Contacts of the helix formed by residues 98 - 124 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96P ALA 3.8 1.5 + - - +
97P TRP* 1.3 76.4 - - - +
99P GLU* 1.3 60.4 + - - +
100P ASN* 4.1 10.5 - - + +
101P VAL* 3.2 16.3 + - + +
102P LYS* 3.0 28.2 + - - +
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Residues in contact with GLU 99 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98P LYS* 1.3 73.7 - - - +
100P ASN* 1.3 57.4 + - - +
102P LYS* 3.8 7.5 - - - +
103P CYS* 2.9 32.2 + - - +
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Residues in contact with ASN 100 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98P LYS* 3.2 6.6 - - + +
99P GLU* 1.3 78.6 - - - +
101P VAL* 1.3 56.1 + - - +
103P CYS* 4.3 2.8 - - - +
104P GLU* 2.9 31.9 + - - +
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Residues in contact with VAL 101 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97P TRP* 6.0 1.6 - - + -
98P LYS* 3.2 20.2 + - + +
100P ASN* 1.3 77.1 - - - +
102P LYS* 1.3 60.9 + - - +
104P GLU* 3.9 4.2 - - - +
105P VAL* 2.9 32.7 + - - +
277P LEU* 5.1 12.3 - - + +
280P LEU* 4.9 20.9 - - + -
281P GLY 5.6 0.9 - - - +
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Residues in contact with LYS 102 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97P TRP* 6.0 4.0 - - + -
98P LYS 3.0 15.9 + - - +
99P GLU* 3.9 7.2 - - - +
101P VAL* 1.3 76.4 - - - +
103P CYS* 1.3 57.6 + - - +
105P VAL* 4.2 1.7 - - - +
106P TRP* 2.9 24.9 + - - +
202P GLY 5.2 1.3 - - - +
203P LEU* 3.0 39.8 - - + +
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Residues in contact with CYS 103 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99P GLU 2.9 19.8 + - - +
100P ASN* 4.3 2.7 - - - +
102P LYS* 1.3 77.6 - - - +
104P GLU* 1.3 56.9 + - - +
106P TRP* 4.2 2.6 - - - +
107P THR* 2.9 31.7 + - - -
142P ARG* 5.4 13.1 - - + +
143P PHE* 5.4 6.1 - - - +
203P LEU 3.8 5.6 + - - -
204P LYS* 5.9 2.0 - - - +
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Residues in contact with GLU 104 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100P ASN 2.9 21.3 + - - +
101P VAL* 3.9 5.2 - - - +
102P LYS 3.2 0.2 - - - -
103P CYS* 1.3 75.0 - - - +
105P VAL* 1.3 59.6 + - - +
107P THR* 3.3 4.8 + - - -
108P ALA* 2.9 29.6 + - - +
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Residues in contact with VAL 105 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101P VAL 2.9 19.0 + - - +
102P LYS* 4.2 2.9 - - - +
104P GLU* 1.3 77.3 - - - +
106P TRP* 1.3 57.6 + - - +
108P ALA* 3.4 7.1 + - - +
109P ILE* 2.9 29.1 + - - +
203P LEU* 5.8 2.7 - - + -
276P ALA* 6.3 3.1 - - + -
277P LEU* 6.1 6.3 - - + -
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Residues in contact with TRP 106 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102P LYS 2.9 20.3 + - - +
103P CYS* 4.2 3.4 - - - +
105P VAL* 1.3 77.0 - - - +
107P THR* 1.3 58.1 + - - +
109P ILE* 3.3 6.0 + - - +
110P ILE* 2.9 30.0 + - - +
203P LEU* 3.6 25.7 - - + +
204P LYS* 4.5 11.0 - - + +
217P ASP* 5.8 7.0 - - + -
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Residues in contact with THR 107 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103P CYS 2.9 21.9 + - - -
104P GLU* 3.7 5.6 - - - -
106P TRP* 1.3 77.5 - - - +
108P ALA* 1.3 56.6 + - - +
