Contacts of the helix formed by residues 115 - 139 (chain D) in PDB entry 2Q7M
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 GLY 115 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90D TYR* 4.7 3.9 - - - -
93D VAL* 4.7 19.9 - - - +
114D PHE* 1.3 81.7 - - - +
116D LYS* 1.3 65.3 + - - -
117D ARG* 3.1 7.4 - - - -
118D ILE* 2.8 25.9 + - - +
119D ILE* 2.8 15.9 - - - +
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Residues in contact with LYS 116 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113D ILE* 4.6 18.8 - - + +
114D PHE 3.1 13.6 + - - +
115D GLY* 1.3 73.1 - - - +
117D ARG* 1.3 59.9 + - + +
119D ILE* 3.0 4.2 - - - +
120D LEU* 2.9 23.4 + - - +
505E 2CS 2.7 98.9 + - + +
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Residues in contact with ARG 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D GLY* 4.7 6.3 - - - -
116D LYS* 1.3 79.8 - - + +
118D ILE* 1.3 62.7 + - + +
120D LEU* 3.4 9.3 - - + +
121D PHE* 2.7 33.5 + - - +
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Residues in contact with ILE 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D ALA* 2.8 32.8 - - + +
89D MET* 3.2 15.3 - - + -
90D TYR* 2.8 50.0 - - + +
93D VAL* 4.4 6.5 - - + -
115D GLY* 2.8 18.5 + - - +
117D ARG* 1.3 77.7 - - + +
119D ILE* 1.3 57.9 + - + +
121D PHE* 3.0 8.0 + - - +
122D LEU* 2.7 46.6 + - + +
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Residues in contact with ILE 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D THR 4.3 4.5 - - - +
67D PHE* 4.1 25.4 - - + -
70D VAL* 3.8 16.7 - - + +
90D TYR* 4.1 25.1 - - + -
114D PHE* 5.3 0.9 - - + -
115D GLY* 2.8 36.8 - - - +
116D LYS* 3.0 23.3 - - - +
118D ILE* 1.3 79.0 - - - +
120D LEU* 1.3 54.9 + - - +
122D LEU* 3.8 0.9 - - - +
123D PHE* 2.7 36.0 + - - +
505E 2CS 3.4 44.7 - - + +
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Residues in contact with LEU 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D LYS* 2.9 22.4 + - - +
117D ARG* 3.4 11.2 - - + +
119D ILE* 1.3 79.6 - - - +
121D PHE* 1.3 58.6 + - + +
123D PHE* 3.1 1.3 + - + +
124D LEU* 2.8 62.9 + - + +
505E 2CS 3.1 49.1 - - + +
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Residues in contact with PHE 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D PRO* 4.5 10.1 - - + -
85D PHE* 6.3 0.4 - + - -
86D ALA* 3.7 30.3 - - + -
117D ARG 2.7 21.4 + - - +
118D ILE* 3.4 4.7 - - - +
120D LEU* 1.3 72.5 - - + +
122D LEU* 1.3 59.8 + - + +
124D LEU* 2.7 36.3 + - + -
125D MET* 3.1 44.4 + - + -
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Residues in contact with LEU 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D PHE* 4.5 5.4 - - + -
70D VAL* 3.5 35.0 - - + +
71D LEU* 4.1 17.5 - - - -
74D ALA* 2.9 24.4 - - + +
83D ALA 3.8 5.4 - - - +
86D ALA* 3.2 26.7 - - + -
87D GLY* 4.0 22.0 - - - +
118D ILE* 2.7 32.7 + - + +
121D PHE* 1.3 74.5 - - + +
123D PHE* 1.3 60.2 + - - +
125D MET* 3.0 30.9 + - + -
126D SER* 2.9 5.5 + - - -
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Residues in contact with PHE 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D VAL* 3.7 9.6 - - + +
119D ILE 2.7 22.6 + - - +
120D LEU* 3.1 4.0 - - + +
122D LEU* 1.3 74.6 - - - +
124D LEU* 1.3 81.0 + - + +
126D SER* 3.0 16.2 + - - -
127D VAL* 3.0 30.2 + - + +
17E LEU* 3.0 57.7 - - + -
18E ILE* 6.4 0.7 - - + -
20E VAL* 3.6 15.7 - - + -
21E VAL* 4.6 9.6 - - + -
505E 2CS 3.0 27.8 - - + -
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Residues in contact with LEU 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D LEU* 2.8 52.3 - - + +
121D PHE* 2.7 26.8 + - + +
123D PHE* 1.3 101.8 - - + +
125D MET* 1.3 58.3 + - - -
127D VAL* 3.0 14.7 - - + +
128D ALA* 3.0 24.8 + - - +
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Residues in contact with MET 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D ALA* 2.8 50.9 - - + +
77D LEU 3.7 0.2 - - - +
78D CYS* 3.3 23.0 - - - +
82D PRO* 3.6 22.7 - - + -
83D ALA* 2.9 28.9 - - + -
121D PHE* 3.2 47.3 - - + +
122D LEU* 3.0 7.4 + - + +
124D LEU* 1.3 74.6 - - - +
126D SER* 1.3 63.0 + - - +
128D ALA* 3.0 22.3 - - - +
129D GLY 3.1 8.0 + - - -
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Residues in contact with SER 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D VAL* 4.3 1.9 - - - +
73D SER* 3.5 38.6 - - - -
74D ALA* 3.7 1.8 + - - +
77D LEU* 4.0 5.3 - - - +
122D LEU 2.9 15.5 + - - -
123D PHE* 3.0 16.5 + - - -
125D MET* 1.3 73.7 - - - +
127D VAL* 1.3 53.9 + - - +
128D ALA 3.0 4.7 - - - -
130D ILE* 3.0 33.0 + - - +
17E LEU* 3.2 23.7 - - - +
