Contacts of the helix formed by residues 113 - 135 (chain D) in PDB entry 3UDB
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 SER 113 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D ARG 4.1 0.8 + - - -
112D PHE* 1.3 77.3 - - - +
114D GLU* 1.3 66.7 + - - +
115D ASP* 3.5 8.1 + - - +
116D GLU* 3.1 32.3 + - - +
117D ALA* 2.9 20.3 + - - +
211D LEU* 4.7 0.2 - - - -
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Residues in contact with GLU 114 (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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112D PHE 3.8 0.6 + - - -
113D SER* 1.3 74.0 - - - +
115D ASP* 1.3 64.2 + - - +
117D ALA* 3.2 3.1 + - - +
118D ARG* 3.0 31.2 + - - +
211D LEU* 3.8 17.0 - - + +
245D HIS 4.1 6.5 - - - +
246D ILE* 3.6 10.3 - - + +
247D SER* 2.6 51.1 + - - -
250D CYS* 4.0 4.0 - - - -
276D TRP* 2.7 31.9 + - + +
279D LYS* 4.5 1.7 + - - -
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Residues in contact with ASP 115 (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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113D SER* 3.2 7.2 + - - +
114D GLU* 1.3 79.7 - - - +
116D GLU* 1.3 58.6 + - + +
118D ARG* 2.9 36.4 + - - +
119D PHE* 3.0 26.7 + - - +
280D ASN* 4.0 15.8 + - - +
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Residues in contact with GLU 116 (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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105D ARG* 3.2 27.4 + - - +
112D PHE* 3.9 19.7 - - + -
113D SER* 3.1 31.1 + - - +
115D ASP* 1.3 74.9 - - - +
117D ALA* 1.3 66.7 + - - +
119D PHE* 3.2 10.7 + - + +
120D PHE* 3.2 32.6 + - + -
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Residues in contact with ALA 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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112D PHE* 4.1 4.2 - - + +
113D SER 2.9 8.3 + - - +
114D GLU 3.6 8.1 - - - +
116D GLU* 1.3 78.4 - - - +
118D ARG* 1.3 51.7 + - - +
120D PHE 3.3 0.7 + - - -
121D PHE* 2.7 36.6 + - - +
207D LEU* 4.4 5.2 - - + -
210D MET* 3.4 35.6 - - + +
211D LEU* 3.6 28.0 - - + -
276D TRP* 4.4 1.3 - - + -
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Residues in contact with ARG 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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114D GLU* 3.0 23.6 + - - +
115D ASP* 2.9 39.1 + - - +
117D ALA* 1.3 74.1 - - - +
119D PHE* 1.3 61.1 + - - +
121D PHE* 3.8 2.0 - - + +
122D GLN* 2.9 49.5 + - + +
276D TRP* 2.9 74.4 + - + +
277D PHE* 4.9 1.3 - - + -
279D LYS* 3.0 52.7 + - - +
280D ASN* 4.7 6.9 - - - +
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Residues in contact with PHE 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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115D ASP 3.0 13.7 + - - +
116D GLU* 3.2 12.5 + - + +
118D ARG* 1.3 77.0 - - - +
120D PHE* 1.3 93.5 + + - +
122D GLN* 3.7 12.9 - - - +
123D GLN* 2.9 52.5 + - - +
153D ALA* 5.6 7.0 - - + -
154D PRO* 3.9 13.7 - - + -
155D ARG* 3.8 22.4 - - - -
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Residues in contact with PHE 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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102D LEU* 4.4 3.1 - - + -
105D ARG* 3.9 17.9 - - - -
112D PHE* 3.6 31.4 - + - -
116D GLU* 3.2 23.3 + - + -
117D ALA 3.8 1.8 - - - +
118D ARG 3.1 0.2 - - - -
119D PHE* 1.3 95.8 - + - +
121D PHE* 1.3 64.0 + - - +
122D GLN 3.3 0.4 - - - -
123D GLN* 3.4 7.0 + - - +
124D LEU* 3.0 17.7 + - - +
148D LEU* 3.6 21.1 - - + -
154D PRO* 3.2 42.6 - - + -
156D LEU* 3.3 31.2 - - + +
210D MET* 3.6 21.1 - - - -
