Contacts of the helix formed by residues 98 - 124 (chain U) 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 U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96U ALA 3.3 6.5 + - - +
97U TRP* 1.3 77.5 - - - +
99U GLU* 1.3 65.5 + - - +
100U ASN* 4.2 9.4 - - + +
101U VAL* 3.5 15.2 + - + +
102U LYS* 3.1 22.3 + - - +
277U LEU 5.9 0.2 + - - -
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Residues in contact with GLU 99 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97U TRP 3.9 0.6 + - - -
98U LYS* 1.3 72.5 - - - +
100U ASN* 1.3 60.8 + - - +
102U LYS* 3.8 6.0 - - - +
103U CYS* 2.9 29.8 + - - +
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Residues in contact with ASN 100 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98U LYS* 3.3 6.1 - - + +
99U GLU* 1.3 79.1 - - - +
101U VAL* 1.3 57.4 + - - +
103U CYS* 3.4 5.5 + - - +
104U GLU* 2.9 29.7 + - - +
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Residues in contact with VAL 101 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97U TRP* 6.1 1.1 - - + -
98U LYS* 3.5 19.8 + - + +
99U GLU 3.4 0.4 - - - -
100U ASN* 1.3 75.1 - - - +
102U LYS* 1.3 61.3 + - - +
104U GLU* 3.3 6.1 + - - +
105U VAL* 2.9 31.5 + - - +
277U LEU* 5.1 12.6 - - + +
280U LEU* 4.8 21.1 - - + -
281U GLY* 5.2 4.5 - - - +
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Residues in contact with LYS 102 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97U TRP* 5.7 5.1 - - + +
98U LYS 3.1 17.5 + - - +
99U GLU* 3.8 7.4 - - - +
101U VAL* 1.3 78.2 - - - +
103U CYS* 1.3 56.2 + - - +
105U VAL* 4.1 3.6 - - - +
106U TRP* 2.9 31.4 + - - +
203U LEU* 4.2 26.0 - - - +
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Residues in contact with CYS 103 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99U GLU 2.9 19.1 + - - +
100U ASN* 3.9 5.4 - - - +
102U LYS* 1.3 73.2 - - - +
104U GLU* 1.3 59.5 + - - +
106U TRP* 3.9 4.8 - - - +
107U THR* 2.9 31.9 + - - -
142U ARG* 5.4 13.1 - - + +
143U PHE 5.7 3.8 - - - +
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Residues in contact with GLU 104 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100U ASN 2.9 17.9 + - - +
101U VAL* 3.7 6.5 - - - +
103U CYS* 1.3 74.8 - - - +
105U VAL* 1.3 61.1 + - - +
107U THR* 3.4 4.8 + - - -
108U ALA* 2.9 29.3 + - - +
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Residues in contact with VAL 105 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101U VAL 2.9 17.9 + - - +
102U LYS* 4.1 3.8 - - - +
104U GLU* 1.3 76.2 - - - +
106U TRP* 1.3 58.3 + - - +
108U ALA* 3.4 6.6 + - - +
109U ILE* 2.9 28.9 + - - +
203U LEU* 5.9 3.4 - - + -
277U LEU* 6.5 0.7 - - + -
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Residues in contact with TRP 106 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102U LYS 2.9 20.1 + - - +
103U CYS* 3.9 5.4 - - - +
105U VAL* 1.3 77.0 - - - +
107U THR* 1.3 56.7 + - - +
109U ILE* 3.2 7.4 + - - +
110U ILE* 2.9 29.5 + - - +
203U LEU* 4.4 24.6 - - + +
204U LYS* 5.2 2.5 - - - +
217U ASP* 6.5 0.2 - - - -
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Residues in contact with THR 107 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103U CYS 2.9 19.6 + - - -
104U GLU* 3.8 5.2 - - - -
106U TRP* 1.3 75.2 - - - +
108U ALA* 1.3 56.8 + - - +
110U ILE* 3.5 5.6 + - - +
