Contacts of the helix formed by residues 134 - 157 (chain D) in PDB entry 1IES
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 LEU 134 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D ASN* 4.5 4.2 + - - +
110D LEU* 3.7 36.1 - - + +
111D LEU* 4.3 17.7 - - + -
114D HIS* 3.9 11.7 - - + -
129D LEU* 3.0 16.1 + - + +
130D GLU* 3.8 27.8 + - + +
133D PHE* 1.3 77.5 - - + +
135D ASP* 1.3 61.9 + - - +
137D GLU* 3.4 6.0 - - - +
138D VAL* 3.1 25.6 + - - +
123F PRO* 3.7 33.0 - - + -
124F HIS* 4.3 13.9 - - + +
127F ASP* 4.9 2.7 - - - +
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Residues in contact with ASP 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D GLU 4.4 7.0 + - - +
131D SER 5.5 3.6 - - - +
132D HIS 5.4 0.4 - - - -
133D PHE 3.4 0.6 - - - +
134D LEU* 1.3 75.5 - - - +
136D GLU* 1.3 67.7 + - - +
138D VAL* 2.9 12.5 + - - +
139D LYS* 2.9 46.0 + - - +
71F GLN* 4.6 1.7 + - - -
124F HIS* 3.1 29.0 + - + +
127F ASP* 4.4 9.4 + - - +
128F PHE* 6.1 0.3 - - - -
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Residues in contact with GLU 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D TYR* 5.6 3.6 + - - -
57D GLU* 4.2 28.8 - - - +
58D LYS* 4.7 12.5 + - - +
61D GLY* 6.1 1.4 - - - -
64D ARG* 5.4 6.9 + - - -
132D HIS 3.6 21.2 + - - +
133D PHE* 3.4 15.2 + - - +
135D ASP* 1.3 77.1 - - - +
137D GLU* 1.3 60.8 + - - +
139D LYS* 3.4 7.1 + - - +
140D LEU* 2.9 35.4 + - + +
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Residues in contact with GLU 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D TYR* 3.7 13.7 + - - -
58D LYS* 3.3 20.3 + - - -
103D GLU* 2.7 40.1 - - - +
106D LEU* 4.7 1.8 - - - +
107D ASN* 3.3 40.4 - - + +
110D LEU* 4.0 6.2 - - + +
133D PHE 3.0 17.7 + - - +
134D LEU 3.4 5.6 - - - +
136D GLU* 1.3 81.8 - - - +
138D VAL* 1.3 62.4 + - - +
140D LEU* 3.3 5.1 + - - +
141D ILE* 3.0 32.2 + - + +
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Residues in contact with VAL 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D ASN* 4.7 12.1 - - - +
134D LEU 3.1 13.4 + - - +
135D ASP 2.9 9.1 + - - +
137D GLU* 1.3 74.7 - - - +
139D LYS* 1.3 62.0 + - - +
141D ILE* 3.7 6.4 + - + +
142D LYS* 3.2 22.7 + - - +
71F GLN* 4.0 27.4 - - + +
72F ARG* 4.0 23.1 - - - +
124F HIS* 3.8 42.0 - - + +
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Residues in contact with LYS 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D ASP* 2.9 44.2 + - - +
136D GLU* 3.8 6.1 - - - +
138D VAL* 1.3 73.7 - - - +
140D LEU* 1.3 59.4 + - - +
142D LYS* 3.2 4.9 + - - +
143D LYS* 2.9 27.9 + - - +
67F LYS* 4.6 12.1 - - - +
71F GLN* 3.4 41.1 + - - +
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Residues in contact with LEU 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D PHE* 5.0 1.1 - - + -
54D LEU* 3.6 33.4 - - + -
57D GLU* 4.9 7.2 - - - +
58D LYS* 4.0 8.3 - - - +
103D GLU* 3.5 33.9 - - + +
136D GLU* 2.9 22.9 + - + +
137D GLU* 3.8 5.6 - - - +
139D LYS* 1.3 74.6 - - - +
141D ILE* 1.3 63.4 + - - +
143D LYS* 3.0 29.8 + - + +
144D MET* 2.9 41.4 + - + +
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Residues in contact with ILE 141 (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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100D ILE* 4.1 15.8 - - + +
103D GLU* 3.8 28.7 - - + -
104D LYS* 4.2 7.6 - - + +
107D ASN* 4.0 20.9 - - + +
137D GLU* 3.0 21.5 + - - +
138D VAL* 4.2 6.3 - - + +
