Contacts of the helix formed by residues 150 - 164 (chain A) in PDB entry 2NTZ
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 SER 150 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A GLN* 3.9 1.6 - - - +
149A HIS* 1.3 84.6 + - - +
151A ILE* 1.3 65.3 + - - +
152A ARG* 3.1 5.3 + - - +
153A GLU* 3.3 33.7 + - - +
154A ILE* 3.8 2.4 - - - +
202A GLN* 4.3 23.2 + - - -
203A SER* 5.8 3.6 - - - +
210A TYR* 5.6 1.1 - - - -
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Residues in contact with ILE 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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149A HIS* 2.4 15.2 + - + +
150A SER* 1.3 69.2 - - - +
152A ARG* 1.3 68.7 + - - +
153A GLU 3.1 1.7 + - - -
154A ILE* 3.1 38.4 + - + +
155A GLY 3.6 2.4 + - - -
181A LYS* 4.3 21.1 - - + -
184A ARG* 5.1 3.1 - - + +
185A ALA* 4.1 29.1 - - + +
188A ALA* 5.0 7.9 - - + -
205A LEU 5.1 3.8 - - - +
207A PHE* 5.4 15.9 - - + +
210A TYR* 4.6 20.9 - - + +
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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
----------------------------------------------------------
150A SER* 4.6 4.7 - - - +
151A ILE* 1.3 81.8 - - - +
153A GLU* 1.3 64.8 + - - +
155A GLY* 3.2 11.7 + - - -
156A LEU* 3.7 4.0 + - - +
185A ALA 5.7 0.4 - - - -
188A ALA* 3.8 25.4 + - - +
189A ALA* 4.0 16.2 + - - +
191A ALA* 3.1 23.2 + - - +
193A GLU* 3.9 20.0 + - - +
196A VAL* 3.4 32.9 - - - +
202A GLN* 4.5 12.8 - - - +
210A TYR* 3.1 45.5 - - + +
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Residues in contact with GLU 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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145A THR* 5.2 9.5 - - - +
146A ALA* 5.6 1.4 - - - -
147A LEU 4.8 8.5 + - - +
148A GLN* 2.7 34.4 - - + +
150A SER* 3.3 18.7 + - - +
151A ILE 3.2 1.0 - - - -
152A ARG* 1.3 74.6 - - - +
154A ILE* 1.3 70.9 + - - +
155A GLY 2.8 2.2 - - - -
156A LEU* 2.6 33.2 + - + +
157A ARG* 3.6 2.3 + - - +
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Residues in contact with ILE 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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148A GLN* 4.6 5.8 - - + +
149A HIS* 4.4 18.2 - - - +
150A SER 3.8 7.0 - - - +
151A ILE* 3.3 32.8 - - + +
153A GLU* 1.3 76.1 - - - +
155A GLY* 1.3 70.0 + - - +
157A ARG* 3.2 11.4 + - + +
158A LEU* 3.0 47.4 + - + +
177A LEU* 4.9 13.7 - - + -
181A LYS* 5.2 11.2 - - - +
185A ALA* 4.9 4.9 - - + -
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Residues in contact with GLY 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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151A ILE 3.6 3.0 + - - -
152A ARG 3.2 3.4 + - - -
153A GLU 2.7 5.3 + - - -
154A ILE* 1.3 80.2 - - - +
156A LEU* 1.3 65.1 + - - -
158A LEU* 2.6 7.5 + - - +
159A MSE 2.6 20.8 + - - -
185A ALA* 4.5 2.8 - - - +
186A LEU* 4.4 14.8 - - - +
189A ALA* 3.3 26.5 - - - -
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Residues in contact with LEU 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 ARG 3.7 4.1 + - - +
153A GLU* 2.6 24.6 + - + +
155A GLY* 1.3 67.4 - - - -
157A ARG* 1.3 58.8 + - + +
159A MSE 2.8 14.8 + - + +
160A ARG* 2.7 50.7 + - + +
189A ALA* 3.7 5.9 - - - +
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Residues in contact with ARG 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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147A LEU* 4.4 20.6 - - - +
153A GLU 3.6 1.9 + - - +
154A ILE* 3.2 13.6 + - - +
155A GLY 2.8 3.8 + - - -
156A LEU* 1.3 78.7 - - + +
158A LEU* 1.3 62.1 + - - +
159A MSE 2.8 4.7 - - - -
160A ARG* 2.6 51.5 + - - +
161A MSE 2.9 26.1 + - + +
175A GLU* 2.7 34.7 + - - +
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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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154A ILE* 3.0 40.4 - - + +
155A GLY* 2.6 10.5 + - - +
157A ARG* 1.3 80.6 - - - +
159A MSE 1.3 50.6 + - - +
161A MSE 3.6 12.2 - - - +
162A LYS* 2.7 34.9 + - - +
171A ILE* 3.8 28.6 - - + +
175A GLU* 3.9 20.9 - - + -
177A LEU* 4.7 11.9 - - + -
182A VAL* 4.7 9.9 - - + +
185A ALA* 4.0 19.1 - - + -
186A LEU* 4.7 12.9 - - + +
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Residues in contact with MSE 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 GLY 2.6 13.7 + - - +
156A LEU* 2.9 20.4 - - + +
158A LEU* 1.3 72.9 - - - +
160A ARG* 1.3 65.9 + - - +
162A LYS* 3.3 36.6 - - + -
163A ASN* 3.2 23.6 + - + +
186A LEU* 3.8 16.8 - - + -
189A ALA* 4.4 15.9 - - + +
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Residues in contact with ARG 160 (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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156A LEU* 2.7 30.4 + - + +
157A ARG* 2.6 36.9 + - - +
159A MSE 1.3 75.3 - - - +
161A MSE 1.3 69.3 + - - +
163A ASN* 3.1 18.3 + - - +
164A ASP* 3.5 11.4 + - - +
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Residues in contact with MSE 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 ARG* 2.9 27.5 + - + +
158A LEU* 3.6 16.4 - - - +
160A ARG* 1.3 77.5 - - + +
162A LYS* 1.3 56.8 + - - +
163A ASN 2.9 1.8 - - - -
164A ASP* 2.7 28.7 + - - +
166A MSE 3.3 56.9 - - + +
171A ILE* 4.0 6.7 - - + -
174A LYS* 4.2 13.0 - - + -
175A GLU* 3.3 40.6 - - - +
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Residues in contact with LYS 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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158A LEU 2.7 22.0 + - - +
159A MSE 3.3 28.0 - - + -
160A ARG 3.4 0.2 - - - -
161A MSE 1.3 73.2 - - - +
163A ASN* 1.3 60.1 + - - +
165A GLY* 3.3 10.9 + - - -
166A MSE 3.8 21.1 + - - +
167A SER* 6.0 0.2 - - - +
168A GLN* 2.5 41.9 + - + +
171A ILE* 4.0 5.4 - - + +
186A LEU* 3.9 16.2 - - + -
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Residues in contact with ASN 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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159A MSE 3.2 14.6 + - + +
160A ARG* 3.1 14.6 + - - +
161A MSE 2.9 0.8 - - - -
162A LYS* 1.3 74.2 - - - +
164A ASP* 1.3 66.6 + - - +
165A GLY 3.0 10.5 + - - -
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Residues in contact with ASP 164 (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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160A ARG* 3.5 12.4 + - - +
161A MSE 2.7 18.8 + - - +
163A ASN* 1.3 78.9 + - - +
165A GLY* 1.3 65.2 + - - +
166A MSE 3.6 13.8 - - + +
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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