Contacts of the helix formed by residues 136 - 157 (chain B) in PDB entry 3PL7
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 ASN 136 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ASN* 3.6 15.0 - - - +
139A ARG* 4.2 9.3 - - - +
135B VAL* 1.3 75.1 - - - +
137B TRP* 1.3 64.0 + - - +
138B GLY* 2.9 7.1 + - - -
139B ARG* 2.7 58.8 + - - +
140B ILE* 3.1 22.9 + - - +
181B TRP* 3.6 17.7 - - + -
68C ASP* 3.4 36.4 + - - +
71C ASP* 4.9 0.4 + - - -
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Residues in contact with TRP 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ASN* 1.3 71.6 - - - +
138B GLY* 1.3 59.8 + - - +
140B ILE* 3.1 25.2 + - + +
141B VAL* 2.8 34.2 + - - +
181B TRP* 3.6 26.0 - + - -
182B ILE* 3.8 24.2 - - + -
185B ASN 5.2 2.0 + - - -
187B GLY* 3.3 27.6 - - - -
188B TRP* 3.6 35.0 - + - -
190B THR* 3.2 25.6 - - + +
191B PHE* 3.7 33.6 - + + +
194B LEU* 3.8 25.4 - - + -
195B TYR* 4.1 17.7 - - + -
68C ASP* 4.9 1.2 + - - +
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Residues in contact with GLY 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B PHE* 4.4 3.1 - - - -
136B ASN* 2.9 8.4 + - - -
137B TRP* 1.3 76.8 - - - +
139B ARG* 1.3 58.2 + - - +
141B VAL* 3.3 4.0 + - - +
142B ALA* 2.9 24.1 + - - +
194B LEU* 5.9 0.2 - - - +
195B TYR* 3.7 16.9 + - - -
65C ARG* 6.5 0.2 - - - -
68C ASP* 4.2 15.9 + - - +
69C GLU* 4.3 5.8 - - - -
72C SER* 3.1 15.7 + - - -
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Residues in contact with ARG 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ASN* 4.6 9.4 - - - +
130B LEU* 3.7 29.3 + - + +
131B PHE* 3.6 20.8 - - + -
133B ASP* 4.0 25.9 + - - +
134B GLY 3.0 34.2 + - - -
135B VAL 4.9 0.4 - - - -
136B ASN* 2.7 38.0 + - - +
138B GLY* 1.3 72.1 - - - -
140B ILE* 1.3 57.4 + - - +
142B ALA* 3.2 6.3 + - - +
143B PHE* 2.9 26.3 + - - +
71C ASP* 2.8 31.1 + - - -
72C SER* 3.2 18.3 + - - +
75C GLU* 4.4 13.9 + - - +
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Residues in contact with ILE 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B LEU* 5.6 0.9 - - + -
131B PHE* 4.2 6.3 - - + -
135B VAL* 3.8 24.9 - - + -
136B ASN 3.1 13.0 + - - +
137B TRP* 3.5 33.9 - - + +
139B ARG* 1.3 74.4 - - - +
141B VAL* 1.3 68.3 + - + +
143B PHE* 3.0 19.9 + - + +
144B PHE* 3.1 35.4 + - + -
174B LEU* 5.3 1.3 - - + -
178B LEU* 4.5 11.0 - - + -
181B TRP* 4.0 3.6 - - + -
182B ILE* 4.0 20.2 - - + -
188B TRP* 4.2 15.3 - - + -
191B PHE* 6.0 0.2 - - + -
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Residues in contact with VAL 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B LEU* 4.5 11.9 - - + -
93B ALA* 3.8 34.1 - - + +
94B GLY* 4.3 2.6 - - - +
97B PHE* 4.1 17.9 - - + -
137B TRP 2.8 20.9 + - - +
138B GLY 3.6 7.0 - - - +
140B ILE* 1.3 72.5 - - + +
142B ALA* 1.3 62.5 + - - +
143B PHE 3.4 0.2 + - - -
144B PHE* 3.5 2.7 + - + +
145B SER* 3.3 21.6 + - - +
191B PHE* 3.7 29.2 - - + -
195B TYR* 3.7 18.2 - - + +
69C GLU* 4.6 2.9 - - - +
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Residues in contact with ALA 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B PHE* 3.7 29.8 - - + -
105B PHE* 3.8 4.5 - - - -
130B LEU* 4.1 14.8 - - + +
138B GLY 2.9 14.5 + - - +
139B ARG* 3.2 11.7 - - - +
140B ILE 3.1 0.2 - - - -
141B VAL* 1.3 76.9 - - - +
143B PHE* 1.3 57.3 + - - +
145B SER* 3.5 2.6 + - - -
146B PHE* 3.0 28.8 + - - +
72C SER* 3.9 11.4 - - - -
76C LEU* 4.8 6.6 - - + +