140D LEU* 1.3 75.7 - - - +
142D LYS* 1.3 57.0 + - - +
144D MET* 3.3 7.8 + - - +
145D GLY 2.8 24.1 + - - -
4F ILE* 3.7 35.1 - - + +
6F GLN* 3.9 21.8 - - - +
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Residues in contact with LYS 142 (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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138D VAL 3.2 15.8 + - - +
139D LYS* 3.7 8.7 - - - +
140D LEU 3.2 0.2 - - - -
141D ILE* 1.3 76.1 - - - +
143D LYS* 1.3 63.0 + - - +
145D GLY* 2.9 2.5 + - - +
146D ASP* 2.8 55.1 + - - +
4F ILE* 3.9 17.9 - - + +
70F ASN* 3.2 39.6 - - - +
71F GLN* 3.5 26.9 + - + +
75F ARG* 6.1 0.9 - - - +
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Residues in contact with LYS 143 (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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50D PHE* 4.1 21.7 - - + -
54D LEU* 6.0 0.8 - - - +
139D LYS 2.9 14.1 + - - +
140D LEU* 3.4 24.5 - - + +
142D LYS* 1.3 74.4 - - - +
144D MET* 1.3 57.6 + - - +
146D ASP* 3.2 11.7 + - + +
147D HIS* 2.9 59.7 + - + +
174D ASP* 5.9 0.7 - - - +
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Residues in contact with MET 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D TYR* 3.6 16.4 - - - +
50D PHE* 4.0 18.6 - - + -
54D LEU* 3.5 32.3 - - + -
96D MET* 4.6 8.3 - - - +
99D ALA* 3.9 11.0 - - + -
100D ILE* 4.0 31.0 - - + -
103D GLU* 3.9 23.6 - - + -
140D LEU* 2.9 26.3 + - + +
141D ILE* 3.6 9.0 - - - +
143D LYS* 1.3 74.5 - - - +
145D GLY* 1.3 64.3 + - - +
147D HIS* 3.1 9.1 + - - +
148D LEU* 2.9 27.1 + - + +
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Residues in contact with GLY 145 (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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100D ILE* 4.1 4.6 - - - +
141D ILE 2.8 11.5 + - - -
142D LYS 2.9 4.4 + - - -
144D MET* 1.3 74.2 - - - +
146D ASP* 1.3 63.3 + - - +
148D LEU* 3.4 1.1 + - - +
149D THR* 3.2 15.1 + - - +
3F GLN* 2.9 35.7 + - - -
4F ILE* 3.5 17.9 - - - +
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Residues in contact with ASP 146 (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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142D LYS* 2.8 51.5 + - - +
143D LYS* 3.4 11.6 - - + +
145D GLY* 1.3 77.6 - - - +
147D HIS* 1.3 64.8 + - + +
149D THR* 3.4 7.5 + - - -
150D ASN* 3.0 34.0 + - - +
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Residues in contact with HIS 147 (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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50D PHE* 3.7 29.1 - + - -
96D MET* 3.9 21.1 - - + -
143D LYS* 2.9 44.4 + - + +
144D MET* 3.1 7.4 + - - +
146D ASP* 1.3 78.4 - - + +
148D LEU* 1.3 52.0 + - - +
150D ASN* 3.1 4.7 + - - +
151D ILE* 2.8 39.2 + - - +
166D PHE* 3.7 22.1 - + + -
170D THR* 4.0 21.5 - - + +
171D LEU* 4.0 12.0 - - + +
174D ASP* 4.3 9.4 - - - -
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Residues in contact with LEU 148 (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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93D LEU* 3.5 27.4 - - + -
96D MET* 3.6 19.5 - - + +
97D LYS* 3.6 23.8 - - + -
100D ILE* 4.0 37.5 - - + -
144D MET* 2.9 13.1 + - + +
145D GLY 3.6 3.6 - - - +
147D HIS* 1.3 74.6 - - - +
149D THR* 1.3 58.8 + - - +
151D ILE* 3.2 5.4 + - - +
152D GLN* 2.7 39.5 + - - +
3F GLN* 3.3 26.7 - - + +
