Contacts of the helix formed by residues 142 - 154 (chain A) in PDB entry 2R0B
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 LYS 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A SO4 3.9 24.5 - - - +
136A MET* 4.3 1.8 - - - -
140A GLY 4.1 1.2 + - - +
141A MET* 1.3 74.6 - - - +
143A TYR* 1.3 67.0 + - - +
144A ARG* 3.4 4.9 - - + +
145A ASP* 3.3 22.8 + - - +
146A ALA* 3.0 21.0 + - - +
171A GLU* 3.8 21.4 + - - +
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Residues in contact with TYR 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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2A SO4 3.5 17.7 + - - +
132A ILE* 3.9 15.3 - - + -
136A MET* 3.9 19.3 - - + +
142A LYS* 1.3 73.3 - - - +
144A ARG* 1.3 65.9 + - + +
146A ALA 3.2 0.9 + - - -
147A PHE* 2.7 72.0 + + + +
159A PRO* 3.8 8.5 - - + +
164A VAL* 3.4 42.6 - - + +
167A LEU* 3.6 36.8 - - + -
168A GLN* 4.1 15.9 - - + -
171A GLU* 5.0 0.6 + - - -
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Residues in contact with ARG 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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2A SO4 2.9 42.3 + - - +
142A LYS* 4.8 5.2 - - + -
143A TYR* 1.3 85.8 - - + +
145A ASP* 1.3 78.4 + - - +
147A PHE* 3.9 5.9 - - - +
148A ALA* 3.0 27.5 + - - +
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Residues in contact with ASP 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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141A MET* 3.4 17.4 - - + +
142A LYS* 3.3 26.0 + - - +
143A TYR 3.2 0.6 - - - -
144A ARG* 1.3 92.4 - - - +
146A ALA* 1.3 61.2 + - - +
148A ALA* 3.5 5.5 + - - +
149A TYR* 3.0 28.4 + - - +
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Residues in contact with ALA 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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132A ILE* 4.0 11.7 - - + +
135A ILE* 3.9 19.7 - - + -
136A MET* 3.7 23.8 - - + -
141A MET* 3.4 14.9 - - + +
142A LYS 3.0 16.1 + - - +
143A TYR 3.8 2.0 - - - +
145A ASP* 1.3 72.9 - - - +
147A PHE* 1.3 67.1 + - - +
149A TYR* 3.3 1.6 + - - +
150A VAL* 3.1 29.4 + - - +
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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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132A ILE* 4.1 10.6 - - + +
143A TYR* 2.7 55.9 + + + +
144A ARG* 3.9 6.5 - - - +
146A ALA* 1.3 72.3 - - - +
148A ALA* 1.3 62.7 + - + +
150A VAL* 3.2 2.4 + - - -
151A GLN* 2.9 64.8 + - + +
157A ILE* 3.6 40.7 - - + +
158A ASN* 4.4 4.0 - - - -
159A PRO* 3.7 15.5 - - + -
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Residues in contact with ALA 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 ARG 3.0 18.3 + - - +
145A ASP* 3.8 7.0 - - - +
146A ALA 3.3 0.2 - - - -
147A PHE* 1.3 83.8 - - + +
149A TYR* 1.3 61.7 + - - +
151A GLN* 3.4 10.8 + - - +
152A GLU* 3.1 31.7 + - + +
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Residues in contact with TYR 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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32A ILE* 2.7 36.8 + - + -
33A LEU* 4.1 12.3 - - + +
34A PRO* 5.4 1.4 - - - +
135A ILE* 4.3 11.9 - - + -
141A MET* 4.0 18.2 - - + -
145A ASP 3.0 19.3 + - - +
146A ALA 3.6 4.0 - - - +
147A PHE 3.3 0.2 - - - -
148A ALA* 1.3 78.1 - - - +
150A VAL* 1.3 75.4 + - + +
152A GLU* 3.4 4.5 + - - -
153A ARG* 2.8 66.0 + - - +
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Residues in contact with VAL 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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32A ILE* 3.9 18.8 - - + -
38A LEU* 4.0 26.0 - - + -
128A ALA* 5.4 0.7 - - + -
131A VAL* 4.4 4.3 - - + -
132A ILE* 4.0 13.2 - - + -
135A ILE* 3.4 33.0 - - + -
146A ALA 3.1 15.3 + - - +
149A TYR* 1.3 77.7 - - + +
151A GLN* 1.3 60.1 + - - +
153A ARG* 2.9 5.3 + - - +
154A ARG* 2.8 25.9 + - + +
157A ILE* 3.5 25.4 - - + -
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Residues in contact with GLN 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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147A PHE* 2.9 50.9 + - + +
148A ALA* 3.7 9.7 - - - +
149A TYR 3.4 0.2 - - - -
150A VAL* 1.3 75.5 - - - +
152A GLU* 1.3 64.2 + - + +
153A ARG 3.2 0.5 + - - -
154A ARG 3.4 8.2 - - - -
155A PHE* 3.4 42.4 + - - +
157A ILE* 3.8 14.9 + - + +
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Residues in contact with GLU 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 ALA* 3.1 20.6 + - + +
149A TYR* 3.7 7.6 - - - +
150A VAL 3.2 0.6 - - - -
151A GLN* 1.3 77.5 - - + +
153A ARG* 1.3 72.8 + - - +
155A PHE* 5.3 0.7 + - - +
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Residues in contact with ARG 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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30A GLN* 3.5 22.2 - - + +
31A GLU 3.9 16.2 - - - +
32A ILE* 3.6 32.8 + - + +
149A TYR* 2.8 79.2 + - - +
150A VAL 2.9 6.5 + - - +
152A GLU* 1.3 96.3 - - - +
154A ARG* 1.3 57.5 + - - +
155A PHE 4.0 1.2 + - - -
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Residues in contact with ARG 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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26A ARG* 2.8 31.3 + - - +
28A GLU 2.9 20.1 + - - -
30A GLN* 2.9 38.3 + - - +
32A ILE* 4.5 9.9 - - + -
38A LEU* 3.7 25.4 + - - +
39A GLY* 4.4 0.9 - - - -
40A PRO* 3.7 11.6 - - - +
122A ALA 2.9 23.4 + - - -
123A GLY* 2.8 25.4 + - - -
150A VAL 2.8 12.4 + - - +
151A GLN* 3.4 11.7 - - - +
153A ARG* 1.3 72.2 - - - +
155A PHE* 1.3 66.4 + - + +
156A CYS* 3.0 22.3 + - - -
157A ILE* 3.3 21.9 + - + +
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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