Contacts of the helix formed by residues 190 - 203 (chain B) in PDB entry 5T0H
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 LEU 190 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187B ILE* 3.6 52.3 - - + +
188B GLY 3.1 7.5 + - - +
189B GLY* 1.3 74.3 - - - +
191B ASP* 1.3 55.2 + - - +
192B ASN* 3.0 4.3 - - - -
193B GLN* 2.6 46.9 + - - +
194B ILE* 3.2 10.1 + - + -
233B THR* 4.0 19.1 - - + -
237B LYS* 4.3 15.0 - - - -
353B PHE* 4.7 11.0 - - + -
354B PRO* 5.3 11.0 - - + -
360B THR* 5.7 3.6 - - + +
364B ILE* 5.8 6.7 - - + -
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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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187B ILE 4.9 3.5 + - - +
188B GLY* 4.7 1.5 - - - -
189B GLY* 3.8 18.8 - - - +
190B LEU* 1.3 77.7 - - - +
192B ASN* 1.3 63.0 + - - +
194B ILE* 3.6 16.2 - - + -
195B GLN* 2.5 50.4 + - + +
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Residues in contact with ASN 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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398A ARG* 5.1 0.5 + - - -
189B GLY 5.3 3.1 - - - +
190B LEU* 4.5 2.0 - - - +
191B ASP* 1.3 85.6 + - - +
193B GLN* 1.3 59.7 + - - +
195B GLN* 3.4 34.3 + - - +
196B GLU* 3.6 9.7 + - - +
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Residues in contact with GLN 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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190B LEU* 2.6 31.1 + - + +
192B ASN* 1.3 73.9 - - - +
194B ILE* 1.3 59.3 + - - +
196B GLU* 3.3 20.1 - - - +
197B ILE* 3.6 4.9 + - - +
237B LYS* 3.2 21.7 + - - +
349B ARG* 4.2 17.1 + - - +
351B ILE* 3.2 26.3 - - + +
352B GLU 2.6 39.6 + - - +
353B PHE* 3.3 15.4 - - - +
354B PRO* 3.6 15.8 - - + +
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Residues in contact with ILE 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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184B TYR* 3.5 44.2 - - + +
187B ILE* 5.0 4.7 - - + +
190B LEU* 3.2 7.9 + - + +
191B ASP* 3.1 24.9 + - + +
193B GLN* 1.3 76.0 - - - +
195B GLN* 1.3 58.6 + - - +
196B GLU 3.1 2.0 - - - -
197B ILE* 3.1 19.7 + - + -
198B LYS* 2.4 41.7 + - + +
201B VAL* 6.0 2.5 - - + -
237B LYS* 3.9 35.7 - - + +
240B ALA* 5.4 0.4 - - + -
241B ASN* 5.8 1.8 - - - +
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Residues in contact with GLN 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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398A ARG* 2.2 41.3 + - - +
191B ASP* 2.5 45.0 + - + +
192B ASN* 3.4 37.0 + - - +
194B ILE* 1.3 70.4 - - + +
196B GLU* 1.3 54.8 - - - +
198B LYS* 3.2 20.0 - - + +
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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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394A MET* 3.3 36.7 - - + +
395A PHE* 5.9 3.6 - - + -
398A ARG* 3.0 26.0 + - - +
192B ASN 3.6 7.8 + - - +
193B GLN 3.3 12.0 + - - +
195B GLN* 1.3 82.1 - - - +
197B ILE* 1.3 80.0 + - - +
198B LYS 3.1 3.8 + - - -
199B GLU 3.5 2.8 + - - -
200B SER* 3.8 2.4 + - - -
346B ARG* 4.3 2.1 + - - -
348B ASP* 4.2 5.2 - - - +
349B ARG* 2.7 60.6 + - - +
351B ILE* 4.1 0.7 - - - +
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Residues in contact with ILE 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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193B GLN 3.6 3.2 + - - +
194B ILE* 3.1 35.4 + - + +
196B GLU* 1.3 85.7 + - - +
198B LYS* 1.3 54.9 + - - +
199B GLU 3.4 0.4 - - - -
200B SER* 3.4 20.4 - - - +
201B VAL* 2.5 55.1 + - + +
222B VAL* 3.7 29.6 - - + -
224B LEU* 4.5 13.9 - - + -
237B LYS* 4.7 15.5 - - + +
241B ASN* 5.3 4.9 - - - +
328B ILE* 5.5 3.8 - - + -
351B ILE* 5.1 5.4 - - + -
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Residues in contact with LYS 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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398A ARG* 4.9 0.2 - - - +
184B TYR* 3.3 42.6 + - + -
194B ILE* 2.4 29.7 + - + +
195B GLN* 3.2 22.0 - - + +
196B GLU 3.0 0.4 - - - -
197B ILE* 1.3 69.9 - - - +
199B GLU* 1.3 54.7 + - - +
201B VAL* 3.1 10.1 - - + +
202B GLU* 2.5 75.0 + - + +
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Residues in contact with GLU 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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394A MET* 4.1 22.7 - - + +
397A ILE* 3.4 37.9 - - + +
398A ARG* 4.1 27.6 - - + +
195B GLN 4.0 0.8 + - - -
196B GLU 3.5 3.5 + - - +
197B ILE 3.4 0.2 - - - -
198B LYS* 1.3 80.1 - - - +
200B SER* 1.3 56.4 + - - +
202B GLU* 4.2 6.9 - - - +
203B LEU* 2.8 72.9 + - + +
207B HIS* 5.1 4.2 + - - -
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Residues in contact with SER 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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394A MET* 4.8 3.5 - - - +
196B GLU* 3.8 8.1 + - - -
197B ILE* 3.0 26.6 + - - +
199B GLU* 1.3 80.4 - - - +
201B VAL* 1.3 58.6 + - - +
204B PRO* 3.1 25.0 - - - +
221B GLY* 3.7 9.0 + - - -
222B VAL* 3.1 25.0 - - - +
326B LYS* 6.0 0.9 - - - -
346B ARG* 4.8 8.5 + - - -
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Residues in contact with VAL 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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194B ILE* 6.0 2.9 - - + -
197B ILE* 2.5 44.2 + - + +
198B LYS* 3.1 28.0 - - + +
200B SER* 1.3 72.8 - - - +
202B GLU* 1.3 71.2 + - + +
204B PRO* 3.8 10.7 - - - +
206B THR* 4.6 1.0 + - - -
241B ASN* 3.4 40.6 - - + +
244B SER* 5.3 8.8 + - - -
328B ILE* 5.8 2.5 - - + -
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Residues in contact with GLU 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B LYS* 2.5 68.6 + - + +
199B GLU* 4.2 7.4 - - - +
201B VAL* 1.3 77.2 - - + +
203B LEU* 1.3 53.7 + - - +
204B PRO 2.6 25.3 - - - +
206B THR* 2.6 49.7 + - - +
207B HIS* 5.1 8.4 - - + +
244B SER* 5.5 2.9 + - - -
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Residues in contact with LEU 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397A ILE* 4.4 5.6 - - + -
199B GLU* 2.8 53.9 + - + +
202B GLU* 1.3 72.2 - - - +
204B PRO* 1.3 62.3 - - + +
205B LEU 3.4 5.2 + - - +
206B THR 3.1 12.0 - - - +
207B HIS* 3.2 24.7 - - - +
208B PRO* 3.5 12.5 - - - +
211B TYR* 3.6 56.5 - - + +
218B PRO* 4.2 18.8 - - + +
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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