Contacts of the helix formed by residues 112 - 134 (chain D) in PDB entry 1ZWS
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 112 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110D SER* 5.1 1.0 + - - -
111D LEU* 1.3 75.9 - - - +
113D GLU* 1.3 53.3 + - - +
114D GLU* 3.7 10.3 + - - +
115D GLU* 2.7 42.9 + - - +
116D ALA* 2.7 33.5 + - - +
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Residues in contact with GLU 113 (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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111D LEU 3.7 2.5 + - - +
112D SER* 1.3 72.0 - - - +
114D GLU* 1.3 54.8 + - - +
116D ALA* 2.8 10.7 + - - +
117D THR* 2.6 40.0 + - - +
211D LEU* 5.0 8.3 - - + -
243D HIS 4.4 0.9 - - - +
244D THR* 3.1 15.5 - - - +
245D SER* 2.5 45.0 + - - -
248D ALA* 4.1 5.4 - - - -
274D TRP* 2.7 34.5 + - + +
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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
----------------------------------------------------------
112D SER* 3.2 9.1 + - - +
113D GLU* 1.3 78.5 - - - +
115D GLU* 1.3 59.0 + - - +
117D THR* 2.4 27.5 + - - +
118D SER* 2.9 13.7 + - - -
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Residues in contact with GLU 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D LYS* 3.0 32.2 + - - +
110D SER 4.0 4.3 - - - +
111D LEU* 3.4 18.2 - - + +
112D SER* 2.7 37.1 + - - +
114D GLU* 1.3 75.2 + - - +
116D ALA* 1.3 57.2 + - - +
118D SER* 2.5 31.0 + - - -
119D PHE* 2.9 24.9 - - + -
154D ILE* 4.3 17.5 - - + +
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Residues in contact with ALA 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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111D LEU* 3.6 22.0 - - + +
112D SER 2.7 16.8 + - - +
113D GLU* 2.8 14.3 + - - +
115D GLU* 1.3 69.2 - - - +
117D THR* 1.3 66.1 + - - +
118D SER 2.9 3.0 + - - -
119D PHE* 3.0 24.4 + - - +
120D ILE* 3.1 16.1 + - - +
210D LEU* 3.7 15.0 - - + +
211D LEU* 4.1 9.6 - - + -
274D TRP* 4.8 2.0 - - + -
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Residues in contact with THR 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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113D GLU 2.6 13.8 + - - +
114D GLU* 2.4 37.3 + - - +
116D ALA* 1.3 72.6 - - - +
118D SER* 1.3 52.2 + - - +
120D ILE* 3.7 9.1 - - - +
121D LYS* 2.7 36.6 + - - +
274D TRP* 3.3 64.8 + - + +
275D ILE* 4.2 10.0 - - + +
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Residues in contact with SER 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 2.9 13.6 + - - -
115D GLU* 2.5 27.0 + - - +
117D THR* 1.3 79.7 + - - +
119D PHE* 1.3 68.2 + - - +
121D LYS* 3.1 6.7 + - - +
122D GLN* 3.1 22.5 + - - +
154D ILE* 4.6 20.2 - - - +
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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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101D LEU* 4.1 24.0 - - + -
104D PHE* 4.6 3.1 - + - -
105D LEU* 3.8 21.1 - - + -
108D LYS* 4.5 9.6 - - - -
111D LEU* 3.8 11.4 - - + -
115D GLU* 2.9 49.8 - - + -
116D ALA* 3.0 11.0 + - - +
118D SER* 1.3 73.4 - - - +
120D ILE* 1.3 69.5 + - - +
122D GLN* 2.6 29.8 + - - +
123D ILE* 3.0 13.8 + - + +
154D ILE* 4.8 13.5 - - + -
155D PRO* 4.4 21.8 - - + -
157D ILE* 3.6 25.1 - - + -
210D LEU* 5.0 9.2 - - + -
