Contacts of the helix formed by residues 189 - 201 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175C ARG* 5.3 11.0 - - - -
185E GLN 2.9 10.2 + - - +
186E ALA* 3.7 15.5 - - - +
187E TRP 3.3 1.4 - - - -
188E GLN* 1.3 73.0 - - - +
190E LEU* 1.3 61.2 + - + +
191E HIS 3.0 7.1 + - - -
192E ARG* 3.4 20.4 + - - +
193E GLU* 2.9 18.9 - - - +
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Residues in contact with LEU 190 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C ASP* 5.4 0.2 - - - +
174C PHE* 3.7 18.8 - - + -
175C ARG* 3.3 42.8 - - + +
178C LEU* 4.6 9.4 - - + -
186E ALA 4.8 4.9 - - - +
187E TRP* 3.6 49.6 - - + +
188E GLN 3.1 0.8 - - - -
189E ALA* 1.3 77.5 - - + +
191E HIS* 1.3 62.8 + - - +
192E ARG 3.3 0.4 - - - -
193E GLU* 3.2 10.5 + - - +
194E GLN* 3.0 35.3 + - - +
291F VAL* 5.3 4.3 - - + -
295F LEU* 4.6 10.5 - - + -
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Residues in contact with HIS 191 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188E GLN* 3.3 15.5 + - - +
189E ALA 3.0 1.4 - - - -
190E LEU* 1.3 79.0 - - - +
192E ARG* 1.3 62.2 + - + +
194E GLN* 3.3 6.0 + - - +
195E ARG* 2.9 45.1 + - + +
291F VAL* 6.4 1.8 - - + -
294F GLU* 2.8 38.3 + - - +
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Residues in contact with ARG 192 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175C ARG* 4.0 27.1 - - - +
189E ALA* 3.4 15.5 + - - +
191E HIS* 1.3 84.9 - - + +
193E GLU* 1.3 78.8 + - - +
195E ARG* 2.8 30.5 + - + +
196E GLU* 2.5 27.6 + - - +
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Residues in contact with GLU 193 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175C ARG* 2.6 46.7 + - + +
178C LEU* 3.9 30.7 - - + -
179C VAL* 4.7 9.6 - - + +
182C VAL* 4.0 6.4 - - + +
189E ALA 2.9 28.6 - - - +
190E LEU* 3.2 8.1 + - - +
192E ARG* 1.3 95.1 + - - +
194E GLN* 1.3 58.4 + - - +
196E GLU* 3.1 17.4 - - - +
197E LEU* 3.0 28.6 + - - +
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Residues in contact with GLN 194 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178C LEU* 3.8 15.7 - - + -
190E LEU* 3.0 26.6 + - - +
191E HIS 3.6 5.6 - - - +
193E GLU* 1.3 76.6 - - - +
195E ARG* 1.3 57.6 - - - +
197E LEU* 3.3 7.8 + - - +
198E VAL* 2.9 35.8 + - - +
291F VAL* 4.4 5.1 + - - +
294F GLU* 3.1 34.2 + - - +
295F LEU* 3.0 46.5 + - + +
298F SER* 3.0 24.1 + - - +
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Residues in contact with ARG 195 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191E HIS* 2.9 33.3 + - + +
192E ARG* 2.8 29.1 + - + +
194E GLN* 1.3 72.7 - - - +
196E GLU* 1.3 63.6 + - + +
198E VAL* 3.3 8.3 + - - +
199E ALA* 3.0 22.3 + - - +
294F GLU* 5.8 0.2 - - - -
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Residues in contact with GLU 196 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C VAL* 6.0 2.3 - - - +
182C VAL* 5.2 14.9 - - + +
186C ARG* 5.2 6.3 - - - +
192E ARG* 2.5 40.3 + - - +
193E GLU* 3.1 23.3 - - - +
195E ARG* 1.3 79.9 - - + +
197E LEU* 1.3 61.8 + - - +
199E ALA* 3.6 11.9 - - + -
200E VAL* 2.9 37.1 + - + +
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Residues in contact with LEU 197 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178C LEU* 5.5 6.1 - - + -
181C LEU* 3.6 28.3 - - + +
182C VAL* 3.5 30.7 - - + -
185C SER* 5.9 1.8 - - - -
193E GLU 3.0 21.4 + - - +
194E GLN* 3.3 10.5 - - - +
195E ARG 3.2 0.2 - - - -
196E GLU* 1.3 78.6 - - - +
198E VAL* 1.3 73.7 + - + +
200E VAL* 3.2 4.6 + - - +
201E LEU* 3.2 38.5 + - + +
298F SER* 4.1 28.9 - - - +
301F GLN* 5.0 1.8 - - + -
302F LEU* 5.0 8.3 - - + -
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Residues in contact with VAL 198 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194E GLN 2.9 16.5 + - - +
195E ARG* 3.3 8.5 + - - +
197E LEU* 1.3 86.3 - - + +
199E ALA* 1.3 60.6 + - - +
201E LEU* 3.4 9.5 + - - +
202E ARG* 3.3 45.5 - - + +
298F SER* 4.1 11.4 - - - +
301F GLN* 4.5 20.4 - - + +
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Residues in contact with ALA 199 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195E ARG 3.0 9.1 + - - +
196E GLU* 3.5 22.2 - - + +
197E LEU 3.2 0.2 - - - -
198E VAL* 1.3 79.8 - - - +
200E VAL* 1.3 63.5 + - + +
201E LEU 3.5 0.2 + - - -
202E ARG* 3.6 18.7 + - - +
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Residues in contact with VAL 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182C VAL* 4.7 8.1 - - + +
185C SER* 4.6 5.4 - - - +
186C ARG* 3.3 66.0 - - + +
189C GLN* 3.7 22.5 + - + +
196E GLU* 2.9 22.4 + - + +
197E LEU* 3.2 6.5 + - - +
199E ALA* 1.3 78.3 - - + +
201E LEU* 1.3 71.4 + - + +
202E ARG 3.2 6.3 + - - +
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Residues in contact with LEU 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C SER* 3.4 25.1 - - - +
189C GLN* 5.0 7.0 - - + +
197E LEU* 3.2 27.5 + - + +
198E VAL 3.4 3.6 + - - +
199E ALA 3.3 0.4 - - - -
200E VAL* 1.3 85.9 - - + +
202E ARG* 1.3 62.4 + - - +
203E GLU 4.4 0.2 + - - -
301F GLN* 3.6 45.1 + - + +
302F LEU* 3.8 22.9 - - + -
305F PHE* 3.9 34.1 - - + -
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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