Contacts of the helix formed by residues 142 - 154 (chain A) in PDB entry 5U07
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 GLY 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A ARG* 1.3 72.1 - - - +
143A ALA* 1.3 59.5 + - - +
145A ALA* 2.8 25.7 + - - +
146A GLU* 3.1 10.4 + - - +
163A THR* 4.3 19.4 + - - -
164A TYR* 6.0 0.4 - - - -
165A ALA* 5.6 2.2 - - - -
14I TYR* 5.9 0.2 - - - -
19I ARG* 5.7 7.2 - - - +
40K C 4.9 2.0 + - - -
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Residues in contact with ALA 143 (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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137A THR* 5.4 10.1 - - + -
141A ARG* 3.5 4.8 - - + +
142A GLY* 1.3 70.3 - - - +
144A ALA* 1.3 66.7 + - - +
146A GLU* 3.1 11.3 + - - +
147A GLU* 2.9 21.7 + - - +
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Residues in contact with ALA 144 (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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127A LYS* 3.8 18.3 - - + +
137A THR* 3.6 23.2 + - - +
138A TRP 3.0 34.9 + - - +
141A ARG* 4.4 0.6 - - - +
142A GLY 3.3 0.8 - - - -
143A ALA* 1.3 77.5 - - - +
145A ALA* 1.3 56.7 + - - +
147A GLU* 3.2 13.2 - - - +
148A TRP* 2.9 25.1 + - - +
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Residues in contact with ALA 145 (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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110A PRO* 5.6 8.7 - - + -
141A ARG 3.9 7.4 + - - +
142A GLY* 2.8 17.4 + - - +
144A ALA* 1.3 78.9 - - - +
146A GLU* 1.3 57.6 + - - +
148A TRP* 3.0 17.5 - - + +
149A TRP* 2.9 22.0 + - - +
163A THR* 4.2 22.6 - - + +
164A TYR 5.3 2.9 - - - +
165A ALA* 5.1 9.9 - - + -
190A PHE* 4.9 10.0 - - + -
14I TYR* 4.8 0.2 + - - -
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Residues in contact with GLU 146 (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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142A GLY 3.1 10.2 + - - +
143A ALA* 3.1 11.4 + - - +
145A ALA* 1.3 75.4 - - - +
147A GLU* 1.3 66.6 + - - +
149A TRP* 2.8 20.6 + - + +
150A HIS* 2.9 26.1 + - - +
14I TYR* 3.1 47.3 + - + +
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Residues in contact with GLU 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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127A LYS* 3.7 24.8 - - - +
143A ALA 2.9 11.6 + - - +
144A ALA* 3.2 16.1 - - - +
146A GLU* 1.3 78.4 + - - +
148A TRP* 1.3 69.8 + - - +
150A HIS* 3.0 44.7 + - - +
151A SER* 3.1 29.2 + - - -
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Residues in contact with TRP 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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108A ALA* 3.4 26.7 - - + -
109A SER 4.0 5.1 + - - -
110A PRO* 3.3 43.0 - - + +
127A LYS* 3.3 36.8 - - + +
144A ALA 2.9 13.5 + - - +
145A ALA* 3.0 20.0 - - - +
147A GLU* 1.3 82.5 + - - +
149A TRP* 1.3 58.9 + - + +
151A SER* 3.5 1.1 + - - -
152A ARG* 2.9 78.7 + - + +
190A PHE* 3.4 35.4 - + - -
210A ILE* 4.8 5.6 - - + -
211A GLY* 4.6 7.2 - - - -
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Residues in contact with TRP 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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145A ALA 2.9 9.0 + - - +
146A GLU* 2.8 24.7 + - + +
148A TRP* 1.3 80.2 - - + +
150A HIS* 1.3 65.0 + - - +
152A ARG* 4.7 3.4 - - - -
153A ALA* 2.8 30.0 + - + +
159A GLU 5.7 2.2 - - - +
161A LEU* 4.9 11.0 - - + -
190A PHE* 6.5 0.9 - - + -
14I TYR* 4.3 9.9 - - + +
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Residues in contact with HIS 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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146A GLU* 2.9 25.6 + - - +
147A GLU* 3.0 59.9 + - + +
149A TRP* 1.3 76.7 - - - +
151A SER* 1.3 80.1 + - - +
153A ALA* 5.0 1.8 - - - -
154A ALA* 3.1 23.0 + - - +
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Residues in contact with SER 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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127A LYS* 4.1 17.4 + - - -
147A GLU* 3.1 32.2 + - - -
148A TRP 3.8 3.4 - - - -
150A HIS* 1.3 88.9 + - - +
152A ARG* 1.3 68.8 + - - +
153A ALA 3.5 0.2 + - - -
154A ALA* 3.7 12.5 + - - +
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Residues in contact with ARG 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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46A ARG* 5.1 12.0 + - - +
109A SER 5.7 0.2 + - - -
111A THR* 4.2 10.1 + - - +
127A LYS* 3.0 27.1 - - - +
148A TRP* 2.9 70.7 + - + +
149A TRP* 4.1 3.1 - - - +
151A SER* 1.3 83.1 - - - +
153A ALA* 1.3 63.3 + - - +
154A ALA* 4.6 1.6 - - - +
156A ASN* 4.5 4.7 + - - -
210A ILE* 3.7 33.6 - - + +
211A GLY* 4.6 10.3 - - - +
212A ARG* 4.0 10.5 - - - +
57K U 4.6 1.8 + - - -
58K G 2.9 40.2 + - - -
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Residues in contact with ALA 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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149A TRP* 2.8 23.3 + - + +
150A HIS* 4.7 2.0 - - - +
152A ARG* 1.3 71.3 - - - +
154A ALA* 1.3 73.8 + - - +
156A ASN* 2.9 34.5 + - + +
157A GLY 4.0 21.1 - - - +
158A LEU* 6.2 0.7 - - + -
210A ILE* 5.9 1.1 - - - -
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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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150A HIS 3.1 18.8 + - - +
151A SER 3.8 11.7 - - - +
152A ARG 4.6 1.3 - - - +
153A ALA* 1.3 82.0 - - - +
155A ALA* 1.3 64.6 + - + +
156A ASN* 3.2 2.2 + - - +
157A GLY 4.8 0.2 + - - -
158A LEU* 4.4 15.4 - - - +
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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