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Residues in contact with ILE 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 ALA 3.1 15.9 + - - +
117D THR* 3.7 10.8 - - - +
119D PHE* 1.3 78.1 - - - +
121D LYS* 1.3 62.9 + - - +
123D ILE* 3.1 21.0 - - + +
124D LEU* 2.9 28.5 + - + +
203D ILE* 4.7 7.6 - - + +
206D ILE* 4.8 3.6 - - + -
207D THR* 3.4 30.7 - - + +
210D LEU* 3.3 27.8 - - + -
251D PHE* 4.0 27.1 - - + -
274D TRP* 4.4 9.4 - - + -
275D ILE* 4.3 7.6 - - + -
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Residues in contact with LYS 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 THR 2.7 22.7 + - - +
118D SER* 3.2 8.1 - - - +
119D PHE 2.7 2.8 + - - -
120D ILE* 1.3 69.0 - - - +
122D GLN* 1.3 58.6 + - + +
124D LEU* 2.7 33.3 + - - +
125D ASP* 2.7 52.9 + - - +
270D LEU* 4.3 10.3 - - + +
275D ILE* 4.0 29.4 - - + +
276D THR* 4.6 7.0 - - - -
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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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74D HIS* 5.2 1.2 + - - -
75D ASN* 3.6 24.2 + - - +
118D SER 3.5 10.1 + - - +
119D PHE* 2.6 19.8 + - - +
121D LYS* 1.3 73.9 - - + +
123D ILE* 1.3 63.6 + - - +
125D ASP* 2.9 21.0 + - - +
126D GLY* 3.0 11.1 + - - -
154D ILE* 4.2 14.8 - - - +
155D PRO 2.9 24.5 + - - +
156D HIS* 3.6 6.6 + - - -
157D ILE* 3.0 44.0 + - + +
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Residues in contact with ILE 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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101D LEU* 4.7 9.6 - - + -
119D PHE* 3.0 8.4 + - + +
120D ILE* 3.1 33.4 - - + +
122D GLN* 1.3 77.2 - - - +
124D LEU* 1.3 54.4 + - - +
126D GLY* 3.4 0.9 + - - -
127D VAL* 2.8 47.4 + - + +
140D LEU* 5.6 1.6 - - + -
145D ILE* 4.1 32.3 - - + -
157D ILE* 4.1 23.1 - - + +
159D LEU* 4.5 7.4 - - + +
203D ILE* 4.1 20.9 - - + -
206D ILE* 4.8 13.0 - - + -
210D LEU* 6.0 0.4 - - + -
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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 ILE* 2.9 20.5 + - + +
121D LYS* 2.7 24.7 + - - +
123D ILE* 1.3 72.3 - - + +
125D ASP* 1.3 50.1 + - - +
127D VAL* 3.3 0.8 + - - -
128D ASN* 2.7 37.6 + - - +
203D ILE* 4.2 26.5 - - + -
251D PHE* 4.3 7.9 - - + -
266D ILE* 3.6 25.8 - - + +
269D ALA* 4.4 14.8 - - + +
270D LEU* 3.4 30.5 - - + -
275D ILE* 4.0 27.1 - - + -
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Residues in contact with ASP 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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73D HIS* 3.3 18.9 + - - +
74D HIS* 5.7 0.9 - - + -
75D ASN* 3.7 13.6 - - - +
121D LYS* 2.7 58.9 + - - +
122D GLN* 2.9 8.7 + - - +
124D LEU* 1.3 72.5 - - - +
126D GLY* 1.3 60.9 + - - +
128D ASN* 3.5 10.3 + - - +
129D TYR 3.3 13.7 + - - -
270D LEU* 4.7 9.4 - - - +
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Residues in contact with GLY 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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73D HIS* 4.1 5.2 - - - -
75D ASN* 3.9 22.6 - - - +
76D VAL* 4.1 13.2 - - - +
122D GLN 3.0 10.1 + - - -
123D ILE 3.9 2.5 - - - -
125D ASP* 1.3 76.6 - - - +
127D VAL* 1.3 65.7 + - - +
129D TYR* 3.2 13.9 + - - +
130D LEU* 3.3 15.9 + - - +
159D LEU* 4.7 4.0 - - - -
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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 ILE* 2.8 44.0 + - + +