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Residues in contact with PHE 143 (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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9B VAL* 5.7 0.2 - - + -
123B PHE* 4.2 17.9 - + - -
127B VAL* 3.6 34.1 - - + -
130B LEU* 4.0 7.2 - - + -
131B PHE* 3.6 16.2 - + + -
139B ARG 2.9 12.3 + - - +
140B ILE* 3.0 7.8 + - + +
142B ALA* 1.3 74.7 - - - +
144B PHE* 1.3 91.0 + + - +
146B PHE* 3.3 6.7 + - - +
147B GLY* 3.1 18.7 + - - -
170B MET* 3.6 45.1 - - + +
173B TYR* 4.1 9.9 - + + -
174B LEU* 4.4 6.5 - - + -
178B LEU* 3.8 21.5 - - + -
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Residues in contact with PHE 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 4.5 4.7 - - + -
9B VAL* 4.1 29.6 - - + -
12B PHE* 3.3 34.7 - + + -
90B LEU* 3.7 37.2 - - + -
140B ILE* 3.1 41.6 + - + -
141B VAL* 4.0 5.4 - - + +
143B PHE* 1.3 88.0 - + - +
145B SER* 1.3 52.7 + - - +
147B GLY* 3.2 2.1 + - - -
148B GLY 2.7 31.7 + - - -
170B MET* 3.8 19.2 - - + +
174B LEU* 4.4 20.2 - - + -
188B TRP* 4.0 17.3 - + - -
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Residues in contact with SER 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PHE* 4.4 6.3 - - - -
16B LYS* 5.7 1.6 + - - -
94B GLY* 3.8 28.6 + - - -
97B PHE* 3.9 9.9 - - - +
98B GLU* 5.3 3.1 - - - +
105B PHE* 3.5 27.1 - - - -
141B VAL 3.3 15.1 + - - -
142B ALA 3.7 0.9 - - - -
143B PHE 3.3 0.2 - - - -
144B PHE* 1.3 75.4 - - - +
146B PHE* 1.3 61.1 + - - +
148B GLY* 3.7 0.8 - - - +
149B ALA* 2.8 32.2 + - - +
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Residues in contact with PHE 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B PHE* 3.5 27.0 - + + -
108B LEU* 4.7 14.4 - - + -
109B THR* 4.8 7.1 - - + +
112B LEU* 3.7 32.1 - - + -
123B PHE* 3.8 19.7 - + - -
126B VAL* 4.0 15.0 - - + -
127B VAL* 4.0 21.3 - - + -
130B LEU* 5.7 2.5 - - + -
142B ALA 3.0 15.5 + - - +
143B PHE* 3.3 12.3 + - - +
145B SER* 1.3 75.4 - - - +
147B GLY* 1.3 59.3 + - - +
149B ALA* 3.1 4.3 + - - +
150B LEU* 2.8 57.1 + - + +
76C LEU* 5.2 6.5 - - + -
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Residues in contact with GLY 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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13B LEU* 4.1 5.6 - - - -
123B PHE* 5.3 0.7 - - - -
143B PHE 3.1 12.0 + - - -
144B PHE 3.6 2.9 - - - -
146B PHE* 1.3 82.3 - - - +
148B GLY* 1.3 62.5 + - - +
150B LEU* 3.1 9.7 + - - +
151B CYS* 3.0 26.9 + - - -
166B ILE* 3.9 4.7 - - - +
170B MET* 3.8 22.2 - - - -
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Residues in contact with GLY 148 (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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12B PHE* 4.4 8.1 - - - -
13B LEU* 3.6 20.5 - - - +
16B LYS* 4.9 13.1 - - - +
144B PHE 2.7 19.2 + - - -
145B SER* 3.7 2.0 - - - -
147B GLY* 1.3 71.6 - - - +
149B ALA* 1.3 56.9 + - - +
151B CYS* 3.4 4.5 + - - +
152B VAL* 3.1 32.3 + - - +
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Residues in contact with ALA 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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105B PHE* 4.3 26.7 - - + -
109B THR* 4.5 8.9 - - + +
145B SER 2.8 17.1 + - - +
146B PHE 3.6 3.1 - - - +
148B GLY* 1.3 76.1 - - - +
150B LEU* 1.3 60.8 + - - +
152B VAL* 3.8 8.6 - - - +
153B GLU* 3.0 30.7 + - - +
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Residues in contact with LEU 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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109B THR* 3.7 28.7 - - + +
