
117m GLN 3.2 0.2 - - - -
118m SER* 1.3 75.3 - - - +
120m TYR* 1.3 58.9 + - - +
122m GLY* 3.8 1.9 - - - +
123m GLU* 2.9 28.2 + - - +
288m ARG* 6.2 2.2 - - + -
289m ILE* 5.1 16.6 - - + +
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Residues in contact with TYR 120 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116m ASN 2.9 17.4 + - - +
117m GLN* 3.2 8.0 + - - +
119m TYR* 1.3 76.7 - - - +
121m LEU* 1.3 60.0 + - - +
123m GLU* 3.3 6.9 + - - +
124m CYS* 2.9 28.5 + - - +
224m PRO* 4.7 14.8 - - + +
228m ARG* 6.4 1.6 - - + -
289m ILE* 5.7 4.2 - - + +
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Residues in contact with LEU 121 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117m GLN 2.9 15.4 + - - +
118m SER* 4.6 0.2 - - - -
120m TYR* 1.3 76.1 - - - +
122m GLY* 1.3 58.9 + - - +
124m CYS* 3.3 8.6 + - - +
125m SER 3.0 7.4 + - - -
126m PHE* 2.9 35.4 + - + +
129m LYS* 4.7 5.6 - - + -
130m SER* 3.6 29.6 - - - +
133m ILE* 6.2 0.9 - - + -
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Residues in contact with GLY 122 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118m SER 2.9 18.2 + - - -
119m TYR* 3.4 2.9 + - - -
120m TYR 3.2 0.2 - - - -
121m LEU* 1.3 75.0 - - - +
123m GLU* 1.3 62.7 + - - +
125m SER* 3.1 13.6 + - - -
126m PHE 4.7 2.5 - - - -
130m SER* 3.8 7.1 - - - -
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Residues in contact with GLU 123 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119m TYR 2.9 16.7 + - - +
120m TYR* 3.3 7.4 + - - +
122m GLY* 1.3 75.9 - - - +
124m CYS* 1.3 58.3 + - - +
125m SER* 3.2 3.3 + - - -
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Residues in contact with CYS 124 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120m TYR 2.9 17.3 + - - +
121m LEU* 3.7 9.2 - - - +
122m GLY 3.2 0.2 - - - -
123m GLU* 1.3 75.3 - - - +
125m SER* 1.3 70.8 + - - +
126m PHE* 3.4 5.2 + - + +
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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