Contacts of the strand formed by residues 180 - 184 (chain B) in PDB entry 4BZ5
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 VAL 180 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B ILE* 4.2 23.1 - - + -
164B LEU* 4.1 24.5 - - + -
165B VAL* 4.2 20.4 - - + +
178B THR* 5.1 0.2 - - + -
179B ARG* 1.3 79.8 - - - +
181B LEU* 1.3 71.9 + - - +
182B TYR 4.4 1.8 - - - +
202B ARG 2.8 12.5 + - - +
203B VAL* 3.3 4.6 - - + -
204B VAL* 2.8 29.1 + - - +
273B ILE* 5.2 1.5 - - - +
275B PRO* 4.5 0.9 - - - -
277B TYR* 3.5 19.3 - - + +
279B VAL* 4.1 22.2 - - + -
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Residues in contact with LEU 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B VAL* 1.3 74.1 - - - +
182B TYR* 1.3 66.5 + - - +
183B VAL* 4.0 15.9 - - + -
204B VAL* 3.5 29.8 - - + +
206B PHE* 4.8 2.0 - - + -
266B LEU* 5.4 0.2 - - + -
269B LEU* 4.0 32.5 - - + +
270B ASN 4.5 3.1 - - - +
273B ILE* 4.0 11.2 - - + -
275B PRO* 3.8 24.7 - - + +
277B TYR 3.0 8.0 + - - +
278B VAL* 3.3 9.2 - - + +
279B VAL 2.9 23.9 + - - -
329B TRP* 4.0 28.5 - - + -
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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
----------------------------------------------------------
141B HIS* 3.7 3.3 - - - +
157B ILE* 3.5 32.2 - - + +
161B ILE* 4.0 14.8 - - + -
180B VAL* 4.0 1.0 + - + -
181B LEU* 1.3 73.4 - - - +
183B VAL* 1.3 64.0 + - - +
184B ASP* 2.6 45.2 + - + -
190B GLY* 5.0 3.6 - - - -
193B VAL* 3.6 30.7 - - + -
203B VAL* 4.8 2.5 - - + -
204B VAL 2.8 16.0 + - - +
205B THR* 3.6 18.1 - - + -
206B PHE* 2.8 31.6 + - - +
207B SER* 5.9 0.7 - - - -
279B VAL* 3.3 29.8 - - + +
281B GLN* 3.4 21.4 - - + +
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Residues in contact with VAL 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B LEU* 4.0 22.2 - - + -
182B TYR* 1.3 81.6 - - - +
184B ASP* 1.3 56.5 + - - +
185B LEU* 3.6 26.7 - - + -
206B PHE* 3.4 11.4 - - + -
266B LEU* 3.8 32.5 - - + -
278B VAL* 4.4 12.6 - - + -
279B VAL 2.8 11.7 + - - +
280B VAL* 3.2 10.0 - - + +
281B GLN* 2.8 32.2 + - - +
326B ILE* 4.3 11.4 - - + -
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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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141B HIS* 2.7 22.0 + - - -
182B TYR* 2.6 33.4 + - + +
183B VAL* 1.3 73.4 - - - +
185B LEU* 1.3 59.0 + - - +
186B ASP* 3.2 26.9 + - - +
188B HIS 4.0 2.4 - - - +
190B GLY* 3.1 18.2 - - - -
206B PHE 2.8 13.7 + - - +
207B SER* 3.7 10.3 - - - +
208B VAL* 3.2 29.5 + - - +
281B GLN* 3.5 6.5 - - - +
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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