110P ILE* 3.4 5.9 + - - +
111P ALA* 2.9 28.9 + - - +
140P LEU* 5.7 3.2 - - - +
141P GLU 5.2 11.2 - - - -
142P ARG* 5.2 8.7 - - - -
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Residues in contact with ALA 108 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104P GLU 2.9 16.5 + - - +
105P VAL* 3.8 6.7 - - - +
106P TRP 3.3 0.2 - - - -
107P THR* 1.3 76.7 - - - +
109P ILE* 1.3 57.6 + - - +
111P ALA* 3.3 8.7 + - - +
112P GLN* 2.9 26.9 + - - +
284P ILE* 4.8 17.9 - - + -
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Residues in contact with ILE 109 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105P VAL 2.9 17.7 + - - +
106P TRP* 3.7 7.9 - - - +
108P ALA* 1.3 74.9 - - - +
110P ILE* 1.3 60.2 + - - +
112P GLN* 3.1 9.4 + - - +
113P LYS* 2.9 27.2 + - - +
217P ASP* 4.3 18.6 - - + +
218P ILE* 6.1 0.2 - - - -
220P GLU* 5.6 3.1 - - + -
221P PRO* 4.7 7.2 - - + +
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Residues in contact with ILE 110 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106P TRP 2.9 16.1 + - - +
107P THR* 3.8 6.7 - - - +
109P ILE* 1.3 75.8 - - - +
111P ALA* 1.3 57.8 + - - +
113P LYS* 3.2 8.0 + - - +
114P ILE* 2.9 30.8 + - - +
149P GLU* 5.2 15.0 - - + +
220P GLU* 5.7 3.3 - - - +
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Residues in contact with ALA 111 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107P THR 2.9 18.4 + - - +
108P ALA* 3.5 9.2 - - - +
109P ILE 3.2 0.2 - - - -
110P ILE* 1.3 77.3 - - - +
112P GLN* 1.3 56.8 + - - +
114P ILE* 3.9 4.7 - - - +
115P LEU* 2.9 30.5 + - - +
137P TYR* 5.0 14.8 - - + +
140P LEU* 5.5 8.5 - - + -
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Residues in contact with GLN 112 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108P ALA 2.9 14.4 + - - +
109P ILE* 3.1 11.9 + - - +
111P ALA* 1.3 74.7 - - - +
113P LYS* 1.3 58.2 + - - +
115P LEU* 3.5 5.9 + - - +
116P ASN* 2.9 29.6 + - - +
221P PRO* 4.5 13.1 - - + +
285P PRO 5.5 3.4 - - - +
286P GLU* 5.4 7.4 - - + -
287P PHE 4.7 18.4 - - - +
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Residues in contact with LYS 113 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109P ILE 2.9 12.3 + - - +
110P ILE* 3.2 11.0 + - - +
112P GLN* 1.3 74.5 - - - +
114P ILE* 1.3 60.0 + - - +
116P ASN* 3.1 4.8 + - - +
117P GLN* 2.9 28.1 + - - +
220P GLU* 3.7 30.1 - - + +
221P PRO* 3.8 12.5 - - + +
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Residues in contact with ILE 114 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110P ILE 2.9 17.0 + - - +
111P ALA* 4.2 3.4 - - - +
113P LYS* 1.3 76.9 - - - +
115P LEU* 1.3 57.0 + - - +
117P GLN* 3.2 8.1 + - - +
118P SER* 2.9 28.8 + - - -
133P ILE* 4.8 9.3 - - + +
136P LEU 5.6 1.1 - - - -
137P TYR* 4.2 23.3 - - + +
148P ARG 6.0 0.2 - - - +
149P GLU* 6.2 2.9 - - - -
152P SER* 4.9 15.9 - - - -
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Residues in contact with LEU 115 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111P ALA 2.9 19.7 + - - +
112P GLN* 3.8 7.4 - - - +
114P ILE* 1.3 78.4 - - - +
116P ASN* 1.3 57.1 + - - +
118P SER* 3.4 7.5 + - - -
119P TYR* 2.9 27.4 + - - +
137P TYR* 4.7 8.2 - - + +
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Residues in contact with ASN 116 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112P GLN 2.9 18.1 + - - +
