Contacts of the strand formed by residues 178 - 184 (chain B) in PDB entry 1R9J
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B ILE* 6.4 0.2 - - + -
123B ALA* 4.0 32.3 - - + +
124B VAL* 4.1 15.7 - - + -
127B ALA* 4.0 11.8 - - + +
149B THR* 3.7 17.7 - - + +
151B VAL* 4.2 10.3 - - + -
167B LEU* 5.4 1.1 - - + -
170B ALA* 3.9 28.3 - - + -
175B LEU* 3.1 17.0 + - + +
176B GLU 4.3 1.2 - - - +
177B LYS* 1.3 77.3 - - - +
179B ILE* 1.3 65.7 + - - +
180B VAL* 4.2 15.0 - - + -
210B PHE* 4.9 1.8 - - + -
239B PRO* 3.7 10.5 - - + +
240B LYS* 2.9 24.8 + - - +
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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* 4.0 18.8 - - + -
149B THR 2.8 9.1 + - - +
150B TYR* 3.4 44.9 - - + +
151B VAL* 3.1 24.0 + - - -
176B GLU 5.0 1.8 - - - +
177B LYS 4.1 7.4 - - - +
178B LEU* 1.3 78.6 - - - +
180B VAL* 1.3 65.2 + - - +
181B ILE* 3.7 5.9 + - + +
229B LEU* 4.8 1.3 - - + +
232B ALA* 3.9 37.9 - - + +
233B LYS* 4.3 7.9 - - + -
240B LYS* 3.7 10.5 - - + -
242B ILE* 4.2 17.7 - - + -
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Residues in contact with VAL 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B ILE* 3.9 13.0 - - + -
151B VAL* 3.6 18.8 - - + +
153B CYS* 3.7 28.3 - - - -
167B LEU* 4.3 12.1 - - + -
178B LEU* 4.2 15.7 - - + -
179B ILE* 1.3 73.2 - - - +
181B ILE* 1.3 59.3 + - - +
210B PHE* 4.2 14.8 - - + -
240B LYS 2.8 18.8 + - - +
241B MET* 3.2 20.8 - - + -
242B ILE* 2.7 34.3 + - - +
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Residues in contact with ILE 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* 3.9 20.3 - - + +
36B MET* 4.0 39.5 - - + -
40B LEU* 4.1 15.3 - - + -
150B TYR* 4.6 9.6 - - + -
151B VAL 2.9 8.6 + - - +
152B TYR* 3.5 31.8 - - + -
153B CYS 3.1 24.2 + - - +
179B ILE* 4.3 13.9 - - + +
180B VAL* 1.3 75.5 - - - +
182B TYR* 1.3 60.4 + - - +
183B ASP 3.6 0.7 + - - -
229B LEU* 4.4 9.2 - - + -
242B ILE* 3.6 11.2 - - + +
244B GLN* 4.0 9.0 - - - +
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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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153B CYS* 3.6 20.2 - - - -
154B GLY 3.7 12.8 - - - -
155B ASP* 2.3 32.8 + - - -
158B LEU* 3.4 32.3 - - + -
180B VAL 3.8 1.2 - - - -
181B ILE* 1.3 71.2 - - - +
183B ASP* 1.3 73.8 + - - +
184B SER* 3.2 22.7 + - - -
197B PHE* 3.8 11.1 - - - -
201B CYS* 4.4 16.1 - - + +
241B MET* 4.2 19.3 - - + -
242B ILE 2.8 13.8 + - - +
243B VAL* 3.7 26.0 - - + -
244B GLN* 3.1 28.4 + - - +
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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 THR* 4.1 13.3 + - - +
32B GLY* 4.5 1.0 - - - +
33B MET* 3.4 37.0 + - + +
64B ASN* 4.8 0.7 - - - +
153B CYS 2.9 17.5 + - - +
154B GLY* 3.9 10.8 - - - -
155B ASP* 4.2 3.8 - - - +
181B ILE 3.6 1.6 + - - -
182B TYR* 1.3 78.2 - - - +
184B SER* 1.3 58.7 + - - +
185B ASN* 3.4 25.9 + - - -
244B GLN* 3.1 19.3 + - - -
246B THR* 2.6 26.4 + - - +
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Residues in contact with SER 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* 4.3 3.3 + - - -
182B TYR* 3.2 33.9 + - - -
183B ASP* 1.3 70.0 - - - +
185B ASN* 1.3 59.1 + - - +
186B TYR* 3.6 22.2 + - - -
243B VAL* 4.2 12.1 - - - +
244B GLN 2.9 15.7 + - - -
245B THR* 3.2 14.0 + - - +
246B THR 3.1 20.2 + - - -
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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