Contacts of the strand formed by residues 153 - 159 (chain B) in PDB entry 5E5R
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 LEU 153 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146B PRO* 5.9 4.7 - - + -
147B PRO 3.4 32.3 - - - +
152B GLU* 1.3 93.9 - - - +
154B SER* 1.3 61.5 + - - +
155B TYR* 3.7 21.1 - - + +
176B GLN* 4.5 7.1 - - - +
198B VAL* 3.8 27.1 - - + -
199B THR 3.3 13.0 - - - +
200B SER* 4.9 11.0 - - - -
201B THR* 4.1 4.9 - - - -
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Residues in contact with SER 154 (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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153B LEU* 1.3 73.6 - - - +
155B TYR* 1.3 66.5 + - - +
176B GLN* 3.6 8.7 - - - -
197B VAL 3.9 0.7 - - - +
198B VAL* 3.5 3.5 - - - +
199B THR* 2.8 53.3 + - - +
201B THR* 4.8 5.0 + - - -
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Residues in contact with TYR 155 (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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144B CYS* 3.9 20.0 - - - -
146B PRO* 3.3 18.7 + - + +
147B PRO* 3.1 33.4 - - + +
153B LEU* 3.7 29.1 - - + +
154B SER* 1.3 75.1 - - - +
156B ALA* 1.3 60.9 + - - +
157B TRP* 5.1 0.2 - - - +
174B VAL* 3.8 7.1 - - + +
175B SER 4.1 4.7 - - - +
176B GLN* 3.0 52.5 + - - +
177B GLU 5.4 1.7 + - - -
178B THR 4.8 0.9 - - - -
179B GLY* 3.5 39.7 - - - +
196B CYS* 4.3 1.8 - - - -
197B VAL 3.7 2.5 - - - +
198B VAL* 4.0 23.3 - - + -
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Residues in contact with ALA 156 (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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155B TYR* 1.3 77.5 - - - +
157B TRP* 1.3 72.0 + - - +
165B PHE* 3.7 28.5 - - + -
174B VAL* 4.6 3.1 - - - -
196B CYS* 3.7 1.9 - - - -
197B VAL* 3.0 39.1 + - + +
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Residues in contact with TRP 157 (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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129B ARG* 6.0 0.7 - - - -
142B LEU* 3.1 41.7 - - + -
143B LEU 3.5 14.8 - - - -
144B CYS 3.9 5.2 - - - -
156B ALA* 1.3 80.9 - - - +
158B VAL* 1.3 62.3 + - - +
165B PHE* 3.2 5.6 - - - -
166B VAL* 2.7 51.3 + - + +
174B VAL* 3.8 24.7 - - + +
179B GLY 2.9 27.1 + - - -
180B HIS 3.7 0.6 - - - -
181B LEU* 3.6 20.9 - - + +
194B TYR* 4.1 24.7 - - + -
195B THR 3.7 16.4 - - - -
196B CYS* 3.5 33.3 - - + -
212B THR* 5.7 2.2 - - - -
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Residues in contact with VAL 158 (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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156B ALA 4.2 0.8 - - - -
157B TRP* 1.3 75.3 - - - +
159B PHE* 1.3 61.8 + - - +
161B GLU 4.1 9.4 - - - +
162B TYR* 4.2 22.9 - - + -
163B PRO* 3.5 29.8 - - + -
165B PHE* 3.4 31.9 - - + +
166B VAL* 4.6 1.1 - - - -
193B ASN 3.8 0.2 - - - +
194B TYR* 3.8 7.8 - - - -
195B THR* 3.1 54.8 + - + +
197B VAL* 4.9 6.7 - - + +
208B LEU* 5.4 3.6 - - + -
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Residues in contact with PHE 159 (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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157B TRP 4.2 0.4 + - - -
158B VAL* 1.3 75.4 - - - +
160B ASN* 1.3 84.0 + - - +
161B GLU* 2.6 30.3 + - - +
163B PRO 5.3 0.7 - - - -
165B PHE 4.3 9.4 + - - +
166B VAL* 4.3 16.8 - - + +
189B SER 4.2 10.3 - - - -
190B ASP 3.8 2.5 - - - -
191B VAL 3.4 21.1 - - - -
192B GLY* 3.5 21.3 - - - -
193B ASN 3.5 10.5 - - - -
194B TYR* 3.6 33.2 - + - -
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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