Contacts of the strand formed by residues 186 - 194 (chain B) in PDB entry 3GW5
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 TYR 186 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181B SER* 3.9 9.2 + - - -
182B ASP 3.3 31.4 - - - -
183B PRO* 2.9 38.6 - - + +
185B HIS* 1.3 77.4 - - - +
187B GLU* 1.3 63.0 + - - +
188B GLY 3.8 19.3 - - - -
189B ASN* 5.2 0.9 - - - -
190B PHE* 3.5 33.5 - + - -
324B TYR* 3.8 23.3 - + + -
337B ALA* 3.7 23.8 - - + -
338B LEU 3.1 15.3 - - - +
340B ARG* 3.0 13.6 + - - -
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Residues in contact with GLU 187 (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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186B TYR* 1.3 81.0 - - - +
188B GLY* 1.3 69.8 + - - +
189B ASN 3.8 0.9 + - - +
337B ALA* 4.2 1.2 - - - +
338B LEU* 2.9 54.7 + - + +
339B ALA 5.1 2.0 - - - +
340B ARG* 3.8 23.4 - - - +
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Residues in contact with GLY 188 (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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186B TYR* 3.8 14.9 - - - -
187B GLU* 1.3 80.0 - - - +
189B ASN* 1.3 70.0 + - - +
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Residues in contact with ASN 189 (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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186B TYR* 5.2 1.1 - - - -
187B GLU 3.8 1.1 + - - +
188B GLY* 1.3 80.2 - - - +
190B PHE* 1.3 69.0 + - - +
191B HIS 3.7 1.4 + - - -
336B PHE 4.0 4.7 - - - +
337B ALA* 4.1 9.5 - - - +
504B GOL 4.4 4.7 + - - -
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Residues in contact with PHE 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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181B SER* 3.5 26.5 - - - -
186B TYR* 3.5 35.4 - + - -
189B ASN* 1.3 79.4 - - - +
191B HIS* 1.3 59.7 + - - +
192B TYR* 3.5 43.7 + + + -
324B TYR* 3.7 26.2 - + - -
326B GLU* 3.9 13.7 - - + -
335B GLY* 3.6 31.9 - - - -
336B PHE 3.5 8.3 - - - -
337B ALA* 3.7 10.8 - - + -
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Residues in contact with HIS 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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189B ASN 3.7 0.2 + - - -
190B PHE* 1.3 73.6 - - - +
192B TYR* 1.3 72.5 + - - +
193B ILE* 3.8 11.5 - - + +
272B LEU 3.3 17.3 - - - -
273B GLY* 3.1 33.5 + - - -
275B LYS* 3.5 39.6 - - + +
277B TYR* 2.7 28.0 + - - +
334B ILE 3.7 1.2 - - - +
335B GLY* 3.3 1.9 - - - -
336B PHE* 2.9 27.6 + - - +
504B GOL 3.6 14.4 - - - +
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Residues in contact with TYR 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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190B PHE* 3.5 35.7 + - + -
191B HIS* 1.3 81.2 + - - +
193B ILE* 1.3 67.7 + - - +
326B GLU* 2.7 33.5 + - + -
328B ASP* 5.1 0.9 - - + -
333B ARG* 3.2 64.0 + - + +
334B ILE 3.5 0.7 - - - -
335B GLY* 3.6 24.7 - - - -
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Residues in contact with ILE 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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191B HIS* 3.8 31.0 - - + +
192B TYR* 1.3 82.0 - - - +
194B ASN* 1.3 77.6 + - + +
203B ILE* 3.8 23.0 - - + +
204B GLN* 5.1 4.5 - - + +
272B LEU* 3.9 24.5 - - + -
273B GLY* 3.9 17.9 - - - +
277B TYR* 4.3 0.2 - - - +
333B ARG* 3.3 5.6 - - - +
334B ILE* 2.9 31.8 + - + +
336B PHE* 4.0 24.2 - - + -
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Residues in contact with ASN 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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193B ILE* 1.3 83.4 - - + +
195B LEU* 1.3 68.2 + - - +
196B ILE 3.9 0.3 + - - -
203B ILE* 3.2 18.5 - - - +
204B GLN 4.9 1.0 + - - -
331B ASN 4.7 5.3 + - - -
332B ASN* 4.1 12.7 + - - +
333B ARG* 4.5 3.0 - - - +
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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
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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