Contacts of the helix formed by residues 231 - 240 (chain B) in PDB entry 5C16
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 ASP 231 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228B LYS* 5.2 5.6 - - - +
229B VAL 3.8 3.4 + - - +
230B TYR* 1.3 78.2 - - - +
232B PRO* 1.3 74.4 - - - +
233B VAL* 3.6 10.9 + - - +
234B SER* 2.6 50.6 + - - +
235B GLU* 3.0 11.8 + - - +
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Residues in contact with PRO 232 (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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230B TYR* 3.5 43.0 - - + +
231B ASP* 1.3 91.4 - - - +
233B VAL* 1.3 61.4 + - + +
235B GLU* 3.1 3.3 + - - +
236B TYR* 2.9 42.0 + - + -
262B PRO* 6.4 1.6 - - + -
264B ILE* 4.3 26.2 - - + +
546B GLU* 5.9 2.5 - - - +
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Residues in contact with VAL 233 (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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231B ASP* 3.3 9.7 + - - +
232B PRO* 1.3 79.4 - - - +
234B SER* 1.3 58.4 + - - +
236B TYR* 3.5 7.5 + - - +
237B LYS* 3.0 32.0 + - + +
241B LEU 4.8 0.7 - - - +
248B ILE* 4.1 23.0 - - + +
250B LYS* 5.4 4.9 - - - +
264B ILE* 3.9 24.7 - - + -
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Residues in contact with SER 234 (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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231B ASP* 2.6 35.9 + - - +
233B VAL* 1.3 76.7 - - - +
235B GLU* 1.3 55.6 + - - +
237B LYS* 3.2 8.9 + - - +
238B ARG* 2.7 35.5 + - - +
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Residues in contact with GLU 235 (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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230B TYR* 3.8 15.0 - - + -
231B ASP 3.0 11.7 + - - +
232B PRO 3.1 7.4 + - - +
234B SER* 1.3 76.9 - - - +
236B TYR* 1.3 63.1 + - + +
238B ARG* 2.8 30.8 + - - +
239B GLN* 2.9 29.7 + - - +
459B TYR* 3.6 11.4 + - - -
460B TYR* 2.5 35.0 + - - -
468B THR* 4.1 8.2 - - + +
472B LYS* 3.7 26.2 - - + -
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Residues in contact with TYR 236 (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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230B TYR* 4.6 3.3 + - - -
232B PRO* 2.9 43.9 + - + +
233B VAL 3.9 4.0 - - - +
235B GLU* 1.3 78.8 - - + +
237B LYS* 1.3 58.6 + - - +
239B GLN* 3.1 10.6 + - - +
240B GLY 3.0 5.0 + - - -
241B LEU* 2.7 57.6 + - + +
248B ILE* 4.4 16.2 - - + -
262B PRO* 5.8 0.3 - - - +
264B ILE* 4.2 20.6 + - + -
265B ILE* 4.9 0.5 - - - -
266B VAL* 3.6 35.4 + - + +
291B LEU* 4.1 25.8 + - + -
472B LYS* 4.5 25.1 + - + +
477B PHE* 4.7 12.0 - - - -
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Residues in contact with LYS 237 (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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233B VAL* 3.0 22.4 + - + +
234B SER* 3.5 8.7 - - - +
236B TYR* 1.3 75.3 - - - +
238B ARG* 1.3 59.5 + - - +
240B GLY* 2.8 20.5 + - - -
241B LEU 3.3 12.9 + - - +
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Residues in contact with ARG 238 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234B SER 2.7 19.5 + - - +
235B GLU* 2.8 45.1 + - - +
237B LYS* 1.3 73.6 - - - +
239B GLN* 1.3 70.7 + - - +
240B GLY 3.6 0.2 + - - -
457B ASP* 3.0 30.5 + - - -
459B TYR* 3.3 46.7 - - - +
460B TYR* 3.2 13.5 + - - -
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Residues in contact with GLN 239 (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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235B GLU* 2.9 37.1 + - - +
236B TYR* 3.1 15.0 + - - +
237B LYS 3.1 1.2 - - - -
238B ARG* 1.3 88.4 - - - +
240B GLY* 1.3 57.8 + - - +
241B LEU* 4.2 7.2 - - + -
291B LEU* 3.9 3.9 - - - +
292B SER 3.3 19.2 + - - +
293B TRP* 3.2 16.3 - - + +
294B ILE* 3.0 56.1 + - + +
296B PRO* 5.3 9.7 - - - +
457B ASP* 5.3 0.2 - - - +
460B TYR* 3.4 5.7 + - - -
472B LYS* 4.1 5.7 - - - +
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Residues in contact with GLY 240 (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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237B LYS 2.8 12.6 + - - -
238B ARG 3.3 0.8 + - - -
239B GLN* 1.3 79.9 - - - +
241B LEU* 1.3 62.4 + - - +
242B PRO 3.8 3.2 - - - +
243B ASN* 3.8 21.8 + - - +
294B ILE* 5.5 0.2 - - - -
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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