Contacts of the helix formed by residues 134 - 157 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A PRO* 3.7 33.4 - - + -
124A HIS* 4.0 15.9 - - + +
127A ASP* 5.5 1.6 - - + +
107B ASN* 4.5 4.6 + - - +
110B LEU* 3.7 36.1 - - + +
111B LEU* 4.2 19.5 - - + -
114B HIS* 3.9 12.6 - - + -
129B LEU* 3.0 15.3 + - + +
130B GLU* 3.8 27.3 + - + +
133B PHE* 1.3 77.6 - - - +
135B ASP* 1.3 61.9 + - - +
137B GLU* 3.6 4.7 - - - +
138B VAL* 3.3 25.3 + - - +
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Residues in contact with ASP 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLN* 4.6 2.4 + - - -
124A HIS* 3.2 27.9 + - + +
127A ASP* 4.6 10.7 + - - +
130B GLU 4.1 8.7 + - - +
131B SER 5.5 3.6 - - - +
133B PHE 3.3 0.4 - - - +
134B LEU* 1.3 75.2 - - - +
136B GLU* 1.3 66.3 + - - +
137B GLU 3.1 1.6 - - - -
138B VAL* 2.9 12.5 + - - +
139B LYS* 2.9 45.5 + - - +
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Residues in contact with GLU 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B TYR* 5.5 4.2 + - - -
57B GLU* 4.0 30.3 - - - +
58B LYS* 4.6 13.2 + - - +
61B GLY* 6.0 1.6 - - - -
132B HIS 3.7 21.0 + - - +
133B PHE* 3.4 14.6 + - - +
135B ASP* 1.3 75.9 + - - +
137B GLU* 1.3 61.9 + - - +
139B LYS* 3.5 8.8 + - - +
140B LEU* 2.9 33.4 + - + +
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Residues in contact with GLU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B TYR* 3.9 11.1 + - - -
58B LYS* 3.3 20.6 + - - -
103B GLU* 2.7 41.7 - - - +
106B LEU* 4.8 2.5 - - - -
107B ASN* 3.3 36.3 - - + +
110B LEU* 3.9 9.4 - - + -
133B PHE 3.1 15.1 - - - +
134B LEU 3.6 5.8 - - - +
136B GLU* 1.3 83.7 - - - +
138B VAL* 1.3 63.1 + - - +
140B LEU* 4.6 4.0 - - - +
141B ILE* 3.1 33.2 + - - +
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Residues in contact with VAL 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLN* 3.9 32.8 - - + +
72A ARG* 4.0 20.6 - - - +
124A HIS* 3.8 40.2 - - + +
107B ASN* 4.8 11.2 - - - +
134B LEU 3.3 12.7 + - - +
135B ASP 2.9 11.9 + - - +
137B GLU* 1.3 74.3 - - - +
139B LYS* 1.3 62.8 + - - +
141B ILE* 4.0 4.9 - - + +
142B LYS* 3.2 21.5 + - - +
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Residues in contact with LYS 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LYS* 5.0 9.5 - - - +
71A GLN* 3.6 35.2 + - - +
135B ASP* 2.9 41.5 + - - +
136B GLU* 3.9 6.3 - - - +
138B VAL* 1.3 75.5 - - - +
140B LEU* 1.3 63.8 + - - +
142B LYS* 3.1 7.3 + - - +
143B LYS* 2.9 23.6 + - - +
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Residues in contact with LEU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B PHE* 4.9 2.0 - - + -
54B LEU* 3.7 32.1 - - + -
57B GLU* 5.0 6.7 - - - +
58B LYS* 4.1 8.1 - - - +
103B GLU* 3.4 35.2 - - + +
136B GLU* 2.9 22.0 + - + +
137B GLU* 4.2 4.7 - - - +
139B LYS* 1.3 75.9 - - - +
141B ILE* 1.3 63.4 + - - +
143B LYS* 3.1 30.6 + - + +
144B MET* 2.9 39.7 + - + +
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Residues in contact with ILE 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ILE* 3.3 37.0 - - + +
6A GLN* 4.0 21.1 - - - +
100B ILE* 4.2 14.5 - - + +
103B GLU* 3.8 27.8 - - + +
104B LYS* 4.2 8.5 - - + +