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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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117D ALA 2.7 18.2 + - - +
118D ARG* 3.3 8.5 + - + +
120D PHE* 1.3 76.0 - - - +
122D GLN* 1.3 65.9 + - - +
124D LEU* 3.2 13.5 + - + +
125D ILE* 2.9 50.1 + - + +
203D CYS* 3.4 29.4 - - + -
207D LEU* 3.6 31.2 - - + -
210D MET* 4.1 5.4 - - + +
253D LEU* 3.9 18.6 - - + -
257D ILE* 4.3 15.9 - - + -
271D ILE* 4.0 10.3 - - + -
276D TRP* 3.8 19.5 - + + -
277D PHE* 3.9 11.7 - + - -
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Residues in contact with GLN 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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118D ARG* 2.9 30.7 + - + +
119D PHE* 3.7 14.9 - - - +
121D PHE* 1.3 77.5 - - - +
123D GLN* 1.3 59.1 + - + +
125D ILE* 3.4 1.7 + - - +
126D SER* 2.9 30.2 + - - -
277D PHE* 3.1 44.9 + - + +
279D LYS 3.3 20.4 + - - -
280D ASN* 3.9 4.5 - - - +
281D LEU* 3.3 38.8 - - + +
282D PRO* 4.1 11.0 - - + +
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Residues in contact with GLN 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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76D ASN* 2.7 47.2 + - - +
119D PHE* 2.9 57.2 + - - +
120D PHE* 3.4 9.4 + - - +
121D PHE 3.2 0.4 - - - -
122D GLN* 1.3 76.0 - - + +
124D LEU* 1.3 66.9 + - - +
126D SER* 3.2 2.1 + - - -
127D GLY* 2.9 23.0 + - - -
154D PRO 4.6 0.2 + - - -
155D ARG* 3.4 24.1 - - - +
156D LEU* 2.7 28.8 + - + -
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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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76D ASN* 5.7 0.2 - - - -
120D PHE 3.0 14.4 + - - +
121D PHE* 3.2 18.1 + - + +
123D GLN* 1.3 75.1 - - - +
125D ILE* 1.3 58.9 + - + +
127D GLY* 3.9 0.7 - - - -
128D VAL* 2.9 37.3 + - + +
143D LEU* 3.2 37.5 - - + -
146D THR* 4.6 4.5 - - + -
156D LEU* 4.0 20.8 - - + +
158D ILE* 4.3 17.8 - - + +
203D CYS* 3.9 25.4 - - + +
206D THR* 3.6 18.8 - - - +
210D MET* 6.0 1.3 - - + -
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Residues in contact with ILE 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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121D PHE* 2.9 52.9 + - + +
124D LEU* 1.3 74.5 - - + +
126D SER* 1.3 61.9 + - - +
128D VAL* 4.0 2.1 - - - +
129D SER* 2.9 28.2 + - - -
203D CYS* 4.1 21.5 - - + -
268D ILE* 3.9 37.2 - - + +
271D ILE* 4.2 16.6 - - + -
272D ARG* 4.3 10.5 - - + -
277D PHE* 3.7 22.9 - - + -
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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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74D HIS* 2.7 35.2 + - - -
76D ASN* 4.6 0.9 - - - -
122D GLN 2.9 18.8 + - - -
123D GLN* 3.7 6.5 - - - -
125D ILE* 1.3 79.3 - - - +
127D GLY* 1.3 62.9 + - - +
129D SER* 3.4 6.1 + - - -
130D TYR* 3.1 19.1 + - - +
272D ARG* 5.4 8.3 - - - +
277D PHE* 5.1 2.2 - - - -
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Residues in contact with GLY 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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74D HIS* 3.8 21.0 - - - -
76D ASN* 4.5 3.6 - - - -
77D ILE* 3.8 8.7 - - - +
123D GLN 2.9 15.2 + - - -
124D LEU 3.9 0.9 - - - -
126D SER* 1.3 76.6 + - - +
128D VAL* 1.3 61.0 + - - +
130D TYR* 3.5 3.8 + - - +
131D ALA* 3.1 21.7 + - - +
158D ILE* 4.1 14.8 - - - +
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Residues in contact with VAL 128 (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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124D LEU* 2.9 25.3 + - + +
