Contacts of the strand formed by residues 193 - 198 (chain B) in PDB entry 1HBX
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 HIS 193 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B ALA* 3.5 0.2 - - - -
189B SER* 2.7 35.0 + - - +
191B THR* 3.2 22.6 + - - -
192B GLY* 1.3 76.9 - - - +
194B VAL* 1.3 61.0 + - - +
195B TYR* 3.2 41.2 - + + +
9C A 4.1 10.6 + - - -
149G SER* 5.8 2.0 - - - -
150G PHE* 3.3 21.3 - - - +
151G THR* 4.1 15.3 - - + +
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Residues in contact with VAL 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B LEU* 4.2 22.2 - - + -
187B VAL 3.6 2.7 - - - +
188B ALA* 4.3 3.4 - - + +
192B GLY 3.4 4.2 + - - +
193B HIS* 1.3 75.2 - - - +
195B TYR* 1.3 62.9 + - - +
196B THR* 4.0 10.3 - - + -
215B ILE* 4.7 3.8 - - + -
219B LEU* 3.7 25.6 - - + -
149G SER* 3.4 1.9 - - - -
150G PHE* 2.8 67.3 + - + -
152G LEU* 3.9 24.9 - - + +
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Residues in contact with TYR 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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161B PHE* 4.5 1.8 - + - -
165B LYS* 3.2 39.7 - - + -
169B MET* 3.8 19.7 - - + -
186B LEU* 3.5 1.7 - - - +
187B VAL* 2.7 40.1 + - + +
189B SER* 4.2 9.4 - - - -
193B HIS* 3.2 50.2 - + + +
194B VAL* 1.3 72.4 - - - +
196B THR* 1.3 68.6 + - - +
8C T 3.3 15.8 + - - -
9C A 4.2 17.0 + - - -
147G TYR* 2.9 24.0 - - - +
148G SER 3.8 3.6 - - - -
149G SER* 3.5 14.4 - - - +
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Residues in contact with THR 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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169B MET* 4.0 4.5 - - - +
185B LEU 3.4 9.6 - - - -
186B LEU* 4.6 9.2 - - + -
194B VAL* 4.0 9.0 - - + -
195B TYR* 1.3 83.3 - - - +
197B PHE* 1.3 62.0 + - - +
206B ILE* 2.8 34.7 - - + +
215B ILE* 6.1 0.2 - - + -
146G LEU 3.9 1.2 + - - +
147G TYR* 3.3 7.8 - - - -
148G SER* 2.7 43.6 + - - +
150G PHE* 3.8 25.6 - - + -
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Residues in contact with PHE 197 (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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169B MET* 3.8 21.0 - - - +
172B ALA* 3.8 19.5 - - + -
173B TYR* 3.8 31.2 - + + -
176B SER* 3.7 17.3 - - - -
183B VAL* 4.1 7.9 - - + -
184B LEU* 2.9 8.0 - - - +
185B LEU* 2.9 35.3 + - + +
196B THR* 1.3 75.2 - - - +
198B ALA* 1.3 65.3 + - - +
199B THR* 3.9 16.4 - - + -
141G TYR* 4.7 11.7 - - + -
144G SER* 4.0 8.3 - - - -
146G LEU* 3.3 50.3 - - + -
147G TYR* 4.3 5.4 - - + -
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Residues in contact with ALA 198 (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 VAL 3.5 7.9 - - - +
184B LEU* 3.7 15.5 - - + -
196B THR* 5.1 2.0 - - - +
197B PHE* 1.3 85.3 - - - +
199B THR* 1.3 60.9 + - - +
202B LEU 3.9 20.2 - - - +
203B GLN* 2.9 32.0 - - - +
206B ILE* 5.0 7.2 - - + -
146G LEU* 3.2 21.8 + - - +
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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