Contacts of the helix formed by residues 216 - 222 (chain B) in PDB entry 3PU3
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 SER 216 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B EDO 5.2 5.9 + - - -
212B VAL* 2.9 20.9 + - - -
213B LYS* 3.7 0.6 + - - -
214B LYS 3.5 1.6 - - - -
215B LEU* 1.3 75.8 - - - +
217B TRP* 1.3 63.7 + - - +
218B VAL* 3.1 12.5 + - - +
219B GLU* 3.0 30.1 + - - +
220B ASN* 2.7 29.7 + - - +
221B TYR* 5.7 0.2 - - - -
336B PHE* 4.1 17.9 - - - +
337B LEU 3.3 7.1 + - - -
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Residues in contact with TRP 217 (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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215B LEU 3.3 4.4 + - - -
216B SER* 1.3 71.8 + - - +
218B VAL* 1.3 59.2 - - - +
221B TYR* 2.8 59.1 + + + +
222B TRP* 3.6 0.7 + - - +
337B LEU* 2.8 41.0 + - + +
338B HIS* 3.2 29.4 - - - -
339B SER* 2.9 21.4 + - - -
342B VAL* 3.8 23.1 - - + -
345B GLN* 3.6 19.1 - - - -
346B MET* 6.4 0.2 - - - -
369B ALA* 4.3 17.3 - - + +
370B CYS* 4.0 22.9 - - - -
373B MET* 3.4 40.1 - - + -
402B LEU* 4.3 10.8 - - + -
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Residues in contact with VAL 218 (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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216B SER* 3.1 7.5 + - - +
217B TRP* 1.3 75.8 - - + +
219B GLU* 1.3 65.5 + - - +
222B TRP* 3.1 41.2 + - + +
230B LYS* 3.7 37.3 - - + -
231B PRO* 4.0 32.5 - - + +
233B VAL* 5.9 2.2 - - + -
234B THR* 6.1 1.1 - - - +
336B PHE* 6.4 1.1 - - - -
337B LEU* 5.7 3.8 - - + +
363B PHE* 4.7 11.9 - - + -
369B ALA* 4.7 10.1 - - + -
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Residues in contact with GLU 219 (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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213B LYS* 3.2 54.9 - - + +
216B SER* 3.0 18.9 + - - +
218B VAL* 1.3 80.2 - - - +
220B ASN* 1.3 60.6 + - - +
222B TRP 4.9 2.4 - - - +
230B LYS* 5.3 6.9 + - - +
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Residues in contact with ASN 220 (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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13B EDO 5.1 2.4 - - - -
213B LYS 3.1 16.5 + - - +
214B LYS* 3.0 28.1 + - - +
215B LEU 4.0 0.8 + - - -
216B SER 2.7 28.2 + - - +
219B GLU* 1.3 80.5 - - - +
221B TYR* 1.3 91.2 + - + +
222B TRP 3.8 0.9 - - - -
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Residues in contact with TYR 221 (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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13B EDO 2.7 46.9 - - - +
45B EDO 5.9 2.8 - - - -
217B TRP* 2.8 41.8 + + + +
220B ASN* 1.3 98.1 - - + +
222B TRP* 1.3 62.4 + - - +
223B PRO* 3.7 1.6 - - - +
339B SER* 4.7 5.8 + - - -
369B ALA 5.9 0.2 - - - +
372B TYR* 3.7 17.9 - - + +
373B MET* 3.5 32.3 - - - +
376B HIS* 3.1 48.5 + + + -
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Residues in contact with TRP 222 (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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217B TRP 3.6 1.8 + - - +
218B VAL* 3.1 28.5 + - + +
219B GLU 4.9 2.8 - - - +
220B ASN 5.3 0.3 - - - -
221B TYR* 1.3 78.7 + - - +
223B PRO* 1.3 86.0 - - + +
224B ASP* 3.6 1.6 + - - +
226B ALA* 3.5 7.9 - - - +
228B LEU* 3.4 25.4 + - + -
229B ALA 3.5 18.4 - - - -
230B LYS* 3.4 38.5 + - + +
231B PRO* 3.5 30.1 - - + -
365B ASN* 3.8 11.9 - - + -
368B THR* 3.4 26.5 - - + -
369B ALA* 3.7 31.0 - - + -
372B TYR* 3.7 17.7 - + + -
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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