Contacts of the helix formed by residues 98 - 124 (chain l) 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 l).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96l ALA 3.2 5.4 + - - +
97l TRP* 1.3 77.6 - - - +
99l GLU* 1.3 65.4 + - - +
100l ASN* 3.3 9.2 - - + +
101l VAL* 3.6 15.0 + - + +
102l LYS* 3.2 22.3 + - - +
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Residues in contact with GLU 99 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97l TRP 3.9 0.6 + - - -
98l LYS* 1.3 70.6 - - - +
100l ASN* 1.3 59.1 - - - +
102l LYS* 3.8 6.4 - - - +
103l CYS* 2.9 31.0 + - - +
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Residues in contact with ASN 100 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98l LYS* 3.3 6.1 - - + +
99l GLU* 1.3 76.4 - - - +
101l VAL* 1.3 60.1 + - - +
103l CYS* 3.4 5.8 + - - +
104l GLU* 2.9 29.5 + - - +
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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 TRP* 6.1 1.3 - - + -
98l LYS* 3.6 19.6 + - + +
99l GLU 3.4 0.2 - - - -
100l ASN* 1.3 76.5 - - - +
102l LYS* 1.3 60.3 + - - +
104l GLU* 3.7 6.2 - - - +
105l VAL* 2.9 31.9 + - - +
277l LEU* 5.1 12.6 - - + +
280l LEU* 4.8 20.6 - - + -
281l GLY* 5.1 4.9 - - - +
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Residues in contact with LYS 102 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97l TRP* 5.7 4.9 - - + +
98l LYS 3.2 18.1 + - - +
99l GLU* 3.8 7.2 - - - +
101l VAL* 1.3 78.3 - - - +
103l CYS* 1.3 57.1 + - - +
105l VAL* 3.9 3.8 - - - +
106l TRP* 2.9 31.7 + - - +
202l GLY 5.6 1.1 - - - +
203l LEU* 4.2 26.4 - - - +
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Residues in contact with CYS 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 GLU 2.9 19.0 + - - +
100l ASN* 3.8 5.6 - - - +
102l LYS* 1.3 73.9 - - - +
104l GLU* 1.3 60.5 + - - +
106l TRP* 3.9 4.8 - - - +
107l THR* 2.9 31.2 + - - -
142l ARG* 5.4 13.1 - - + +
143l PHE 5.8 3.6 - - - +
203l LEU 5.7 0.2 - - - -
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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 ASN 2.9 17.5 + - - +
101l VAL* 3.7 7.2 - - - +
103l CYS* 1.3 75.2 - - - +
105l VAL* 1.3 61.2 + - - +
107l THR* 3.4 4.9 + - - -
108l ALA* 2.9 30.3 + - - +
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Residues in contact with VAL 105 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101l VAL 2.9 17.8 + - - +
102l LYS* 4.1 4.0 - - - +
104l GLU* 1.3 75.4 - - - +
106l TRP* 1.3 59.2 + - - +
108l ALA* 3.4 6.6 + - - +
109l ILE* 2.9 29.5 + - - +
203l LEU* 5.9 0.4 - - - -
277l LEU* 6.5 0.7 - - + -
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Residues in contact with TRP 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 LYS 2.9 20.4 + - - +
103l CYS* 3.9 5.4 - - - +
105l VAL* 1.3 76.3 - - - +
107l THR* 1.3 57.5 + - - +
109l ILE* 3.2 7.1 + - - +
110l ILE* 2.9 30.2 + - - +
203l LEU* 4.4 24.8 - - + +
204l LYS* 5.2 2.9 - - - +
217l ASP* 6.4 0.2 - - + -
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Residues in contact with THR 107 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103l CYS 2.9 19.6 + - - -
104l GLU* 3.8 5.2 - - - -
106l TRP* 1.3 75.0 - - - +
108l ALA* 1.3 58.2 + - - +
110l ILE* 3.4 6.0 + - - +
111l ALA* 2.9 30.2 + - - +
140l LEU* 5.9 2.4 - - - +
141l GLU 5.3 10.1 - - - -
142l ARG* 5.3 10.1 - - - -