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Residues in contact with THR 149 (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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145D GLY 3.2 5.2 + - - +
146D ASP* 3.5 9.4 + - - -
148D LEU* 1.3 75.8 - - - +
150D ASN* 1.3 61.2 + - - +
152D GLN* 3.4 12.3 + - - +
153D ARG* 3.0 42.4 + - - +
3F GLN* 3.3 29.4 - - - +
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Residues in contact with ASN 150 (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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146D ASP* 3.0 25.0 + - - +
147D HIS* 3.5 7.0 + - - +
149D THR* 1.3 76.3 + - - +
151D ILE* 1.3 65.0 + - - +
153D ARG* 2.8 41.8 + - - +
154D LEU* 3.2 28.4 + - + +
166D PHE* 4.0 17.7 - - + -
170D THR* 5.6 3.5 - - - +
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Residues in contact with ILE 151 (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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92D THR* 3.6 24.9 - - + +
93D LEU* 4.2 24.5 - - + +
96D MET* 3.4 35.4 - - + -
147D HIS 2.8 25.1 + - - +
148D LEU* 3.8 4.9 - - - +
150D ASN* 1.3 71.0 - - - +
152D GLN* 1.3 62.5 + - - +
154D LEU* 3.2 8.5 + - + +
155D VAL* 2.9 45.5 + - + +
163D GLU* 5.4 2.9 - - + -
166D PHE* 3.7 28.0 - - + -
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Residues in contact with GLN 152 (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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93D LEU* 3.8 19.8 - - + +
97D LYS* 3.7 30.9 - - - +
148D LEU* 2.7 32.5 + - - +
149D THR* 3.7 12.4 - - - +
151D ILE* 1.3 72.4 - - - +
153D ARG* 1.3 60.5 + - - +
155D VAL* 4.5 3.8 - - - +
156D GLY* 3.3 19.6 + - - -
3F GLN* 5.0 3.3 - - - +
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Residues in contact with ARG 153 (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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149D THR* 3.0 27.1 + - - +
150D ASN* 2.8 57.3 - - - +
152D GLN* 1.3 73.0 - - - +
154D LEU* 1.3 67.5 + - + +
156D GLY* 4.1 0.5 - - - -
157D SER* 3.4 23.6 + - - -
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Residues in contact with LEU 154 (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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150D ASN* 3.2 20.5 + - + +
151D ILE* 3.2 4.9 + - - +
153D ARG* 1.3 84.0 - - + +
155D VAL* 1.3 63.3 + - + +
157D SER* 3.3 7.1 + - - -
158D GLN 3.2 23.9 + - - +
162D GLY* 3.7 26.3 - - - +
165D LEU* 4.9 14.6 - - + -
166D PHE* 3.7 39.3 - - + +
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Residues in contact with VAL 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D LEU* 4.6 22.4 - - + -
151D ILE* 2.9 31.7 + - + +
152D GLN* 4.5 2.7 - - - +
154D LEU* 1.3 74.4 - - + +
156D GLY* 1.3 66.4 + - - +
159D ALA* 3.2 50.4 + - + +
162D GLY 4.5 0.9 - - - -
163D GLU* 4.1 17.7 - - + +
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Residues in contact with GLY 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152D GLN 3.3 16.4 + - - -
153D ARG* 4.1 1.1 - - - -
154D LEU 3.2 1.2 - - - -
155D VAL* 1.3 79.4 - - - +
157D SER* 1.4 68.1 + - - +
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Residues in contact with SER 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153D ARG 3.4 14.0 + - - -
154D LEU* 3.3 8.4 + - - -
156D GLY* 1.4 77.9 - - - +
158D GLN* 1.3 70.3 + - - +
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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