Contacts of the strand formed by residues 179 - 184 (chain B) in PDB entry 3BEQ
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 SER 179 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B LEU* 4.2 1.3 - - - -
177B ALA* 3.6 2.0 - - - +
178B TRP* 1.3 88.3 - - - +
180B ALA* 1.3 64.8 + - - +
193B GLY* 3.7 0.3 - - - -
194B ILE* 2.9 35.7 + - - +
224B ARG* 3.7 1.7 - - - +
225B THR* 3.0 27.3 + - - -
227B GLU* 2.5 28.1 + - - -
3001B ACT 3.7 14.4 - - - -
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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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119B GLU* 4.5 2.5 - - - +
121B PHE* 4.4 2.9 - - + -
134B LEU* 4.0 11.9 - - + -
158B LEU* 3.7 32.5 - - + -
177B ALA* 4.3 3.4 - - + -
179B SER* 1.3 77.9 + - - +
181B SER* 1.3 62.0 + - - +
192B ILE 3.2 13.2 - - - +
225B THR* 3.5 7.8 - - - +
227B GLU* 2.9 42.9 + - - +
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Residues in contact with SER 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B PHE* 3.8 7.2 - - - -
158B LEU* 4.2 4.0 - - - +
180B ALA* 1.3 76.7 - - - +
182B ALA* 1.3 67.7 + - - +
191B THR* 3.5 0.5 - - - -
192B ILE* 2.8 49.3 + - - +
225B THR* 4.0 8.7 - - - +
226B GLN* 3.3 13.2 + - - -
228B SER 2.8 21.7 + - - -
230B CYS* 3.2 17.6 + - - +
239B THR* 4.4 2.0 - - - -
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Residues in contact with ALA 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B PHE* 3.6 10.4 - - + -
123B SER* 3.5 4.0 + - - -
132B PHE* 3.7 39.3 - - + -
158B LEU* 4.9 0.7 - - + -
181B SER* 1.3 79.7 + - - +
183B CYS* 1.3 67.0 + - - +
189B TRP* 4.7 0.4 - - + -
190B LEU 3.2 14.8 - - - +
191B THR* 3.8 6.7 - - + +
229B GLU* 3.2 23.7 - - - +
230B CYS* 3.3 5.2 - - - -
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Residues in contact with CYS 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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123B SER* 3.6 11.9 - - - +
182B ALA* 1.3 73.2 - - - +
184B HIS* 1.3 61.4 + - - +
185B ASP 4.2 0.3 + - - -
188B GLY 4.0 0.2 - - - +
189B TRP* 3.6 6.0 - - - -
190B LEU* 2.8 39.9 + - - +
229B GLU* 5.2 0.7 - - - +
230B CYS* 2.0 62.6 - - - +
232B CYS* 3.4 24.2 - - - -
237B CYS* 3.7 10.1 - - - -
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Residues in contact with HIS 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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85B LEU* 3.4 18.6 - - - +
123B SER* 4.4 0.2 + - - -
124B CYS 3.6 22.4 + - - +
125B SER* 3.4 23.3 - - - -
126B HIS* 3.7 18.3 + + - -
183B CYS* 1.3 75.7 - - - +
185B ASP* 1.3 58.5 + - - +
186B GLY* 2.9 48.0 + - - -
187B MET 3.7 2.6 + - - -
188B GLY* 3.4 33.1 - - - -
189B TRP* 3.6 30.9 - + + -
232B CYS* 3.4 11.0 - - - +
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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
------------------------------------------------------------
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