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Residues in contact with ALA 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 19.5 + - - +
105l VAL* 3.7 7.2 - - - +
106l TRP 3.3 0.2 - - - -
107l THR* 1.3 76.5 - - - +
109l ILE* 1.3 57.3 + - - +
111l ALA* 3.4 6.8 + - - +
112l GLN* 2.9 28.9 + - - +
284l ILE* 4.7 18.4 - - + -
285l PRO 6.2 0.7 - - - +
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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 VAL 2.9 17.8 + - - +
106l TRP* 3.6 7.0 - - - +
108l ALA* 1.3 74.5 - - - +
110l ILE* 1.3 60.8 + - - +
112l GLN* 3.2 7.2 + - - +
113l LYS* 2.9 29.2 + - - +
217l ASP* 4.1 19.5 - - + +
218l ILE* 5.8 2.0 - - - +
220l GLU* 5.0 6.0 - - + +
221l PRO* 4.6 8.1 - - + +
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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 TRP 2.9 16.9 + - - +
107l THR* 3.9 6.5 - - - +
109l ILE* 1.3 76.7 - - - +
111l ALA* 1.3 57.2 + - - +
113l LYS* 3.3 5.7 + - - +
114l ILE* 2.9 32.1 + - - +
149l GLU* 5.2 15.6 - - + +
220l GLU* 6.0 1.3 - - - -
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Residues in contact with ALA 111 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107l THR 2.9 19.0 + - - +
108l ALA* 3.7 7.0 - - - +
110l ILE* 1.3 77.7 - - - +
112l GLN* 1.3 56.2 + - - +
114l ILE* 4.1 4.7 - - - +
115l LEU* 2.9 31.5 + - - +
137l TYR* 5.0 14.8 - - + +
140l LEU* 5.6 8.2 - - + +
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Residues in contact with GLN 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 ALA 2.9 17.9 + - - +
109l ILE* 3.2 6.5 + - - +
111l ALA* 1.3 77.2 - - - +
113l LYS* 1.3 56.5 + - - +
115l LEU* 3.5 5.1 + - - +
116l ASN* 2.9 30.0 + - - +
221l PRO* 4.0 18.6 - - + -
286l GLU* 5.7 4.3 - - + -
287l PHE 4.4 19.8 - - - +
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Residues in contact with LYS 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 2.9 16.1 + - - +
110l ILE* 3.8 6.7 - - - +
112l GLN* 1.3 73.9 - - - +
114l ILE* 1.3 59.7 + - - +
116l ASN* 3.2 5.9 + - - +
117l GLN* 2.9 27.9 + - - +
220l GLU* 3.5 31.0 - - + +
221l PRO* 4.1 7.6 - - - +
224l PRO* 5.4 1.9 - - - +
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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
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110l ILE 2.9 17.4 + - - +
111l ALA* 4.1 3.1 - - - +
113l LYS* 1.3 76.3 - - - +
115l LEU* 1.3 57.7 + - - +
117l GLN* 3.2 8.2 + - - +
118l SER* 2.9 29.5 + - - -
133l ILE* 4.8 7.3 - - + +
136l LEU* 5.7 0.7 - - + -
137l TYR* 4.3 21.3 - - + +
148l ARG 6.1 0.2 - - - +
149l GLU* 6.0 5.2 - - + -
152l SER* 5.1 14.6 - - - -
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Residues in contact with LEU 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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111l ALA 2.9 20.8 + - - +
112l GLN* 3.8 6.1 - - - +
114l ILE* 1.3 77.1 - - - +
116l ASN* 1.3 57.1 + - - +
118l SER* 3.9 5.4 - - - +
119l TYR* 2.9 30.5 + - - +
137l TYR* 4.6 10.0 - - + +
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Residues in contact with ASN 116 (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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112l GLN 2.9 18.3 + - - +
113l LYS* 3.2 4.9 + - - +
115l LEU* 1.3 76.5 - - - +
117l GLN* 1.3 58.5 + - - +
119l TYR* 3.8 5.6 - - - +
120l TYR* 2.9 30.1 + - - +
221l PRO 4.1 17.0 - - - +
224l PRO* 4.5 14.2 - - + +
