Contacts of the helix formed by residues 146 - 163 (chain A) in PDB entry 4V0P
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 PHE 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A PHE* 3.5 35.7 - + - -
109A LEU* 4.1 23.1 - - + -
142A ASN* 4.0 15.9 - - + -
143A TRP* 2.8 27.3 + + + +
145A TYR* 1.3 94.1 - + + +
147A PHE* 1.3 65.8 + - - +
148A PRO* 3.2 4.5 - - - -
149A VAL* 3.1 17.1 - - + +
150A ILE* 3.1 21.4 + - + +
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Residues in contact with PHE 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A LEU* 4.4 11.4 - - + -
132A LYS* 4.0 36.8 - - + -
135A MET* 3.8 24.9 - - + -
136A LEU* 3.7 46.2 - - + -
139A VAL* 4.2 13.0 - - + -
143A TRP 3.5 4.2 + - - -
144A GLN* 3.1 17.3 + - - +
146A PHE* 1.3 77.5 - - - +
148A PRO* 1.4 67.9 - - + +
150A ILE* 4.1 6.3 - - + -
151A PHE* 2.7 57.9 + + + +
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Residues in contact with PRO 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A GLN 4.5 0.9 - - - +
145A TYR 3.9 10.3 - - - +
146A PHE 3.4 4.7 - - - -
147A PHE* 1.4 99.8 - - + +
149A VAL* 1.3 55.9 + - - +
151A PHE* 3.8 5.0 - - + +
152A SER* 3.1 28.2 + - - -
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Residues in contact with VAL 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A LEU* 4.5 17.9 - - + -
146A PHE* 3.1 28.9 + - + +
148A PRO* 1.3 76.3 - - - +
150A ILE* 1.3 66.7 + - + +
152A SER* 3.2 9.0 + - - +
153A LYS* 2.9 53.4 + - + +
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Residues in contact with ILE 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A LEU* 3.8 22.9 - - + -
112A LYS* 3.7 41.1 - - + +
113A VAL* 4.1 17.9 - - + +
116A LEU* 3.8 20.0 - - + -
139A VAL* 4.5 18.8 - - + -
143A TRP* 3.9 19.3 - - + +
146A PHE* 3.1 18.8 + - + +
147A PHE* 3.7 6.3 - - + +
149A VAL* 1.3 77.6 - - - +
151A PHE* 1.3 56.3 + - - +
153A LYS* 3.9 1.0 - - - +
154A ALA* 2.9 28.4 + - - +
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Residues in contact with PHE 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A LEU* 3.9 11.0 - - + -
120A LEU* 5.5 1.6 - - + -
132A LYS* 6.2 1.6 - - + -
135A MET* 3.4 36.3 - - + -
147A PHE* 2.7 45.0 + + + +
148A PRO* 3.8 5.4 - - + +
150A ILE* 1.3 74.9 - - - +
152A SER* 1.3 64.5 + - - +
154A ALA* 3.2 1.7 + - - +
155A SER* 2.8 40.9 + - - -
166A LEU* 3.8 24.5 - - + -
176A TYR* 4.0 28.0 - + - -
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Residues in contact with SER 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A PRO 3.1 13.1 + - - -
149A VAL* 3.2 16.8 + - - +
151A PHE* 1.3 86.9 - - - +
153A LYS* 1.3 61.3 + - - +
155A SER* 3.8 5.3 - - - -
156A SER* 3.0 32.7 + - - -
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Residues in contact with LYS 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A GLN* 5.1 10.9 - - - +
109A LEU* 5.8 7.8 - - + +
110A SER* 5.2 7.4 + - - -
113A VAL* 4.0 27.5 - - + +
149A VAL* 2.9 38.3 + - + +
150A ILE 4.0 2.7 - - - +
152A SER* 1.3 78.3 + - - +
154A ALA* 1.3 58.8 + - - +
156A SER* 3.4 5.3 + - - -
157A SER* 2.9 30.3 + - - -
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Residues in contact with ALA 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A VAL* 3.9 5.3 - - + +
116A LEU* 3.8 27.4 - - + -
117A VAL* 3.9 25.5 - - + +
120A LEU* 4.6 6.3 - - + -
150A ILE 2.9 19.4 + - - +
151A PHE 3.7 2.7 - - - +
153A LYS* 1.3 76.3 - - - +
155A SER* 1.3 62.3 + - - +
157A SER* 3.3 2.9 + - - -
158A LEU* 3.0 29.5 + - - +
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Residues in contact with SER 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A LEU* 5.4 0.4 - - - +
