Contacts of the helix formed by residues 247 - 253 (chain B) in PDB entry 1Z6T
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 247 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B LYS* 2.7 33.1 + - - +
190B GLN 4.4 5.2 + - - +
245B VAL* 3.5 9.5 - - - +
246B TRP* 1.3 93.6 - - - +
248B SER* 1.3 64.9 + - - +
249B TRP* 3.2 33.8 + - + +
250B VAL* 3.1 25.7 + - + +
251B LEU 3.6 0.7 + - - -
269B VAL* 3.8 6.0 - - - +
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Residues in contact with SER 248 (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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247B ASP* 1.3 69.6 - - - +
249B TRP* 1.3 67.7 + - - +
251B LEU* 3.1 12.7 + - - +
252B LYS* 3.2 7.4 + - - -
268B SER 4.5 4.0 - - - -
269B VAL* 3.1 35.3 + - - +
271B ASP* 5.3 2.0 - - - -
272B SER* 3.0 36.1 + - - -
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Residues in contact with TRP 249 (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 GLN 3.5 21.3 + - - -
191B ASP* 3.6 28.9 - - - -
192B LYS* 3.3 42.6 - - + +
195B LEU* 3.7 24.5 - - + -
220B ILE* 4.1 6.5 - - + -
247B ASP* 3.2 33.0 + - + +
248B SER* 1.3 84.5 + - - +
250B VAL* 1.3 75.1 + - + +
252B LYS* 3.4 38.2 + - - +
253B ALA* 3.6 5.0 + - + +
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Residues in contact with VAL 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B VAL* 4.0 26.7 - - + -
188B GLY 5.7 0.9 - - - +
190B GLN* 4.9 12.6 - - + +
195B LEU* 4.0 17.3 - - + -
245B VAL* 4.3 12.6 - - + -
246B TRP* 5.5 2.0 - - + +
247B ASP* 3.1 22.3 + - + +
249B TRP* 1.3 112.4 - - + +
251B LEU* 1.3 61.8 + - - +
253B ALA* 3.1 14.4 + - - +
254B PHE* 3.2 19.0 - - + -
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Residues in contact with LEU 251 (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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149B TRP* 3.7 33.0 - - + -
242B LEU* 3.8 23.1 - - + -
245B VAL* 3.9 23.8 - - + -
247B ASP 3.6 1.2 + - - +
248B SER 3.1 10.4 + - - +
250B VAL* 1.3 77.3 - - + +
252B LYS* 1.3 59.2 + - - +
254B PHE* 3.1 20.1 + - - +
255B ASP* 3.3 8.8 + - - +
262B LEU* 4.2 9.6 - - + -
269B VAL* 3.3 29.6 - - + +
270B THR* 3.7 26.5 - - + -
273B VAL* 4.2 11.2 - - + -
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Residues in contact with LYS 252 (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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224B LYS* 2.7 35.7 + - - +
248B SER* 3.2 2.5 + - - +
249B TRP* 3.4 30.2 - - - +
250B VAL 3.2 0.4 - - - -
251B LEU* 1.3 74.9 - - - +
253B ALA* 1.3 61.2 + - - +
255B ASP* 3.2 14.0 + - + +
272B SER* 3.4 44.8 - - - +
273B VAL* 4.4 2.2 - - + +
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Residues in contact with ALA 253 (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 LEU* 3.8 22.9 - - + -
199B LEU* 4.2 10.3 - - + +
220B ILE* 4.1 20.6 - - + -
224B LYS* 3.4 33.9 - - + +
227B LEU* 4.4 5.2 - - - +
249B TRP* 3.6 4.3 + - + +
250B VAL 3.1 14.8 + - - +
252B LYS* 1.3 79.3 - - - +
254B PHE* 1.3 61.4 + - + +
255B ASP 3.5 0.2 - - - -
256B SER* 4.4 1.0 + - - -
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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