113P LYS 3.1 5.8 + - - +
115P LEU* 1.3 74.2 - - - +
117P GLN* 1.3 60.9 + - - +
119P TYR* 3.3 8.2 + - - +
120P TYR* 2.9 27.7 + - - +
221P PRO* 4.1 19.3 - - + +
224P PRO* 4.4 11.8 - - + +
287P PHE 4.8 10.3 - - - +
288P ARG* 5.6 1.8 - - - +
289P ILE* 5.3 13.3 - - + +
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Residues in contact with GLN 117 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113P LYS 2.9 12.9 + - - +
114P ILE* 3.2 11.9 + - - +
116P ASN* 1.3 75.4 - - - +
118P SER* 1.3 58.9 + - - +
120P TYR* 3.2 7.5 + - - +
121P LEU* 2.9 29.5 + - - +
133P ILE* 5.2 7.9 - - + -
152P SER* 5.7 5.8 - - - +
156P TYR* 5.2 13.9 - - + -
224P PRO* 4.8 6.7 - - + +
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Residues in contact with SER 118 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114P ILE 2.9 16.0 + - - -
115P LEU* 3.7 8.1 - - - -
117P GLN* 1.3 77.0 - - - +
119P TYR* 1.3 58.2 + - - +
121P LEU* 4.6 0.2 - - - -
122P GLY* 2.9 22.9 + - - -
130P SER* 3.5 34.3 - - - +
133P ILE* 4.4 4.6 - - - +
134P MET* 4.2 18.4 - - - -
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Residues in contact with TYR 119 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115P LEU 2.9 17.9 + - - +
116P ASN* 3.6 9.4 - - - +
117P GLN 3.2 0.2 - - - -
118P SER* 1.3 75.5 - - - +
120P TYR* 1.3 59.1 + - - +
122P GLY* 3.8 1.4 - - - -
123P GLU* 2.9 29.1 + - - +
288P ARG* 6.2 2.0 - - + -
289P ILE* 5.1 16.6 - - + +
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Residues in contact with TYR 120 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116P ASN 2.9 17.3 + - - +
117P GLN* 3.2 8.3 + - - +
119P TYR* 1.3 73.9 - - - +
121P LEU* 1.3 60.0 + - - +
123P GLU* 3.3 6.8 + - - +
124P CYS* 2.9 27.4 + - - +
224P PRO* 4.7 15.7 - - + +
228P ARG* 6.4 1.3 - - + -
289P ILE* 5.7 4.7 - - + +
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Residues in contact with LEU 121 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117P GLN 2.9 14.9 + - - +
118P SER* 4.6 0.2 - - - -
120P TYR* 1.3 75.7 - - - +
122P GLY* 1.3 58.1 + - - +
124P CYS* 3.3 9.1 + - - +
125P SER 3.0 7.8 + - - -
126P PHE* 2.9 35.3 + - + +
129P LYS* 4.7 5.4 - - + -
130P SER* 3.6 30.3 - - - +
133P ILE* 6.2 0.7 - - + -
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Residues in contact with GLY 122 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118P SER 2.9 17.8 + - - -
119P TYR* 3.4 2.9 + - - -
121P LEU* 1.3 75.2 - - - +
123P GLU* 1.3 62.7 + - - +
125P SER* 3.1 13.6 + - - -
126P PHE 4.7 2.5 - - - -
130P SER* 3.8 7.8 - - - -
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Residues in contact with GLU 123 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119P TYR 2.9 17.3 + - - +
120P TYR* 3.3 7.2 + - - +
122P GLY* 1.3 76.2 - - - +
124P CYS* 1.3 58.5 + - - +
125P SER* 3.2 3.3 + - - -
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Residues in contact with CYS 124 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120P TYR 2.9 16.9 + - - +
121P LEU* 3.7 9.9 - - - +
122P GLY 3.2 0.4 - - - -
123P GLU* 1.3 74.7 - - - +
125P SER* 1.3 70.8 + - - +
126P PHE* 3.4 4.8 + - + +
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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