125D ILE* 4.0 4.3 - - - +
126D SER 3.3 0.2 - - - -
127D GLY* 1.3 74.4 - - - +
129D SER* 1.3 59.2 + - - +
131D ALA* 3.3 6.7 + - - +
132D HIS* 3.0 54.4 + - + +
141D LEU* 3.1 33.0 - - + -
158D ILE* 4.0 12.1 - - + -
199D ASP* 4.5 3.1 - - + -
203D CYS* 4.1 18.6 - - - -
268D ILE* 4.0 14.8 - - + -
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Residues in contact with SER 129 (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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125D ILE 2.9 19.4 + - - -
126D SER* 3.6 7.4 - - - -
128D VAL* 1.3 79.1 - - - +
130D TYR* 1.3 61.4 + - - +
132D HIS* 3.3 9.3 + - - +
133D ALA* 3.1 22.0 + - - +
268D ILE* 3.7 25.3 - - - +
272D ARG* 4.2 19.2 + - - -
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Residues in contact with TYR 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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71D SER 3.2 12.0 + - - -
72D LEU* 3.6 17.5 - - + -
73D ARG* 3.0 43.9 + - + +
74D HIS* 3.6 36.8 - + + -
77D ILE* 4.2 4.7 - - + -
126D SER 3.1 6.1 + - - +
127D GLY 3.5 7.9 - - - +
129D SER* 1.3 73.8 + - - +
131D ALA* 1.3 66.4 + - - +
132D HIS 3.1 0.2 - - - -
133D ALA* 3.1 8.0 + - + +
134D MET* 3.0 58.3 + - + +
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Residues in contact with ALA 131 (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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72D LEU* 4.8 4.0 - - + -
77D ILE* 4.5 7.2 - - + -
127D GLY 3.1 11.5 + - - +
128D VAL* 3.7 11.0 - - - +
130D TYR* 1.3 84.3 - - - +
132D HIS* 1.3 63.1 + - + +
134D MET* 4.5 3.8 - - - +
135D GLN* 3.0 42.6 + - - +
141D LEU* 5.8 4.7 - - + -
158D ILE* 6.3 0.7 - - + -
160D ASP* 3.9 21.8 - - - +
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Residues in contact with HIS 132 (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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128D VAL* 3.0 31.4 + - + +
129D SER* 3.4 11.2 - - - +
130D TYR 3.1 0.2 - - - -
131D ALA* 1.3 81.9 - - + +
133D ALA* 1.3 60.5 + - - +
135D GLN 3.4 12.6 - - - +
138D HIS* 5.0 4.3 - + - -
141D LEU* 6.0 0.7 - - + -
196D LYS* 3.2 75.1 + - + +
199D ASP* 2.5 31.7 + - + -
268D ILE* 4.0 21.3 - - + +
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Residues in contact with ALA 133 (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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129D SER 3.1 11.8 + - - +
130D TYR* 3.1 12.0 + - + +
132D HIS* 1.3 78.2 - - - +
134D MET* 1.3 64.3 + - + +
135D GLN 3.3 0.4 - - - -
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Residues in contact with MET 134 (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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71D SER* 4.2 21.3 + - - +
72D LEU* 4.2 17.3 - - + -
130D TYR* 3.0 56.9 + - + +
131D ALA 4.3 1.1 - - - +
132D HIS 3.3 0.4 - - - -
133D ALA* 1.3 86.0 - - + +
135D GLN* 1.3 63.1 + - + +
136D VAL* 3.9 5.5 + - - +
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Residues in contact with GLN 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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68D ASN* 5.2 19.2 + - - +
71D SER* 6.0 0.9 - - - +
72D LEU* 3.9 21.6 - - + +
131D ALA* 3.0 28.5 + - - +
132D HIS* 3.4 14.7 - - - +
133D ALA 3.3 0.8 - - - -
134D MET* 1.3 86.1 - - + +
136D VAL* 1.3 65.9 + - - +
137D ALA 4.3 13.5 - - - +
138D HIS* 5.1 1.3 + - - -
139D ARG* 3.2 37.6 + - - +
160D ASP* 3.5 16.3 + - - +
196D LYS* 4.9 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
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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