Contacts of the helix formed by residues 151 - 163 (chain J) in PDB entry 2AAZ
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 ASP 151 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132J ARG* 2.7 59.7 + - - +
149J GLY 3.7 3.9 + - - +
150J VAL* 1.3 71.8 - - - +
152J GLN* 1.3 62.6 + - - +
153J LEU 3.4 1.9 + - - -
154J GLN* 3.1 26.0 + - + +
155J ARG* 3.2 18.7 + - - +
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Residues in contact with GLN 152 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174I TRP* 4.6 1.2 + - - -
176I PRO* 3.6 29.7 - - + +
130J GLN 2.8 22.8 + - - -
131J TRP* 3.0 10.2 + - - +
134J PHE* 3.6 13.7 - - - +
150J VAL* 4.0 12.6 - - + +
151J ASP* 1.3 72.4 - - - +
153J LEU* 1.3 58.9 + - - +
155J ARG* 3.2 7.5 + - - +
156J VAL* 2.9 34.5 + - - +
170J ILE 3.9 10.4 - - - +
171J LEU* 3.8 11.8 - - + -
172J SER* 2.7 47.8 + - - +
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Residues in contact with LEU 153 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84J VAL* 3.8 27.4 - - + -
131J TRP* 3.4 8.4 + - + +
132J ARG* 3.6 31.6 - - - +
151J ASP* 3.3 1.0 + - - -
152J GLN* 1.3 78.5 - - - +
154J GLN* 1.3 62.8 + - - +
156J VAL* 3.1 17.7 + - + +
157J ILE* 3.1 18.0 + - + +
171J LEU* 3.9 28.4 - - + +
234J LEU* 4.7 5.6 - - + -
238J ILE* 4.4 22.0 - - + -
292J ILE* 3.7 33.2 - - + -
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Residues in contact with GLN 154 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132J ARG* 4.4 4.2 - - - +
151J ASP* 3.1 31.3 + - + +
153J LEU* 1.3 77.3 - - - +
155J ARG* 1.3 55.7 - - - +
157J ILE* 3.1 17.5 + - - +
158J ASP* 2.9 56.9 + - - +
291J ASP* 5.3 7.9 - - - +
292J ILE* 4.0 22.4 - - - +
293J ASP* 5.1 1.4 + - - -
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Residues in contact with ARG 155 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150J VAL* 5.9 5.3 - - + +
151J ASP 3.2 14.0 + - - +
152J GLN* 3.5 11.9 - - - +
153J LEU 3.2 0.4 - - - -
154J GLN* 1.3 77.5 - - - +
156J VAL* 1.3 55.1 + - + +
158J ASP* 3.4 13.7 + - - +
159J THR* 2.7 50.4 + - - +
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Residues in contact with VAL 156 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152J GLN 2.9 20.5 + - - +
153J LEU* 3.1 13.0 + - + +
155J ARG* 1.3 77.2 - - + +
157J ILE* 1.3 63.6 + - + +
159J THR* 3.8 2.2 - - - -
160J ILE* 3.0 44.6 + - + +
169J ILE* 3.6 30.2 - - + +
170J ILE 3.7 25.8 - - - +
171J LEU* 4.5 8.5 - - + -
193J PHE* 3.8 17.5 - - + -
238J ILE* 4.6 9.4 - - + -
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Residues in contact with ILE 157 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153J LEU* 3.1 16.7 + - + +
154J GLN* 3.1 29.6 + - - +
156J VAL* 1.3 77.5 - - - +
158J ASP* 1.3 64.3 - - - +
160J ILE* 3.3 2.1 + - - +
161J LYS* 3.2 37.0 + - + +
238J ILE* 3.6 44.4 - - + +
241J ILE* 4.0 18.4 - - + -
242J THR* 3.8 16.8 - - + +
292J ILE* 4.6 18.6 - - + -
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Residues in contact with ASP 158 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154J GLN* 2.9 47.2 + - - +
155J ARG* 3.8 16.6 + - - +
157J ILE* 1.3 77.0 - - - +
159J THR* 1.3 58.3 + - - +
161J LYS* 3.4 8.7 + - - +
162J ASN* 2.9 45.9 + - - +
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Residues in contact with THR 159 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155J ARG* 2.7 37.7 + - - +
156J VAL* 3.8 4.7 - - - -
158J ASP* 1.3 74.5 - - - +
160J ILE* 1.3 59.7 + - - +
162J ASN* 5.3 0.4 - - - -
163J ASN* 2.7 58.3 + - + +
166J ASP* 3.5 25.1 - - + +
169J ILE* 3.8 18.8 - - + -
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Residues in contact with ILE 160 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156J VAL* 3.0 34.0 + - + +
157J ILE 3.3 4.5 + - - +
159J THR* 1.3 75.8 - - - +
161J LYS* 1.3 61.0 + - - +
164J PRO* 3.5 24.4 - - - +
169J ILE* 4.2 13.5 - - + -
193J PHE* 4.4 5.4 - - + -
195J VAL* 3.8 23.5 - - + +
209J LEU* 3.9 16.4 - - + -
238J ILE* 3.6 29.6 - - + -
242J THR* 3.7 23.8 - - + +
244J THR* 4.0 13.9 - - + +
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Residues in contact with LYS 161 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157J ILE* 3.2 34.3 + - + +
158J ASP* 3.8 8.9 + - - +
159J THR 3.2 0.4 - - - -
160J ILE* 1.3 78.8 - - - +
162J ASN* 1.3 71.2 + - - +
164J PRO* 4.6 3.4 - - - +
241J ILE* 4.1 17.9 + - - +
242J THR* 3.8 25.6 - - + +
286J LYS* 5.8 3.9 - - - +
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Residues in contact with ASN 162 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158J ASP* 2.9 33.1 + - - +
159J THR* 5.3 0.4 - - - -
161J LYS* 1.3 90.1 - - - +
163J ASN* 1.3 64.0 + - + +
164J PRO* 3.7 5.0 - - - +
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Residues in contact with ASN 163 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159J THR* 2.7 25.7 + - + +
162J ASN* 1.3 78.5 - - + +
164J PRO* 1.3 62.6 - - - +
165J THR* 3.3 13.1 + - - -
166J ASP* 3.0 56.1 + - - +
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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