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Residues in contact with VAL 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D PHE* 3.0 27.7 + - + +
124D LEU* 3.0 42.0 - - + +
126D SER* 1.3 75.5 - - - +
128D ALA* 1.3 63.3 + - - +
130D ILE* 3.5 20.5 - - + +
131D PHE* 3.5 10.0 + - + +
17E LEU* 4.6 3.3 - - - +
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Residues in contact with ALA 128 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78D CYS* 4.9 7.2 - - - -
124D LEU 3.0 20.2 + - - +
125D MET* 3.0 11.9 - - - +
126D SER 3.0 1.4 - - - -
127D VAL* 1.3 76.3 - - - +
129D GLY* 1.3 67.3 + - - +
131D PHE* 2.9 15.3 + - - -
132D ASN* 2.8 22.5 + - - +
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Residues in contact with GLY 129 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77D LEU* 2.9 26.2 + - - -
78D CYS* 4.4 2.1 - - - +
125D MET 3.1 6.9 + - - -
128D ALA* 1.3 78.7 - - - +
130D ILE* 1.3 55.3 + - - +
132D ASN* 3.6 13.3 - - - +
133D TYR* 2.7 37.1 + - - +
6E VAL* 6.4 0.4 - - - -
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Residues in contact with ILE 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D LEU* 3.7 23.9 + - + +
126D SER 3.0 17.8 + - - +
127D VAL* 3.5 22.4 - - + +
128D ALA 3.1 0.2 - - - -
129D GLY* 1.3 75.4 - - - +
131D PHE* 1.3 64.9 + - + +
133D TYR* 3.9 3.0 - - + +
134D TYR* 3.4 19.8 + - + -
6E VAL* 6.3 0.2 - - - -
10E VAL* 3.4 48.0 - - + +
13E ALA* 4.4 6.1 - - + -
14E ILE* 3.9 23.8 - - + +
17E LEU* 6.1 3.8 - - + -
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Residues in contact with PHE 131 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127D VAL* 3.7 9.9 - - + +
128D ALA* 2.9 16.8 + - + +
130D ILE* 1.3 81.4 - - + +
132D ASN* 1.3 70.8 + - + +
133D TYR 2.7 4.9 + - - -
134D TYR* 2.5 39.2 + - + +
135D LEU* 3.3 35.1 + - + -
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Residues in contact with ASN 132 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128D ALA 2.8 15.9 + - - +
129D GLY* 3.6 12.7 - - - +
131D PHE* 1.3 96.7 - - + +
133D TYR* 1.3 60.5 + - - +
135D LEU* 2.8 27.4 - - - +
136D ILE* 2.9 27.3 - - - +
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Residues in contact with TYR 133 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129D GLY 2.7 19.8 + - - +
130D ILE* 3.9 5.6 - - - +
131D PHE 2.7 4.9 + - - -
132D ASN* 1.3 69.3 + - - +
134D TYR* 1.3 94.8 + + - +
135D LEU 2.9 5.4 - - - -
136D ILE* 3.2 16.1 + - + -
137D PHE* 2.9 38.9 + - + +
3E GLN* 3.2 45.2 + - + -
6E VAL* 3.0 31.2 - - + -
7E GLY* 2.9 24.9 + - - -
10E VAL* 3.6 19.1 - - + -
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Residues in contact with TYR 134 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130D ILE* 3.4 22.4 - - + -
131D PHE* 2.5 20.9 + - + +
133D TYR* 1.3 94.6 - + - +
135D LEU* 1.3 61.8 + - + +
137D PHE* 3.5 22.4 - + - +
138D PHE* 3.3 33.9 + + + -
10E VAL* 2.8 31.6 - - + +
11E LEU* 4.4 8.3 - - - +
14E ILE* 3.9 14.1 - - + +
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Residues in contact with LEU 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D PHE* 3.3 38.1 + - + -
132D ASN* 2.8 17.7 + - + +
134D TYR* 1.3 74.9 - - + +
136D ILE* 1.3 55.8 + - + +
137D PHE 2.9 3.8 - - - -
138D PHE* 2.6 10.7 + - - -
139D PHE* 2.5 56.2 + - + +
140D GLY 3.9 0.9 - - - -
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Residues in contact with ILE 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D ASN* 2.9 29.6 - - - +
133D TYR* 3.2 28.0 - - + -
135D LEU* 1.3 73.8 - - + +
137D PHE* 1.3 57.1 - - - +
140D GLY* 2.8 38.2 + - - -
141D SER* 3.8 2.3 + - - -
3E GLN* 3.4 30.9 + - + +
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Residues in contact with PHE 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D TYR* 2.9 31.8 + - + +
134D TYR* 3.5 25.1 - + - +
135D LEU 2.9 0.6 + - - -
136D ILE* 1.3 78.3 - - - +
138D PHE* 1.3 88.0 + + - +
141D SER* 4.2 6.6 + - - -
3E GLN* 3.5 17.2 - - - +
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Residues in contact with PHE 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D TYR* 3.3 21.3 + + + +
135D LEU* 2.6 12.1 + - - +
137D PHE* 1.3 113.6 - + + +
139D PHE* 1.3 81.9 + + + +
140D GLY 3.2 3.1 - - - -
141D SER* 3.3 20.4 + - - +
142D ASP* 4.1 4.9 - - - +
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Residues in contact with PHE 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D LEU* 2.5 35.6 + - + +
136D ILE* 4.4 0.2 - - - -
138D PHE* 1.3 95.0 - + + +
140D GLY* 1.3 63.5 + - - +
141D SER 3.0 7.0 - - - +
142D ASP* 3.4 18.3 - - - +
143D PHE* 3.4 13.9 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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