124D LEU* 3.7 3.6 - - - +
126D GLY* 1.3 74.0 - - - +
128D ASN* 1.3 64.8 + - - +
130D LEU* 2.9 24.5 + - + +
131D HIS* 2.9 46.5 + - + +
140D LEU* 4.4 7.9 - - + -
159D LEU* 4.0 14.0 - - + +
199D ASP* 4.9 4.7 - - + +
200D MET* 5.2 1.3 - - - -
203D ILE* 4.1 17.7 - - + -
266D ILE* 4.1 15.3 - - + -
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Residues in contact with ASN 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 2.7 23.5 + - - +
125D ASP* 3.5 12.1 + - - +
127D VAL* 1.3 73.6 - - - +
129D TYR* 1.3 65.2 + - - +
131D HIS* 3.4 2.5 + - - +
132D THR* 2.7 35.6 + - - -
266D ILE* 3.8 25.1 - - + +
267D GLN* 3.7 20.6 + - - +
270D LEU* 4.2 18.0 - - + +
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Residues in contact with TYR 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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70D GLN 3.6 3.8 + - - -
71D VAL* 3.7 22.4 - - + -
72D LEU* 3.6 38.6 + - - +
73D HIS* 3.5 41.3 - + + -
76D VAL* 5.2 1.8 - - + -
125D ASP 3.3 2.0 + - - -
126D GLY 3.2 10.6 + - - +
128D ASN* 1.3 80.8 - - - +
130D LEU* 1.3 72.3 + - + +
132D THR* 3.2 12.7 + - - -
133D LYS* 3.2 43.9 + - + +
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Residues in contact with LEU 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 VAL* 3.9 26.2 - - + -
76D VAL* 4.7 9.2 - - + -
126D GLY 3.5 8.7 - - - +
127D VAL* 2.9 26.1 + - + +
129D TYR* 1.3 79.3 - - + +
131D HIS* 1.3 56.7 + - + +
133D LYS* 2.4 37.4 + - - +
134D LYS 3.1 4.7 + - - -
135D ILE* 3.5 26.5 + - + +
137D HIS* 4.4 26.7 - - + +
159D LEU* 4.6 13.0 - - + -
162D PHE* 4.0 22.7 - - + -
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Residues in contact with HIS 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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127D VAL* 2.9 36.2 + - + +
128D ASN 3.8 3.6 - - - +
130D LEU* 1.3 79.6 - - + +
132D THR* 1.3 54.2 + - - +
134D LYS* 2.6 27.9 + - - +
135D ILE 3.3 16.9 + - - +
196D LEU* 3.4 53.1 + - + +
199D ASP* 3.1 30.8 - - + +
200D MET* 4.5 8.1 - - + -
266D ILE* 4.2 32.1 - - + -
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Residues in contact with THR 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 ASN* 2.7 31.1 + - - -
129D TYR* 3.3 11.2 - - - -
130D LEU 2.6 4.9 + - - -
131D HIS* 1.3 70.1 - - - +
133D LYS* 1.3 56.8 - - + -
134D LYS* 2.8 22.2 + - - +
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Residues in contact with LYS 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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70D GLN* 3.3 41.6 + - + +
71D VAL* 5.4 1.6 - - + -
129D TYR* 3.4 46.2 + - + +
130D LEU* 2.4 17.9 + - - +
132D THR* 1.3 72.3 - - + +
134D LYS* 1.3 72.2 + - - +
135D ILE* 3.6 21.9 - - + +
167D GLU* 4.6 6.4 - - - +
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Residues in contact with LYS 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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131D HIS* 2.6 17.8 + - - +
132D THR 2.8 12.6 + - - +
133D LYS* 1.3 86.6 - - - +
135D ILE* 1.3 59.8 + - - +
167D GLU* 3.5 6.7 - - + +
168D ILE* 3.4 39.6 + - + +
169D GLU* 6.5 0.4 - - - +
170D ASP* 5.1 18.1 + - - +
196D LEU* 4.4 14.6 - - + -
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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