Contacts of the strand formed by residues 178 - 184 (chain B) in PDB entry 2R5N
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 178 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120B ILE* 4.7 7.6 - - + -
123B ALA* 4.2 17.0 - - + +
124B VAL* 3.8 27.8 - - + -
127B ALA* 4.0 11.8 - - + +
149B THR* 3.4 32.8 - - + +
151B ALA* 5.0 2.2 - - + -
170B ALA* 4.2 6.7 - - + -
175B LEU* 3.1 15.9 + - + +
176B GLY 4.5 1.2 - - - +
177B LYS* 1.3 78.5 - - - +
179B ILE* 1.3 69.4 + - - +
210B TRP* 3.7 31.4 - - + -
238B PRO* 3.4 8.5 - - + +
239B SER 3.0 23.0 + - - -
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Residues in contact with ILE 179 (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 TYR* 3.8 23.1 - - + -
149B THR 3.0 7.7 + - - +
150B TYR* 3.3 23.1 - - + +
151B ALA 3.0 21.7 + - - +
176B GLY 4.9 2.2 - - - +
177B LYS 3.7 0.9 + - - -
178B LEU* 1.3 80.6 - - - +
180B ALA* 1.3 61.6 + - - +
181B PHE* 4.0 21.9 - - + -
228B VAL* 4.8 2.7 - - + +
231B ALA* 3.8 20.4 - - + +
232B ARG* 3.7 32.8 - - + +
239B SER* 3.5 7.2 - - - +
241B LEU* 4.0 25.4 - - + -
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Residues in contact with ALA 180 (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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120B ILE* 4.3 13.0 - - + -
151B ALA* 3.3 8.7 - - + +
153B MET* 4.2 16.8 - - - -
178B LEU* 4.2 1.3 - - + -
179B ILE* 1.3 73.9 - - - +
181B PHE* 1.3 63.2 + - - +
210B TRP* 4.0 13.0 - - + -
239B SER 2.8 12.5 + - - +
240B LEU* 3.4 17.2 - - + +
241B LEU* 2.8 29.3 + - - +
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Residues in contact with PHE 181 (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 MET* 4.4 6.9 - - + +
36B ILE* 3.5 25.1 - - + -
40B LEU* 3.9 33.9 - - + -
150B TYR* 4.0 16.6 - + + -
151B ALA 2.7 16.3 + - - -
152B PHE* 3.5 25.0 - + + -
153B MET* 3.0 30.1 + - - +
179B ILE* 4.0 12.1 - - + -
180B ALA* 1.3 75.4 - - - +
182B TYR* 1.3 60.5 + - - +
183B ASP 3.7 0.5 + - - -
224B ILE* 4.7 3.1 - - + -
228B VAL* 3.7 24.0 - - + -
241B LEU* 3.5 31.4 - - + -
243B CYS* 4.0 13.0 - - - -
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Residues in contact with TYR 182 (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 MET* 5.1 0.2 - - - -
153B MET* 3.4 10.8 - - - -
154B GLY 3.7 11.0 - - - -
155B ASP* 2.5 29.1 + - - -
158B MET* 3.6 35.7 - - + -
180B ALA 4.0 1.2 + - - -
181B PHE* 1.3 72.1 - - - +
183B ASP* 1.3 68.1 + - - +
184B ASP* 3.0 36.5 + - + -
197B PHE* 3.5 14.4 - + - -
201B THR* 4.1 11.2 + - + -
240B LEU* 3.9 18.2 - - + -
241B LEU 2.9 15.0 + - - +
242B MET* 3.7 31.4 - - + -
243B CYS* 3.0 29.5 + - - +
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Residues in contact with ASP 183 (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 ALA* 4.3 10.0 - - - +
32B GLY* 4.5 1.7 - - - +
33B MET* 3.3 42.1 + - - +
64B ASN* 4.1 9.0 + - - +
153B MET 2.8 18.3 + - - +
154B GLY* 4.2 8.1 - - - -
155B ASP* 4.3 2.8 - - - +
181B PHE 3.7 1.4 + - - -
182B TYR* 1.3 77.3 - - - +
184B ASP* 1.3 57.8 + - - +
185B ASN* 3.1 28.8 + - - +
243B CYS* 4.0 2.2 - - - -
245B THR* 2.5 36.4 + - - +
672B TPP 4.4 1.9 + - - -
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Residues in contact with ASP 184 (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 ASP* 4.7 0.7 - - - +
182B TYR* 3.0 35.0 + - + +
183B ASP* 1.3 69.1 - - - +
185B ASN* 1.3 56.2 + - - +
186B GLY* 4.3 5.0 + - - -
242B MET* 3.9 21.1 - - - +
243B CYS 2.8 26.0 + - - +
244B LYS* 2.9 41.8 + - - -
245B THR 3.3 9.6 + - - -
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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