Contacts of the helix formed by residues 189 - 201 (chain B) in PDB entry 5LSJ
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 ALA 189 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A ARG* 6.3 3.8 - - + -
185B GLN 2.9 13.9 + - - +
186B ALA* 3.7 11.4 - - - +
187B TRP 3.2 1.2 - - - -
188B GLN* 1.3 73.4 - - - +
190B LEU* 1.3 64.4 + - + +
191B HIS 3.1 3.1 + - - -
192B ARG* 3.1 45.2 + - - +
193B GLU* 4.3 2.0 + - - +
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Residues in contact with LEU 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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174A PHE* 3.7 18.2 - - + -
175A ARG* 3.4 42.6 - - + +
178A LEU* 5.0 5.4 - - + -
186B ALA 4.6 6.1 - - - +
187B TRP* 3.5 49.8 - - + +
188B GLN 3.2 0.8 - - - -
189B ALA* 1.3 77.7 - - + +
191B HIS* 1.3 62.3 + - - +
192B ARG 3.3 0.2 - - - -
193B GLU* 3.1 11.5 + - + +
194B GLN* 3.0 39.2 + - + +
291D VAL* 5.4 2.9 - - + -
295D LEU* 4.6 12.1 - - + -
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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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188B GLN 3.4 14.9 + - - +
189B ALA 3.1 1.4 - - - -
190B LEU* 1.3 78.0 - - - +
192B ARG* 1.3 60.4 + - + +
194B GLN* 3.2 4.9 + - - +
195B ARG* 2.9 62.5 + - + +
294D GLU* 2.6 40.1 + - - +
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Residues in contact with ARG 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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175A ARG* 3.6 33.7 - - - +
189B ALA* 3.1 33.0 + - - +
191B HIS* 1.3 83.3 - - + +
193B GLU* 1.3 92.9 + - - +
195B ARG* 3.0 10.9 + - - +
196B GLU* 2.9 24.1 + - - +
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Residues in contact with GLU 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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175A ARG* 4.3 32.7 + - + +
178A LEU* 3.7 29.2 - - + -
179A VAL* 4.7 14.7 - - - +
182A VAL* 4.0 6.3 - - + +
189B ALA 4.3 4.5 - - - +
190B LEU* 3.1 12.5 + - - +
192B ARG* 1.3 111.7 + - + +
194B GLN* 1.3 58.3 + - - +
196B GLU* 3.3 20.1 + - - +
197B LEU* 2.9 27.2 + - - +
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Residues in contact with GLN 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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178A LEU* 4.1 11.0 - - + -
190B LEU* 3.0 27.6 + - + +
191B HIS* 3.6 5.8 - - - +
193B GLU* 1.3 75.5 - - - +
195B ARG* 1.3 59.5 + - - +
197B LEU* 3.2 8.6 + - - +
198B VAL* 2.9 34.0 + - - +
291D VAL* 4.6 4.2 + - - +
294D GLU* 3.1 41.1 + - + +
295D LEU* 3.0 51.9 + - + +
298D SER* 3.2 17.7 + - - +
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Residues in contact with ARG 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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191B HIS* 2.9 50.4 + - + +
192B ARG* 3.0 12.3 + - - +
194B GLN* 1.3 77.8 - - + +
196B GLU* 1.3 57.9 + - - +
198B VAL* 3.4 7.3 + - - +
199B ALA* 2.9 27.1 + - - +
202B ARG* 5.6 0.2 + - - -
294D GLU* 5.3 0.2 - - - +
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Residues in contact with GLU 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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179A VAL* 5.4 3.2 - - - +
182A VAL* 4.1 21.7 - - + +
183A GLN* 5.8 1.4 + - - -
186A ARG* 3.6 28.7 + - - +
192B ARG 2.9 13.5 + - - +
193B GLU* 3.5 21.9 - - - +
195B ARG* 1.3 73.4 - - - +
197B LEU* 1.3 60.8 + - - +
199B ALA* 3.6 8.3 - - + +
200B VAL* 2.9 29.6 + - + +
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Residues in contact with LEU 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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178A LEU* 5.0 6.7 - - + -
181A LEU* 3.5 32.3 - - + +
182A VAL* 3.4 28.4 - - + +
185A SER* 5.4 2.7 - - - +
193B GLU 2.9 9.8 + - - +
194B GLN* 3.3 12.1 - - - +
196B GLU* 1.3 77.8 - - - +
198B VAL* 1.3 69.2 + - + +
200B VAL* 3.2 6.2 + - - +
201B LEU* 3.0 40.6 + - + +
298D SER* 3.9 29.8 - - - +
301D GLN* 5.0 1.8 - - + -
302D LEU* 4.4 14.6 - - + +
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Residues in contact with VAL 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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194B GLN 2.9 17.7 + - - +
195B ARG* 3.8 7.4 - - - +
197B LEU* 1.3 86.0 - - + +
199B ALA* 1.3 62.7 + - - +
201B LEU* 3.3 6.3 + - - +
202B ARG* 3.3 33.2 + - + +
298D SER* 4.2 10.5 - - - +
301D GLN* 3.6 31.6 - - + +
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Residues in contact with ALA 199 (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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195B ARG 2.9 17.8 + - - +
196B GLU* 3.6 10.8 - - + +
197B LEU 3.2 0.2 - - - -
198B VAL* 1.3 74.6 - - - +
200B VAL* 1.3 65.7 + - + +
201B LEU 3.4 0.3 + - - -
202B ARG* 3.5 38.3 + - - +
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Residues in contact with VAL 200 (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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182A VAL* 4.5 9.2 - - + +
185A SER* 4.3 13.5 - - - +
186A ARG* 3.3 65.5 - - + +
189A GLN* 3.3 26.1 + - + -
196B GLU* 2.9 22.5 + - + +
197B LEU* 3.2 7.2 + - + +
199B ALA* 1.3 76.6 - - + +
201B LEU* 1.3 62.0 + - + +
202B ARG 3.2 5.4 + - - +
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Residues in contact with LEU 201 (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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185A SER* 3.9 10.8 - - - +
189A GLN* 4.3 8.5 - - - +
197B LEU* 3.0 22.0 + - + +
198B VAL* 3.3 8.3 + - - +
199B ALA 3.2 0.6 - - - -
200B VAL* 1.3 77.6 - - + +
202B ARG* 1.3 58.1 + - - +
203B GLU 4.2 1.0 + - - -
301D GLN* 3.2 45.3 + - + +
302D LEU* 3.8 20.4 - - + -
305D PHE* 3.5 49.0 - - + -
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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