107B ASN* 4.0 20.2 - - + +
137B GLU* 3.1 23.1 + - - +
138B VAL* 4.2 5.2 - - - +
140B LEU* 1.3 76.2 - - - +
142B LYS* 1.3 61.2 + - - +
144B MET* 3.9 7.8 - - - +
145B GLY 3.0 17.7 + - - -
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Residues in contact with LYS 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ILE* 4.0 19.0 - - + +
70A ASN* 3.4 37.4 - - + +
71A GLN* 3.5 24.4 + - + +
75A ARG* 6.1 1.6 - - - +
138B VAL 3.2 14.2 + - - +
139B LYS* 3.1 11.0 + - - +
141B ILE* 1.3 76.2 - - - +
143B LYS* 1.3 58.0 + - - +
145B GLY* 3.0 2.8 + - - -
146B ASP* 2.8 62.5 + - - +
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Residues in contact with LYS 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B PHE* 4.1 21.2 - - + -
54B LEU* 5.8 0.8 - - - +
139B LYS 2.9 12.8 + - - +
140B LEU* 3.1 27.4 + - + +
142B LYS* 1.3 74.2 - - - +
144B MET* 1.3 56.9 + - - +
146B ASP* 3.1 12.6 + - + +
147B HIS* 2.9 58.1 + - + +
174B ASP* 5.9 1.3 - - - +
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Residues in contact with MET 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B TYR* 3.8 15.0 - - - +
50B PHE* 4.1 16.8 - - + -
54B LEU* 3.5 31.4 - - + -
96B MET* 4.5 9.3 - - - +
99B ALA* 4.0 10.1 - - + -
100B ILE* 4.0 34.3 - - + -
103B GLU* 3.9 18.8 - - + -
140B LEU* 2.9 32.7 + - + +
141B ILE* 3.9 4.5 - - - +
143B LYS* 1.3 74.8 - - - +
145B GLY* 1.3 61.1 + - - +
147B HIS* 3.3 8.6 + - - +
148B LEU* 2.9 26.0 + - - +
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Residues in contact with GLY 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GLN* 3.0 33.0 + - - -
4A ILE* 3.7 17.7 - - - -
100B ILE* 4.0 5.3 - - - +
141B ILE 3.0 7.5 + - - -
142B LYS* 3.0 7.6 + - - -
144B MET* 1.3 75.6 - - - +
146B ASP* 1.3 62.8 + - - +
148B LEU* 3.4 0.4 + - - -
149B THR* 3.2 15.4 + - - +
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Residues in contact with ASP 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B LYS* 2.8 49.0 + - - +
143B LYS* 3.3 13.9 - - + +
145B GLY* 1.3 76.2 - - - +
147B HIS* 1.3 64.5 + - - +
149B THR* 3.4 7.6 + - - -
150B ASN* 3.1 32.8 + - - +
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Residues in contact with HIS 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B PHE* 3.9 19.2 - + - -
96B MET* 3.7 31.9 - - + -
143B LYS* 2.9 47.6 + - + +
144B MET* 3.6 7.0 - - - +
146B ASP* 1.3 75.0 - - + +
148B LEU* 1.3 56.9 + - - +
150B ASN* 3.2 3.3 + - - +
151B ILE* 2.8 34.9 + - - +
166B PHE* 3.8 22.9 - + + -
170B THR* 4.0 22.1 - - + +
171B LEU* 3.9 10.4 - - + +
174B ASP* 4.2 10.3 - - - -
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Residues in contact with LEU 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GLN* 3.5 24.5 - - + +
93B LEU* 3.4 29.2 - - + -
96B MET* 4.0 16.8 - - + +
97B LYS* 3.6 25.6 - - + -
100B ILE* 4.1 37.2 - - + -
144B MET 2.9 16.2 + - - +
145B GLY 3.4 6.5 + - - +
147B HIS* 1.3 71.1 - - - +
149B THR* 1.3 57.3 + - - +
151B ILE* 3.9 5.4 - - - +
152B GLN* 2.8 40.1 + - - +
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Residues in contact with THR 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A GLN* 3.4 27.1 - - - +
145B GLY 3.2 6.9 + - - +