287l PHE 5.3 4.0 - - - +
288l ARG* 5.6 1.3 - - - +
289l ILE* 4.9 23.5 - - + +
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Residues in contact with GLN 117 (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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113l LYS 2.9 13.2 + - - +
114l ILE* 3.2 11.2 + - - +
116l ASN* 1.3 74.0 - - - +
118l SER* 1.3 60.5 + - - +
120l TYR* 3.3 6.3 + - - +
121l LEU* 2.9 28.3 + - - +
133l ILE* 5.2 6.1 - - + -
152l SER* 5.9 3.6 - - - +
156l TYR* 4.6 21.1 - - + +
224l PRO* 4.7 9.8 - - + +
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Residues in contact with SER 118 (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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114l ILE 2.9 15.4 + - - -
115l LEU* 4.0 6.1 - - - -
117l GLN* 1.3 76.7 - - - +
119l TYR* 1.3 58.9 + - - +
121l LEU* 3.3 1.0 + - - -
122l GLY* 2.9 23.0 + - - -
130l SER* 3.2 37.9 - - - +
133l ILE* 3.8 16.9 - - - +
134l MET* 3.8 14.8 - - - -
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Residues in contact with TYR 119 (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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115l LEU 2.9 19.1 + - - +
116l ASN* 3.9 6.5 - - - +
118l SER* 1.3 77.3 - - - +
120l TYR* 1.3 55.8 + - - +
122l GLY* 3.1 3.4 + - - +
123l GLU* 2.9 26.9 + - - +
289l ILE* 5.7 8.5 - - + +
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Residues in contact with TYR 120 (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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116l ASN 2.9 18.7 + - - +
117l GLN* 3.7 7.0 - - - +
119l TYR* 1.3 76.5 - - - +
121l LEU* 1.3 57.3 + - - +
123l GLU* 3.2 9.5 + - - +
124l CYS* 2.9 26.7 + - - +
224l PRO* 5.0 11.9 - - + +
228l ARG* 6.1 5.2 - - + -
289l ILE* 5.9 1.0 - - - +
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Residues in contact with LEU 121 (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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117l GLN 2.9 17.6 + - - +
118l SER* 3.3 5.6 + - - +
120l TYR* 1.3 75.5 - - - +
122l GLY* 1.3 60.3 + - - +
124l CYS* 3.3 9.3 + - - +
125l SER 3.2 4.5 + - - -
126l PHE* 3.1 34.8 + - + +
129l LYS* 4.8 5.4 - - + -
130l SER* 3.6 21.1 - - - +
133l ILE* 6.2 0.4 - - + -
156l TYR* 6.5 0.9 - - - -
159l THR* 5.6 7.4 - - - -
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Residues in contact with GLY 122 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118l SER 2.9 14.0 + - - -
119l TYR* 3.1 5.3 + - - -
121l LEU* 1.3 75.8 - - - +
123l GLU* 1.3 59.2 + - - +
125l SER* 3.1 17.2 + - - -
126l PHE 4.4 3.4 - - - -
127l PHE* 6.1 0.4 - - - -
130l SER* 3.7 8.9 - - - -
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Residues in contact with GLU 123 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119l TYR 2.9 13.1 + - - +
120l TYR* 3.2 12.1 + - - +
122l GLY* 1.3 76.1 - - - +
124l CYS* 1.3 59.5 + - - +
125l SER* 3.2 2.9 + - - -
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Residues in contact with CYS 124 (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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120l TYR 2.9 15.1 + - - +
121l LEU* 3.6 10.1 - - - +
122l GLY 3.2 0.4 - - - -
123l GLU* 1.3 74.5 - - - +
125l SER* 1.3 70.1 + - - +
126l PHE* 3.3 5.1 + - + +
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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