151A PHE* 2.8 34.9 + - - -
152A SER* 3.8 8.1 - - - -
154A ALA* 1.3 77.1 - - - +
156A SER* 1.3 61.3 + - - +
158A LEU* 3.4 13.4 + - - +
159A GLN* 3.4 29.7 + - - +
164A ILE 4.7 0.2 - - - +
166A LEU* 4.5 21.6 + - - +
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Residues in contact with SER 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A SER 3.0 19.1 + - - -
153A LYS* 3.8 5.4 - - - -
155A SER* 1.3 74.0 - - - +
157A SER* 1.3 60.1 + - - +
159A GLN* 3.3 14.7 + - - +
160A LEU* 2.9 33.7 + - - +
293A ILE 5.2 10.2 + - - +
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Residues in contact with SER 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A VAL* 4.9 5.0 - - - +
117A VAL* 4.1 20.1 - - - +
153A LYS 2.9 19.0 + - - -
154A ALA* 3.5 5.6 - - - -
156A SER* 1.3 77.0 - - - +
158A LEU* 1.3 57.7 + - - +
160A LEU* 4.9 1.3 - - - -
161A VAL* 2.8 50.4 + - - +
162A PHE* 3.7 4.2 - - - -
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Residues in contact with LEU 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A VAL* 4.3 16.2 - - + +
120A LEU* 3.7 35.0 - - + -
121A LEU* 3.9 28.3 - - + -
124A TYR* 6.5 0.2 - - + -
154A ALA 3.0 17.8 + - - +
155A SER* 3.6 8.1 - - - +
156A SER 3.2 0.2 - - - -
157A SER* 1.3 74.7 - - - +
159A GLN* 1.3 58.8 + - - +
162A PHE* 3.1 17.7 + - + +
163A GLY 2.9 11.6 + - - -
164A ILE* 2.8 43.4 + - + +
166A LEU* 4.6 19.1 - - + -
178A PHE* 4.7 8.3 - - + -
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Residues in contact with GLN 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A SER* 3.4 19.4 + - - +
156A SER* 3.3 15.5 + - - +
157A SER 3.2 0.4 - - - -
158A LEU* 1.3 77.1 - - - +
160A LEU* 1.3 63.8 + - - +
163A GLY* 3.1 19.8 + - - -
164A ILE 3.5 14.6 - - - +
165A GLU* 2.7 39.3 + - - +
166A LEU 5.5 1.1 - - - +
181A CYS* 3.9 10.1 - - - -
200A GLY* 4.7 1.4 - - - -
289A HIS* 4.8 0.9 + - - -
292A LYS* 3.9 13.5 - - - +
293A ILE* 3.9 32.9 - - + +
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Residues in contact with LEU 160 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A SER* 2.9 17.7 + - - +
157A SER* 4.4 0.9 - - - +
159A GLN* 1.3 79.5 - - + +
161A VAL* 1.3 69.1 + - + +
200A GLY* 4.3 6.4 - - - +
204A ILE* 4.2 23.0 - - + +
290A MET* 4.5 13.5 - - + -
293A ILE* 3.7 39.9 - - + +
294A SER* 5.8 2.7 - - - -
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Residues in contact with VAL 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A SER* 2.8 36.8 + - - +
160A LEU* 1.3 82.4 - - + +
162A PHE* 1.3 80.0 + - + +
163A GLY 3.6 0.2 - - - -
196A MET* 3.6 32.7 - - + +
197A PRO 4.6 0.3 - - - +
200A GLY* 3.9 8.1 + - - -
201A LEU* 4.3 6.2 + - - +
230A VAL* 6.1 1.3 - - + -
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Residues in contact with PHE 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A VAL* 3.8 22.2 - - + -
118A HIS* 5.2 7.0 - + - -
121A LEU* 3.9 23.1 - - + -
157A SER* 3.7 15.3 - - - -
158A LEU* 3.1 22.5 + - + +
161A VAL* 1.3 96.8 - - + +
163A GLY* 1.3 64.4 + - - +
164A ILE* 3.4 22.5 + - + +
187A ASP* 6.1 0.2 - - - +
196A MET* 3.9 24.2 - - + -
197A PRO* 3.7 37.3 - - + +
199A ALA* 4.1 5.0 + - - +
200A GLY 3.6 10.2 + - - -
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Residues in contact with GLY 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A LEU 2.9 3.4 + - - -
159A GLN 3.1 17.1 + - - -
162A PHE* 1.3 78.4 - - - +
164A ILE* 1.3 58.3 + - - +
180A THR* 3.6 12.8 - - - +
181A CYS* 2.9 36.7 + - - +
199A ALA* 4.0 2.3 - - - +
200A GLY* 3.5 20.7 - - - -
203A ILE* 5.1 0.4 - - - -
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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