111U ALA* 2.9 30.5 + - - +
140U LEU* 5.9 2.5 - - - +
141U GLU 5.3 4.5 - - - -
142U ARG* 5.3 16.2 - - - -
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Residues in contact with ALA 108 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104U GLU 2.9 18.7 + - - +
105U VAL* 3.7 7.2 - - - +
107U THR* 1.3 77.5 - - - +
109U ILE* 1.3 58.0 + - - +
111U ALA* 3.4 6.5 + - - +
112U GLN* 2.9 27.9 + - - +
284U ILE* 4.7 18.2 - - + -
285U PRO 6.2 0.2 - - - +
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Residues in contact with ILE 109 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105U VAL 2.9 18.1 + - - +
106U TRP* 3.2 8.0 + - - +
108U ALA* 1.3 74.3 - - - +
110U ILE* 1.3 60.6 + - - +
112U GLN* 3.1 7.9 + - - +
113U LYS* 2.9 29.3 + - - +
217U ASP* 4.1 19.7 - - + +
218U ILE* 5.8 1.8 - - - +
220U GLU* 5.4 5.6 - - + -
221U PRO* 4.6 8.0 - - + +
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Residues in contact with ILE 110 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106U TRP 2.9 17.1 + - - +
107U THR* 3.9 6.3 - - - +
109U ILE* 1.3 75.4 - - - +
111U ALA* 1.3 57.7 + - - +
113U LYS* 3.8 5.9 - - - +
114U ILE* 2.9 32.1 + - - +
149U GLU* 5.2 14.9 - - + +
220U GLU* 6.0 1.6 - - - -
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Residues in contact with ALA 111 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107U THR 2.9 18.5 + - - +
108U ALA* 3.6 8.1 - - - +
110U ILE* 1.3 77.7 - - - +
112U GLN* 1.3 56.3 + - - +
114U ILE* 4.1 4.5 - - - +
115U LEU* 2.9 32.4 + - - +
137U TYR* 5.0 14.1 - - + +
140U LEU* 5.6 8.1 - - + -
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Residues in contact with GLN 112 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108U ALA 2.9 17.2 + - - +
109U ILE* 3.1 7.1 + - - +
111U ALA* 1.3 77.7 - - - +
113U LYS* 1.3 57.3 + - - +
115U LEU* 3.5 4.9 + - - +
116U ASN* 2.9 29.6 + - - +
221U PRO* 4.0 19.5 - - + +
286U GLU* 5.7 4.0 - - + -
287U PHE 4.4 19.7 - - - +
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Residues in contact with LYS 113 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109U ILE 2.9 15.6 + - - +
110U ILE* 3.8 6.3 - - - +
112U GLN* 1.3 76.0 - - - +
114U ILE* 1.3 58.2 + - - +
116U ASN* 3.2 5.4 + - - +
117U GLN* 2.9 28.3 + - - +
220U GLU* 3.6 31.6 - - + +
221U PRO* 4.1 8.0 - - - +
224U PRO* 5.4 1.9 - - - +
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Residues in contact with ILE 114 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110U ILE 2.9 18.1 + - - +
111U ALA* 4.1 3.6 - - - +
113U LYS* 1.3 75.9 - - - +
115U LEU* 1.3 57.1 + - - +
117U GLN* 3.2 7.7 + - - +
118U SER* 2.9 30.1 + - - -
133U ILE* 4.8 7.8 - - + +
136U LEU* 5.8 0.7 - - + -
137U TYR* 4.3 20.9 - - + +
148U ARG 6.1 0.2 - - - +
149U GLU* 6.0 5.6 - - + -
152U SER* 5.1 15.0 - - - -
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Residues in contact with LEU 115 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111U ALA 2.9 20.6 + - - +
112U GLN* 3.8 6.1 - - - +
114U ILE* 1.3 77.7 - - - +
116U ASN* 1.3 57.0 + - - +
118U SER* 3.5 5.6 + - - -
119U TYR* 2.9 30.0 + - - +
137U TYR* 4.7 9.5 - - + +
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Residues in contact with ASN 116 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112U GLN 2.9 18.5 + - - +
113U LYS* 3.2 5.1 + - - +
115U LEU* 1.3 76.7 - - - +
