Contacts of the strand formed by residues 189 - 194 (chain B) in PDB entry 2W3S
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 GLY 189 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B PRO* 3.8 3.1 - - - +
186B ALA* 2.8 34.6 + - - -
187B GLU 3.0 2.2 + - - -
188B GLY* 1.3 78.3 + - - +
190B VAL* 1.3 62.0 + - - +
212B LEU* 4.5 5.4 - - - -
216B ASP* 3.3 24.0 + - - -
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Residues in contact with VAL 190 (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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183B ALA* 4.1 6.5 - - + -
184B LEU 3.4 20.9 - - - +
185B PRO* 4.3 3.6 - - + -
186B ALA* 4.2 1.1 - - - +
189B GLY* 1.3 75.4 - - - +
191B VAL* 1.3 86.2 + - - +
192B ILE* 3.8 14.1 - - + -
206B VAL* 4.0 15.0 - - + -
210B LEU* 3.9 26.7 - - + -
212B LEU* 4.6 0.4 - - + -
216B ASP 3.0 11.3 + - - +
217B VAL* 4.1 11.4 - - + -
218B ARG* 3.2 18.9 + - - +
243B ALA* 5.0 5.8 - - + +
246B ALA* 5.5 2.0 - - + -
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Residues in contact with VAL 191 (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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182B LEU 3.7 1.0 - - - +
183B ALA* 3.3 3.1 - - - -
184B LEU* 2.7 51.6 + - + +
186B ALA* 4.4 15.5 - - + -
190B VAL* 1.3 79.4 - - - +
192B ILE* 1.3 65.0 + - - +
193B HIS* 4.0 24.9 + - + +
218B ARG* 3.6 26.7 - - + +
220B GLU* 4.0 18.6 - - + +
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Residues in contact with ILE 192 (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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181B ALA* 4.9 2.0 - - + -
182B LEU 3.3 4.0 - - - +
183B ALA* 3.8 25.4 - - + -
190B VAL* 3.8 13.9 - - + -
191B VAL* 1.3 74.1 - - - +
193B HIS* 1.3 78.9 + - - +
194B CYS* 4.1 9.2 - - + -
202B ILE* 4.0 17.9 - - + -
206B VAL* 3.9 34.8 - - + -
217B VAL* 4.6 4.9 - - + -
218B ARG 2.8 16.5 + - - +
219B VAL* 3.4 13.5 - - + +
220B GLU* 3.0 28.1 + - - +
239B ALA* 4.3 10.8 - - + +
242B CYS* 5.5 0.4 - - + -
243B ALA* 4.3 4.3 - - + -
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Residues in contact with HIS 193 (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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23B LEU* 3.1 11.7 - - + +
26B LEU* 4.1 22.7 - - + +
181B ALA* 3.3 0.2 - - - -
182B LEU* 2.7 52.6 + - + +
184B LEU* 3.7 31.3 - - + +
191B VAL* 4.0 8.6 - - + +
192B ILE* 1.3 75.4 - - - +
194B CYS* 1.3 62.9 + - - +
220B GLU* 3.3 46.4 + - + +
221B MET* 5.8 0.2 - - - -
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Residues in contact with CYS 194 (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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23B LEU* 3.2 14.3 - - - +
180B ALA 3.4 8.7 - - - +
181B ALA* 3.8 10.5 - - + -
192B ILE* 4.1 7.0 - - + -
193B HIS* 1.3 78.7 - - - +
195B SER* 1.3 59.9 + - - +
196B SER* 3.2 30.4 + - - -
199B PRO* 5.6 0.2 - - - -
202B ILE* 4.3 12.1 - - + -
219B VAL* 4.1 23.6 - - - -
220B GLU 3.7 3.0 + - - -
221B MET* 3.2 24.1 - - - +
223B ARG 5.2 0.2 - - - +
235B GLY* 6.0 1.6 - - - +
239B ALA* 5.3 0.9 - - + -
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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