112B LEU* 4.8 0.7 - - + -
114B ILE* 4.3 33.7 - - + -
123B PHE* 4.1 18.4 - - + -
146B PHE* 2.8 47.0 + - + +
147B GLY* 3.1 10.3 + - - +
149B ALA* 1.3 74.9 - - - +
151B CYS* 1.3 65.2 + - - +
153B GLU* 3.5 3.9 + - + +
154B SER* 2.8 28.7 + - - +
166B ILE* 3.6 21.3 - - + -
169B TRP* 5.5 1.6 - - + -
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Residues in contact with CYS 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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13B LEU* 3.7 32.8 - - + -
17B LEU* 4.4 14.4 - - + -
147B GLY 3.0 17.8 + - - -
148B GLY* 3.6 9.0 - - - +
150B LEU* 1.3 77.6 - - - +
152B VAL* 1.3 63.0 + - - +
154B SER* 3.0 13.9 + - - -
155B VAL* 3.2 19.7 + - - +
163B VAL* 3.9 29.2 - - + -
166B ILE* 3.7 20.0 - - - -
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Residues in contact with VAL 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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16B LYS* 4.6 11.4 - - + +
17B LEU* 4.8 14.6 - - + -
20B LYS* 4.0 42.0 - - + -
22B TYR* 5.1 4.3 - - + -
148B GLY 3.1 20.8 + - - +
149B ALA* 3.8 7.9 - - - +
150B LEU 3.2 0.2 - - - -
151B CYS* 1.3 78.0 - - - +
153B GLU* 1.3 61.9 + - - +
155B VAL* 3.3 4.5 + - - +
156B ASP* 3.2 39.0 + - - +
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Residues in contact with GLU 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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109B THR* 4.4 34.3 - - - +
110B SER* 4.7 9.3 + - - -
149B ALA 3.0 17.5 + - - +
150B LEU* 4.1 5.4 - - + +
152B VAL* 1.3 77.3 - - - +
154B SER* 1.3 61.2 + - - +
156B ASP* 3.5 15.0 + - - +
157B LYS* 3.2 51.9 + - + +
159B MET* 6.0 2.9 - - + -
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Residues in contact with SER 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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114B ILE* 5.1 2.1 - - - +
150B LEU* 2.8 22.9 + - - +
151B CYS* 3.0 9.4 + - - -
153B GLU* 1.3 75.4 - - - +
155B VAL* 1.3 62.0 + - - +
157B LYS 3.6 0.5 + - - -
158B GLU 3.3 1.9 + - - -
159B MET* 2.8 54.4 + - - +
162B LEU* 3.5 29.8 - - - +
163B VAL* 4.8 4.9 - - - -
166B ILE* 3.8 5.6 - - - +
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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
----------------------------------------------------------
17B LEU* 4.3 6.5 - - + -
22B TYR* 3.5 41.5 - - + -
27B PHE* 3.6 30.5 - - + -
151B CYS 3.2 14.3 + - - +
152B VAL 3.3 5.4 + - - +
154B SER* 1.3 73.7 - - - +
156B ASP* 1.3 61.2 + - - +
158B GLU* 2.8 25.7 + - - +
160B GLN* 4.1 21.5 + - + +
163B VAL* 3.6 17.0 - - + -
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Residues in contact with ASP 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B TYR* 3.3 23.6 + - - -
152B VAL* 3.2 29.4 + - - +
153B GLU* 3.6 19.1 - - - +
155B VAL* 1.3 78.7 - - - +
157B LYS* 1.3 69.3 + - + +
158B GLU* 3.5 6.6 + - - +
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Residues in contact with LYS 157 (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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153B GLU* 3.2 44.2 + - + +
154B SER 3.6 0.2 + - - -
155B VAL 3.1 0.6 - - - -
156B ASP* 1.3 85.6 - - + +
158B GLU* 1.3 66.6 + - - +
159B MET* 3.1 38.6 + - + +
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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