117U GLN* 1.3 58.2 + - - +
119U TYR* 3.9 5.5 - - - +
120U TYR* 2.9 30.7 + - - +
221U PRO 4.2 17.3 - - - +
224U PRO* 4.5 13.1 - - + +
287U PHE 5.4 4.0 - - - +
288U ARG* 5.6 1.3 - - - +
289U ILE* 4.9 22.8 - - + +
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Residues in contact with GLN 117 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113U LYS 2.9 12.9 + - - +
114U ILE* 3.2 11.9 + - - +
116U ASN* 1.3 74.1 - - - +
118U SER* 1.3 60.1 + - - +
120U TYR* 3.3 6.0 + - - +
121U LEU* 2.9 28.9 + - - +
133U ILE* 5.2 5.4 - - + -
152U SER* 5.9 3.4 - - - +
156U TYR* 4.6 21.4 - - + +
224U PRO* 4.6 9.1 - - + +
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Residues in contact with SER 118 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114U ILE 2.9 16.1 + - - -
115U LEU* 3.9 5.8 - - - -
117U GLN* 1.3 75.8 - - - +
119U TYR* 1.3 57.3 + - - +
121U LEU* 3.3 1.0 + - - -
122U GLY* 2.9 23.2 + - - -
130U SER* 3.2 37.2 - - - +
133U ILE* 3.8 17.6 - - - +
134U MET* 3.8 14.1 - - - -
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Residues in contact with TYR 119 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115U LEU 2.9 19.2 + - - +
116U ASN* 3.9 6.1 - - - +
118U SER* 1.3 77.5 - - - +
120U TYR* 1.3 57.3 + - - +
122U GLY* 3.1 3.5 + - - +
123U GLU* 2.9 26.5 + - - +
289U ILE* 5.7 8.5 - - + +
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Residues in contact with TYR 120 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116U ASN 2.9 18.5 + - - +
117U GLN* 3.3 6.9 + - - +
119U TYR* 1.3 75.0 - - - +
121U LEU* 1.3 56.6 + - - +
123U GLU* 3.2 10.2 + - - +
124U CYS* 2.9 26.9 + - - +
224U PRO* 5.0 12.1 - - + +
228U ARG* 6.1 4.7 - - + -
289U ILE* 5.9 5.5 - - + +
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Residues in contact with LEU 121 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117U GLN 2.9 17.6 + - - +
118U SER* 3.6 6.1 - - - +
120U TYR* 1.3 76.5 - - - +
122U GLY* 1.3 56.9 + - - +
124U CYS* 3.3 8.9 + - - +
125U SER 3.1 7.1 + - - -
126U PHE* 3.0 34.1 + - + +
129U LYS* 4.8 5.2 - - + -
130U SER* 3.6 20.9 - - - +
133U ILE* 6.2 0.2 - - + -
156U TYR* 6.5 0.7 - - - -
159U THR* 5.5 7.4 - - - -
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Residues in contact with GLY 122 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118U SER 2.9 15.0 + - - -
119U TYR* 3.1 5.3 + - - -
121U LEU* 1.3 75.6 - - - +
123U GLU* 1.3 59.0 + - - +
125U SER* 3.1 17.1 + - - -
126U PHE 4.4 3.6 - - - -
127U PHE* 6.0 0.4 - - - -
130U SER* 3.7 9.1 - - - -
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Residues in contact with GLU 123 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119U TYR 2.9 13.0 + - - +
120U TYR* 3.2 12.1 + - - +
122U GLY* 1.3 76.7 - - - +
124U CYS* 1.3 59.6 + - - +
125U SER* 3.2 3.8 + - - -
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Residues in contact with CYS 124 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120U TYR 2.9 16.4 + - - +
121U LEU* 3.7 10.1 - - - +
122U GLY 3.2 0.4 - - - -
123U GLU* 1.3 74.3 - - - +
125U SER* 1.3 69.6 + - - +
126U PHE* 3.4 4.9 + - + +
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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
------------------------------------------------------------
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