Contacts of the strand formed by residues 159 - 170 (chain B) in PDB entry 1NE2
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 159 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B PHE* 4.3 0.7 - - - -
155B PHE 2.8 12.9 + - - +
156B SER* 3.2 22.5 - - - +
158B ARG* 1.3 81.4 - - - +
160B ASP* 1.3 60.7 + - - +
161B VAL 3.8 0.2 + - - -
192B VAL* 3.9 6.1 - - - -
193B ARG 3.1 14.1 - - - -
195B HIS* 3.4 20.0 + - - -
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Residues in contact with ASP 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B GLY* 1.3 70.3 - - - +
161B VAL* 1.3 61.9 + - - +
162B PHE* 3.2 10.6 + - + +
192B VAL* 3.3 2.7 - - - +
193B ARG* 2.8 53.0 + - + +
195B HIS* 3.2 28.7 + - - -
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Residues in contact with VAL 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B ARG* 4.5 8.7 - - + +
155B PHE* 3.8 29.4 - - + -
156B SER* 3.8 22.8 - - - +
159B GLY 3.8 0.6 + - - -
160B ASP* 1.3 70.6 - - - +
162B PHE* 1.3 58.9 + - - +
163B ARG 3.4 26.9 - - - +
164B GLU* 4.5 8.3 - - + +
190B PHE* 4.0 17.9 - - + -
191B GLY 3.6 5.6 - - - +
192B VAL* 4.2 3.8 - - + -
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Residues in contact with PHE 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ASP* 3.6 21.8 - - - -
138B TRP* 3.6 26.7 - + - -
140B TYR* 3.5 21.1 - + - -
160B ASP* 3.2 13.5 + - + +
161B VAL* 1.3 73.9 - - - +
163B ARG* 1.3 75.3 + - + +
191B GLY* 2.9 26.6 + - - -
192B VAL 3.5 24.2 - - - -
193B ARG* 3.9 4.3 - - + -
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Residues in contact with ARG 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B GLU* 3.5 41.1 + - - +
41B ILE* 5.3 0.2 - - - +
44B ASP* 2.8 43.4 + - - -
140B TYR* 3.7 16.0 - - - -
161B VAL* 3.4 11.6 - - - +
162B PHE* 1.3 93.6 + - + +
164B GLU* 1.3 63.0 + - - +
165B GLU* 3.7 18.1 + - + -
189B ILE* 3.7 19.7 - - + +
190B PHE* 3.2 6.2 - - - -
191B GLY* 2.9 30.6 + - - +
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Residues in contact with GLU 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B ARG* 2.9 38.9 + - - +
152B ARG* 2.7 49.0 + - - +
161B VAL* 4.5 7.3 - - + +
163B ARG* 1.3 74.9 - - - +
165B GLU* 1.3 59.1 + - - +
166B LYS 4.2 0.2 + - - -
188B VAL* 4.0 2.9 - - + -
189B ILE 3.2 4.7 - - - -
190B PHE* 3.3 27.3 - - + -
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Residues in contact with GLU 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B TYR* 2.5 33.2 + - - -
40B GLU* 2.5 30.6 - - - +
148B ARG* 4.7 0.4 - - - -
163B ARG* 3.7 17.4 + - + -
164B GLU* 1.3 73.8 - - - +
166B LYS* 1.3 75.0 + - - +
167B VAL* 3.6 8.4 + - + +
188B VAL* 3.3 6.9 - - - -
189B ILE* 2.8 42.2 + - + +
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Residues in contact with LYS 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B ARG* 4.4 17.5 - - - +
164B GLU 4.2 1.0 + - - -
165B GLU* 1.3 81.4 - - - +
167B VAL* 1.3 64.6 + - - +
168B TYR* 2.7 43.8 + - + +
186B GLU* 3.3 41.9 + - + +
187B ALA 3.7 4.5 - - - -
188B VAL* 4.8 0.4 - - - +
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Residues in contact with VAL 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B THR* 5.5 4.0 - - + -
36B TYR* 4.4 9.2 - - + -
142B ILE* 4.6 8.7 - - + -
165B GLU* 4.2 13.2 - - - +
166B LYS* 1.3 82.1 - - - +
168B TYR* 1.3 65.3 + - - +
169B ILE* 5.0 6.3 - - + -
186B GLU* 3.8 2.1 - - - +
187B ALA* 2.8 55.3 + - + +
188B VAL 4.2 0.9 - - - +
189B ILE* 3.5 37.5 - - + -
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Residues in contact with TYR 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B THR* 5.2 1.4 + - - -
166B LYS* 2.7 51.2 + - + +
167B VAL* 1.3 77.0 - - - +
169B ILE* 1.3 68.7 + - - +
184B ARG* 3.2 56.4 + - + +
185B ILE 3.5 14.6 - - - +
186B GLU* 4.3 14.9 + - + -
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Residues in contact with ILE 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B THR* 6.3 2.9 - - + -
30B ASP* 4.7 6.1 - - - +
33B THR* 3.9 33.2 - - + +
142B ILE* 6.0 0.7 - - + -
167B VAL* 5.0 3.8 - - + -
168B TYR* 1.3 84.0 - - - +
170B THR* 1.3 73.2 + - - +
184B ARG* 3.1 5.9 - - - +
185B ILE* 2.8 50.6 + - + +
187B ALA* 3.8 26.0 - - + -
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Residues in contact with THR 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B ILE* 1.3 87.2 - - - +
171B VAL* 1.3 74.9 + - - +
172B PRO* 3.6 14.3 - - + +
176B ARG* 4.6 5.8 - - - +
183B ALA* 3.9 5.6 - - + +
184B ARG* 2.8 35.8 + - + +
185B ILE* 5.1 0.5 - - - +
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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