146B ASP* 3.5 9.5 + - - -
147B HIS 3.3 0.2 - - - -
148B LEU* 1.3 75.2 - - - +
150B ASN* 1.3 60.6 + - - +
152B GLN* 3.5 10.8 + - - +
153B ARG* 3.0 43.7 + - - +
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Residues in contact with ASN 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B ASP* 3.1 24.8 + - - +
147B HIS* 3.6 3.7 + - - +
149B THR* 1.3 75.3 + - - +
151B ILE* 1.3 64.8 + - - +
153B ARG* 2.7 43.3 + - - +
154B LEU* 3.3 28.2 + - + +
166B PHE* 4.0 17.5 - - + -
170B THR* 5.5 4.6 - - - +
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Residues in contact with ILE 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B THR* 3.7 22.2 - - + +
93B LEU* 4.2 26.2 - - + +
96B MET* 3.4 35.9 - - + -
147B HIS 2.8 27.0 + - - +
148B LEU* 3.9 4.3 - - - +
150B ASN* 1.3 69.8 - - - +
152B GLN* 1.3 64.0 + - - +
154B LEU* 3.1 5.9 + - + -
155B VAL* 2.9 46.6 + - + +
163B GLU* 5.5 1.6 - - + -
166B PHE* 3.7 31.9 - - + -
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Residues in contact with GLN 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A GLN* 4.8 5.8 + - - +
93B LEU* 3.8 19.8 - - + +
97B LYS* 3.8 29.1 - - - +
148B LEU* 2.8 34.7 + - - +
149B THR* 3.8 10.1 - - - +
150B ASN 3.4 0.2 - - - -
151B ILE* 1.3 72.2 - - - +
153B ARG* 1.3 61.0 + - - +
155B VAL* 4.7 5.1 - - + +
156B GLY* 3.2 19.2 + - - -
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Residues in contact with ARG 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B THR* 3.0 24.1 + - - +
150B ASN* 2.7 58.0 + - - +
151B ILE 3.3 0.2 - - - -
152B GLN* 1.3 76.2 - - - +
154B LEU* 1.3 66.3 + - + +
156B GLY* 4.1 0.9 - - - -
157B SER* 3.4 23.2 + - - -
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Residues in contact with LEU 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B ASN* 3.3 17.6 + - + +
151B ILE* 3.1 5.5 + - - +
153B ARG* 1.3 80.7 - - + +
155B VAL* 1.3 66.0 + - + +
157B SER* 3.0 16.1 + - - -
158B GLN 3.1 16.6 + - - +
162B GLY* 3.6 25.4 - - - +
165B LEU* 4.7 17.0 - - + -
166B PHE* 3.7 41.1 - - + +
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Residues in contact with VAL 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B THR* 6.5 0.4 - - - -
93B LEU* 4.6 24.2 - - + +
151B ILE* 2.9 33.0 + - + +
152B GLN* 4.9 2.9 - - + +
154B LEU* 1.3 74.7 - - - +
156B GLY* 1.3 67.7 + - - +
159B ALA* 3.4 48.8 + - + +
162B GLY 4.5 0.4 - - - -
163B GLU* 4.0 19.1 - - + +
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Residues in contact with GLY 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B GLN 3.2 19.0 + - - -
153B ARG 4.1 1.3 - - - -
154B LEU 3.2 0.8 - - - -
155B VAL* 1.3 81.2 - - - +
157B SER* 1.4 63.1 + - - +
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Residues in contact with SER 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ARG 3.4 12.9 + - - -
154B LEU* 3.0 10.7 + - - -
155B VAL 4.4 0.3 - - - +
156B GLY* 1.4 80.8 - - - +
158B GLN* 1.3 69.8 + - - +
159B ALA 4.0 0.6 + - - -
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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
------------------------------------------------------------
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