Contacts of the strand formed by residues 180 - 186 (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 ALA 180 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B LEU* 3.7 27.4 - - + -
24B ASP* 5.2 3.1 - - + +
177B GLU* 5.0 2.7 - - + +
178B GLY 3.7 7.6 + - - +
179B GLN* 1.3 79.5 + - - +
181B ALA* 1.3 62.9 + - - +
194B CYS* 3.4 1.2 - - - +
195B SER* 2.9 35.0 + - - +
238B LEU* 3.5 6.5 - - - +
255B MET 3.3 9.0 - - - -
256B ARG* 3.9 13.9 - - + -
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Residues in contact with ALA 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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23B LEU* 3.5 6.1 - - - +
180B ALA* 1.3 77.7 - - - +
182B LEU* 1.3 61.8 + - - +
192B ILE* 4.9 1.6 - - + -
193B HIS 3.3 11.0 - - - +
194B CYS* 3.8 9.6 - - + -
235B GLY 5.4 0.4 - - - +
238B LEU* 4.1 6.5 - - + -
239B ALA* 4.1 29.4 - - + +
242B CYS* 3.8 10.3 - - + -
254B LYS* 3.1 22.0 - - - +
255B MET 2.9 16.9 + - - -
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Residues in contact with LEU 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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23B LEU* 4.3 7.0 - - + +
26B LEU* 4.3 20.4 - - + +
27B PRO 4.8 1.1 - - - +
28B CYS* 4.5 22.7 - - + -
32B THR* 4.2 11.9 - - + -
181B ALA* 1.3 76.6 - - - +
183B ALA* 1.3 64.5 + - - +
184B LEU* 4.1 23.1 - - + -
191B VAL 3.7 0.9 - - - +
192B ILE* 3.3 5.3 - - - +
193B HIS* 2.7 60.5 + - + +
242B CYS* 4.3 1.6 - - - -
253B CYS 3.5 20.4 - - - +
254B LYS* 4.2 16.2 - - + -
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Residues in contact with ALA 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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182B LEU* 1.3 73.5 - - - +
184B LEU* 1.3 63.7 + - - +
185B PRO* 3.5 2.6 - - - +
190B VAL* 4.1 4.5 - - + -
191B VAL 3.3 4.3 - - - -
192B ILE* 3.8 15.0 - - + -
242B CYS* 3.5 37.0 - - + +
243B ALA* 3.8 7.4 - - - +
246B ALA* 4.3 2.9 - - + +
252B PRO* 3.3 8.7 - - - +
253B CYS 3.0 28.0 + - - +
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Residues in contact with LEU 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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28B CYS* 5.2 0.9 - - + -
29B PRO* 4.6 15.0 - - + -
182B LEU* 4.1 19.5 - - + -
183B ALA* 1.3 76.0 - - - +
185B PRO* 1.3 71.7 - - + +
186B ALA* 3.4 3.4 + - + +
190B VAL* 3.4 2.9 - - - +
191B VAL* 2.7 50.4 + - + +
193B HIS* 3.7 28.7 - - + +
252B PRO* 3.7 25.8 - - + -
27D PRO* 6.4 1.3 - - + -
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Residues in contact with PRO 185 (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 3.5 10.5 - - - +
184B LEU* 1.3 86.2 - - - +
186B ALA* 1.3 59.9 + - - +
187B GLU 4.0 1.1 - - - -
189B GLY 3.8 6.3 - - - +
190B VAL* 4.3 4.4 - - + -
246B ALA* 4.0 19.3 - - + +
247B ARG* 6.1 0.9 - - - -
250B GLY* 3.8 23.6 - - - +
251B ARG* 4.0 9.2 - - - +
252B PRO* 3.8 15.3 - - + -
21D ARG* 4.4 11.1 + - - -
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Residues in contact with ALA 186 (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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184B LEU* 4.0 8.3 - - + +
185B PRO* 1.3 75.4 - - - +
187B GLU* 1.3 76.5 + - - +
189B GLY* 2.8 26.4 + - - +
190B VAL 4.8 0.2 - - - +
191B VAL* 4.4 18.2 - - + -
21D ARG* 4.2 18.2 - - - +
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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