Contacts of the strand formed by residues 188 - 196 (chain B) in PDB entry 5I75
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 188 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179B TRP* 4.0 21.5 - - + +
184B LEU 4.9 0.4 - - - +
185B SER* 3.9 33.7 + - - +
186B SER 3.9 0.2 - - - -
187B SER* 1.3 76.8 - - - +
189B HIS* 1.3 62.5 + - - +
190B THR* 4.0 12.5 + - - +
204B SER* 3.8 15.7 - - - +
205B SER 3.2 15.9 - - - +
206B VAL* 3.6 26.0 - - + +
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Residues in contact with HIS 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B SER* 3.3 27.9 + - - -
188B VAL* 1.3 74.9 + - - +
190B THR* 1.3 61.6 + - - +
191B PHE* 3.9 14.4 - - + -
204B SER* 3.6 1.7 - - - -
205B SER* 2.9 48.2 + - - +
207B THR* 4.5 10.7 + - - -
157C ASN* 4.6 11.9 - - + +
158C ASN* 3.8 28.9 + - - -
184C THR* 6.1 1.6 - - + -
187C ASP* 4.8 13.9 + - - -
192C THR* 5.4 3.1 - - - -
194C SER* 3.4 28.5 + - - -
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Residues in contact with THR 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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177B VAL* 5.5 4.2 + - + -
188B VAL* 4.0 11.8 + - - +
189B HIS* 1.3 72.6 - - - +
191B PHE* 1.3 67.8 + - - +
192B PRO* 3.9 1.6 - - - +
202B MET* 3.8 24.5 - - + -
203B SER 4.2 2.5 - - - +
204B SER* 3.9 12.7 + - - -
184C THR* 3.4 16.8 - - - +
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Residues in contact with PHE 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 HIS* 3.9 10.3 - - + -
190B THR* 1.3 75.6 - - - +
192B PRO* 1.3 73.4 - - + +
193B ALA 3.6 1.6 + - - -
202B MET* 3.7 16.3 - - - +
203B SER* 3.0 41.8 + - - +
205B SER* 3.8 16.6 - - - -
155C PHE* 3.4 35.7 - + - -
157C ASN* 4.0 14.4 - - - -
182C SER* 4.0 5.4 - - - +
184C THR* 3.6 16.4 - - + -
194C SER* 4.1 6.7 - - - -
195C MET* 3.3 31.2 - - - -
196C SER* 3.5 24.2 - - - +
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Residues in contact with PRO 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 THR 3.9 2.0 - - - +
191B PHE* 1.3 86.3 - - - +
193B ALA* 1.3 68.9 + - - +
194B LEU* 3.7 7.8 + - + +
201B THR 4.4 2.1 - - - +
202B MET* 4.4 1.9 - - - +
182C SER* 3.2 28.0 + - - +
183C TRP 3.8 15.5 - - - +
184C THR* 3.5 24.7 - - + -
185C ASP* 5.3 2.9 - - - +
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Residues in contact with ALA 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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170B TYR* 3.3 26.9 - - - +
173B GLU* 5.8 3.4 - - + -
175B VAL* 5.8 0.2 - - + -
191B PHE 3.6 1.8 + - - -
192B PRO* 1.3 79.3 - - - +
194B LEU* 1.3 64.9 + - - +
195B LEU 4.3 0.3 + - - -
200B TYR* 4.3 19.2 - - + -
201B THR 3.5 8.1 - - - +
202B MET* 3.6 10.7 - - + +
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Residues in contact with LEU 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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192B PRO* 4.1 12.6 - - + +
193B ALA* 1.3 81.7 - - - +
195B LEU* 1.3 63.4 + - - +
196B GLN* 3.9 3.8 + - + +
199B LEU 3.7 0.9 - - - +
200B TYR* 3.3 4.0 - - - -
201B THR* 2.9 38.6 + - - +
180C LEU* 3.9 43.3 - - + -
181C ASN 4.3 9.4 - - - +
182C SER* 4.3 22.0 - - - +
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Residues in contact with LEU 195 (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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171B PHE* 4.6 5.6 - - + -
193B ALA 4.3 0.2 + - - -
194B LEU* 1.3 73.1 - - - +
196B GLN* 1.3 64.0 + - - +
198B GLY* 3.6 14.1 - - - +
199B LEU 3.6 34.5 - - - +
200B TYR* 3.6 43.9 - - + +
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Residues in contact with GLN 196 (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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168B LYS* 5.9 0.8 - - - +
194B LEU* 4.3 4.9 - - + +
195B LEU* 1.3 80.1 - - - +
197B SER* 1.3 78.2 + - - +
198B GLY 3.1 1.8 - - - -
199B LEU* 2.9 29.2 + - + +
201B THR* 3.6 27.4 + - - +
180C LEU* 3.5 30.5 - - - +
200C THR* 5.8 1.8 + - - -
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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