Contacts of the helix formed by residues 193 - 206 (chain B) in PDB entry 5A86
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 ARG 193 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192B SER* 1.4 114.9 + - - +
194B GLU* 1.3 69.7 + - + +
195B GLU 3.3 0.9 - - - +
196B ALA* 3.4 8.8 + - - +
197B ALA* 3.0 26.6 + - - +
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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
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192B SER* 4.2 2.3 + - - +
193B ARG* 1.3 83.7 - - + +
195B GLU* 1.3 65.5 + - - +
197B ALA* 3.0 26.8 + - + +
198B LYS* 3.2 14.1 + - + +
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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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192B SER* 3.7 21.3 + - - +
193B ARG 3.3 0.2 - - - -
194B GLU* 1.3 77.8 - - - +
196B ALA* 1.3 61.6 + - - +
198B LYS* 3.0 49.3 + - + +
199B TRP* 3.0 34.7 + - - -
417B ILE* 3.8 9.5 - - - +
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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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192B SER 4.6 7.1 - - - +
193B ARG* 3.4 16.6 + - - +
194B GLU 3.3 0.2 - - - -
195B GLU* 1.3 79.2 + - - +
197B ALA* 1.3 61.7 + - - +
199B TRP* 3.0 23.4 + - - +
200B SER* 3.1 12.1 + - - -
203B ARG* 5.2 0.5 + - - -
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Residues in contact with ALA 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 ARG 3.0 13.0 + - - +
194B GLU* 3.0 24.3 + - + +
196B ALA* 1.3 76.3 - - - +
198B LYS* 1.3 59.5 + - - +
200B SER* 3.3 9.8 + - - -
201B GLN* 3.2 20.4 + - - +
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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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194B GLU* 3.8 10.1 - - + +
195B GLU* 3.0 35.7 + - - +
197B ALA* 1.3 78.3 - - + +
199B TRP* 1.4 50.9 + - - +
201B GLN* 3.1 10.1 + - - +
202B VAL* 2.8 38.5 + - + +
413B ARG* 5.7 2.3 - - - +
416B ASP* 2.8 32.3 + - - +
417B ILE* 4.1 14.1 - - + +
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Residues in contact with TRP 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 GLU* 3.0 42.3 + - - -
196B ALA* 3.0 13.3 + - - +
198B LYS* 1.4 75.1 - - - +
200B SER* 1.3 60.1 + - - +
202B VAL* 3.1 7.6 + - + +
203B ARG* 2.8 50.8 + - + +
232B GLY 6.0 0.4 - - - -
233B GLY* 2.7 36.6 - - - -
234B LYS* 4.1 13.9 - - + -
236B ILE* 4.8 6.3 - - + -
237B PHE* 4.0 21.8 - + - -
417B ILE* 3.7 30.1 - - + +
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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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196B ALA 3.1 11.1 + - - -
197B ALA* 3.6 12.1 - - - -
199B TRP* 1.3 75.2 - - - +
201B GLN* 1.3 62.5 + - - +
203B ARG* 3.6 30.2 + - - +
204B LYS* 3.3 46.9 + - - +
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Residues in contact with GLN 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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197B ALA 3.2 9.0 + - - +
198B LYS* 3.1 11.5 + - - +
200B SER* 1.3 77.1 - - - +
202B VAL* 1.3 64.6 + - - +
204B LYS* 3.0 25.3 + - - +
205B ASP* 2.9 42.7 + - - +
413B ARG* 3.4 34.7 + - - +
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Residues in contact with VAL 202 (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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198B LYS* 2.8 20.0 + - + +
199B TRP* 3.1 5.1 + - + +
201B GLN* 1.3 71.5 - - - +
203B ARG* 1.3 58.6 + - - +
205B ASP* 3.0 24.4 + - - +
206B LEU* 3.2 14.6 + - + +
236B ILE* 4.4 4.9 - - + -
237B PHE* 3.6 37.5 - - + -
413B ARG* 3.8 34.3 - - + +
414B ILE* 4.0 12.3 - - + +
417B ILE* 3.7 23.3 - - + -
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Residues in contact with ARG 203 (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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196B ALA 5.2 1.0 + - - -
199B TRP* 2.8 36.6 + - + +
200B SER* 3.7 38.5 + - - +
202B VAL* 1.3 76.8 - - + +
204B LYS* 1.3 61.8 + - + +
206B LEU* 3.5 12.8 + - - +
207B CYS* 3.7 13.7 + - - +
230B ASP* 3.5 36.9 + - - +
232B GLY* 5.1 9.9 - - - -
233B GLY 5.6 1.1 - - - +
236B ILE* 4.1 20.2 - - + -
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Residues in contact with LYS 204 (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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200B SER* 3.3 36.0 + - - +
201B GLN* 3.0 31.1 + - - +
203B ARG* 1.3 79.7 - - + +
205B ASP* 1.3 53.6 + - - +
207B CYS* 2.7 31.6 + - - +
410B ARG* 4.6 1.2 + - - -
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Residues in contact with ASP 205 (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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201B GLN* 2.9 30.5 + - - +
202B VAL* 3.0 12.0 + - - +
204B LYS* 1.3 78.6 - - - +
206B LEU* 1.3 60.4 + - - +
207B CYS 3.4 0.4 - - - -
209B LEU* 4.6 6.4 - - - +
410B ARG* 3.1 53.6 + - + +
413B ARG* 2.9 49.5 + - - +
414B ILE* 4.8 7.4 - - + +
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Residues in contact with LEU 206 (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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202B VAL 3.2 12.2 + - - +
203B ARG* 3.9 6.3 - - - +
204B LYS 3.3 0.8 - - - -
205B ASP* 1.3 76.5 - - - +
207B CYS* 1.3 59.0 + - - +
209B LEU* 3.0 49.5 + - + +
210B LYS* 3.6 13.1 + - + +
236B ILE* 3.3 44.4 - - + +
237B PHE* 3.6 25.4 - - + -
240B LEU* 4.9 7.2 - - + -
414B ILE* 3.5 32.5 - - + -
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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