Contacts of the helix formed by residues 190 - 197 (chain B) in PDB entry 4BZ5
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 190 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141B HIS* 3.6 11.4 - - - -
182B TYR* 4.9 3.1 - - - -
184B ASP* 3.1 26.4 + - - -
188B HIS 3.4 1.8 + - - -
189B HIS* 1.3 72.7 + - - +
191B ASP* 1.3 62.4 + - - -
192B GLY 3.5 2.4 + - - -
193B VAL* 3.7 6.0 + - - +
194B GLU* 3.1 23.9 + - - +
207B SER* 3.2 16.1 + - - -
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Residues in contact with ASP 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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142B HIS* 2.6 35.6 + - - +
144B LYS* 3.6 23.0 + - - +
149B SER* 4.8 4.5 + - - -
189B HIS* 2.9 30.0 + - + +
190B GLY* 1.3 70.2 - - - +
192B GLY* 1.3 64.6 + - - +
194B GLU* 3.7 0.3 - - - +
195B GLU* 2.9 38.0 + - + +
217B PRO* 3.4 23.2 - - - +
219B THR* 3.6 10.2 + - + +
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Residues in contact with GLY 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B PHE* 4.6 2.8 - - - -
141B HIS 3.0 12.7 + - - -
142B HIS 4.2 0.7 - - - -
143B ALA 3.8 8.8 - - - +
144B LYS* 3.7 24.0 - - - +
155B ASN* 3.9 6.2 + - - -
158B VAL* 4.2 1.0 - - - +
191B ASP* 1.3 86.0 + - - +
193B VAL* 1.3 62.3 + - - +
195B GLU* 3.7 2.1 - - - +
196B ALA* 3.1 24.1 + - - +
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Residues in contact with VAL 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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141B HIS* 3.3 15.6 + - + +
155B ASN* 3.9 7.9 - - - +
157B ILE* 3.8 27.1 - - + -
158B VAL* 3.9 8.1 - - + -
161B ILE* 4.1 10.8 - - + -
182B TYR* 3.6 47.3 - - + +
190B GLY 3.7 3.2 + - - +
192B GLY* 1.3 73.7 - - - +
194B GLU* 1.3 66.7 + - - +
196B ALA 3.3 8.0 + - - -
197B PHE* 3.3 31.7 + - + +
205B THR* 4.1 3.3 - - + +
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Residues in contact with GLU 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B HIS* 3.0 27.5 + - - -
190B GLY 3.1 16.5 + - - +
191B ASP 3.7 4.2 - - - +
193B VAL* 1.3 79.4 - - - +
195B GLU* 1.3 59.8 + - + +
197B PHE* 3.3 3.5 + - - +
198B TRP* 2.9 60.9 + - + +
205B THR* 4.0 19.0 + - - +
207B SER* 5.4 1.3 - - - -
219B THR* 5.3 0.9 - - - -
220B GLY 5.1 1.2 + - - -
244B ALA* 4.0 12.3 - - + +
245B PHE 4.5 1.7 - - - +
246B ASN* 2.8 31.5 + - - +
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Residues in contact with GLU 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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9A ASP* 5.6 2.1 - - - +
62B PHE* 6.3 0.2 - - + -
144B LYS* 2.5 46.6 + - + +
191B ASP* 2.9 22.4 + - + +
192B GLY* 3.7 5.4 - - - +
194B GLU* 1.3 78.3 - - + +
196B ALA* 1.3 67.0 + - - +
197B PHE 3.2 0.7 + - - -
198B TRP* 3.2 23.0 + - + +
199B TYR* 5.3 2.9 - - - -
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Residues in contact with ALA 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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62B PHE* 3.6 31.6 - - + -
158B VAL* 3.6 25.6 - - + -
192B GLY 3.1 14.3 + - - +
193B VAL 3.3 3.3 + - - +
195B GLU* 1.3 79.4 - - - +
197B PHE* 1.3 69.0 + - + +
198B TRP 3.8 0.3 + - - -
199B TYR* 5.2 1.9 + - - -
200B SER* 5.6 0.2 - - - -
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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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158B VAL* 3.8 41.3 - - + -
161B ILE* 3.5 36.3 - - + -
162B HIS* 4.3 10.8 - - + -
165B VAL* 5.5 2.5 - - + -
193B VAL* 3.3 25.3 + - + +
194B GLU 3.3 5.9 + - - +
195B GLU 3.1 0.2 - - - -
196B ALA* 1.3 83.4 - - + +
198B TRP* 1.3 62.6 + - - +
199B TYR 3.1 3.6 - - - -
200B SER* 2.9 33.2 + - - +
203B VAL* 3.7 47.1 - - + +
205B THR* 4.6 4.9 - - + -
243B SER* 4.6 2.8 + - - -
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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