Contacts of the helix formed by residues 185 - 192 (chain B) in PDB entry 4LXZ
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 185 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B HIS* 3.4 13.0 - - - -
177B TYR* 4.7 4.6 - - - -
179B ASP* 3.2 23.7 + - - -
183B HIS 3.5 1.8 + - - -
184B HIS* 1.3 74.8 - - - +
186B ASP* 1.3 57.9 + - - -
187B GLY 3.5 1.8 - - - -
188B VAL* 3.5 6.1 + - - +
189B GLU* 3.0 28.8 + - - +
200B THR* 5.8 0.2 - - - -
202B SER* 3.4 13.8 + - - -
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Residues in contact with ASP 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B HIS* 2.7 29.6 + - - +
148B LYS* 3.4 23.5 + - - +
153B SER* 4.9 2.6 + - - -
184B HIS* 2.9 18.4 + - + +
185B GLY* 1.3 68.3 - - - +
187B GLY* 1.3 64.5 + - - -
189B GLU* 3.7 1.0 - - - +
190B GLU* 2.8 33.7 + - - +
211B PRO* 3.5 26.1 - - + +
213B THR* 3.4 25.8 + - + +
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Residues in contact with GLY 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B TYR* 4.3 4.7 + - - -
145B HIS 3.1 13.7 + - - -
146B HIS 4.2 0.7 - - - -
147B ALA 3.9 15.1 - - - +
148B LYS* 3.9 16.6 - - - +
159B ASN* 3.8 6.0 + - - -
162B VAL* 3.9 2.4 - - - +
186B ASP* 1.3 84.5 + - - +
188B VAL* 1.3 60.8 + - - +
190B GLU* 3.9 1.8 - - - +
191B ALA* 3.1 23.0 + - - +
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Residues in contact with VAL 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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145B HIS* 4.0 9.4 - - + +
159B ASN* 3.9 8.1 - - - +
161B ILE* 3.8 32.1 - - + -
162B VAL* 3.9 7.2 - - + -
165B ILE* 3.8 24.5 - - + -
177B TYR* 3.6 43.7 - - + +
185B GLY 3.5 3.0 + - - +
186B ASP 3.3 0.4 - - - -
187B GLY* 1.3 72.9 - - - +
189B GLU* 1.3 65.9 + - - +
191B ALA 3.4 5.4 + - - -
192B PHE* 3.3 26.8 - - + +
200B THR* 4.0 6.0 - - + +
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Residues in contact with GLU 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B HIS* 2.8 29.1 + - - +
185B GLY 3.0 17.5 + - - +
186B ASP 3.7 4.9 - - - +
188B VAL* 1.3 77.8 - - - +
190B GLU* 1.3 56.0 + - - +
192B PHE 3.5 1.7 - - - -
193B TYR* 2.8 60.6 + - + -
200B THR* 3.9 27.3 + - - +
202B SER* 5.6 0.3 - - - -
213B THR* 5.4 1.2 - - - -
218B ASP* 4.4 7.1 - - - +
228B ALA* 4.3 5.1 - - + +
229B VAL 5.0 0.7 - - - +
230B ASN* 2.8 32.1 + - - +
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Residues in contact with GLU 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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72B TYR* 4.4 8.6 + - - +
148B LYS* 3.6 40.1 + - - +
149B LYS* 5.0 2.3 + - - +
186B ASP 2.8 22.5 + - - +
187B GLY 3.9 3.5 - - - +
189B GLU* 1.3 72.2 - - - +
191B ALA* 1.4 65.8 + - - +
192B PHE 3.2 1.2 + - - -
193B TYR* 3.3 20.3 + - + +
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Residues in contact with ALA 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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72B TYR* 3.5 34.8 + - + +
162B VAL* 3.7 25.6 - - + -
187B GLY 3.1 16.4 + - - +
188B VAL 3.4 4.4 + - - +
190B GLU* 1.4 76.0 - - - +
192B PHE* 1.4 68.6 + - + +
193B TYR 4.1 0.2 + - - -
194B THR* 5.5 0.9 + - - -
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Residues in contact with PHE 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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162B VAL* 3.9 24.9 - - + -
165B ILE* 3.5 38.6 - - + -
166B LEU* 4.0 15.5 - - + -
169B LEU* 4.0 18.4 - - + -
188B VAL* 3.3 28.9 + - + +
189B GLU 3.4 5.1 + - - +
190B GLU 3.2 0.4 - - - -
191B ALA* 1.4 88.8 - - + +
193B TYR* 1.3 58.8 + - - +
194B THR 3.2 4.0 + - - -
195B THR* 3.2 26.6 + - + +
198B VAL* 3.7 32.1 - - + +
200B THR* 4.7 2.7 - - + -
403B NA 2.5 29.6 - - - -
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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