Contacts of the strand formed by residues 246 - 250 (chain B) in PDB entry 1ZQ1
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 CYS 246 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B MSE 4.1 8.7 - - - -
218B ASN* 3.2 31.6 - - - -
221B CYS* 3.4 40.8 - - + -
236B VAL* 3.9 7.0 - - + -
237B MSE 3.1 15.5 - - - +
238B HIS* 3.7 5.6 - - - -
239B GLY 3.9 0.7 - - - +
245B TYR* 1.3 82.4 - - - +
247B LEU* 1.3 66.0 + - - +
276B ILE* 2.8 33.3 + - + -
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Residues in contact with LEU 247 (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 VAL 3.2 2.4 - - - +
236B VAL* 3.1 24.3 - - - -
237B MSE 2.6 16.1 + - - +
239B GLY* 4.2 7.2 - - - +
245B TYR* 3.3 32.8 - - + +
246B CYS* 1.3 77.4 - - - +
248B ALA* 1.3 58.2 + - - +
249B HIS* 3.3 36.4 - - + +
266B ARG* 4.3 26.9 - - - +
272B PRO* 3.8 22.2 - - + -
274B ALA 3.9 0.7 - - - +
275B LYS* 3.7 19.7 - - + -
276B ILE* 5.5 0.4 - - - -
285B LEU* 4.6 4.3 - - + -
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Residues in contact with ALA 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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225B MSE 3.8 31.2 - - + -
234B MSE 4.2 7.6 - - - -
235B VAL 3.3 5.4 - - - -
236B VAL* 4.0 13.7 - - + -
247B LEU* 1.3 72.5 - - - +
249B HIS* 1.3 57.8 + - - +
272B PRO 3.6 0.9 - - - -
273B ILE* 2.7 36.0 + - + +
274B ALA 3.1 21.5 + - - +
276B ILE* 5.4 1.8 - - + -
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Residues in contact with HIS 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B MSE 3.1 5.6 - - - -
235B VAL* 2.6 44.3 + - + +
237B MSE 4.8 5.5 + - - -
238B HIS 4.9 1.6 + - - -
247B LEU* 3.3 46.8 + - + +
248B ALA* 1.3 72.4 - - - +
250B ARG* 1.3 64.5 + - - +
251B GLY 3.0 0.9 + - - -
254B VAL* 3.2 33.4 - - + +
265B PHE* 3.1 33.2 + - + +
266B ARG* 4.2 0.4 - - - -
267B SER* 2.5 39.7 + - - +
272B PRO* 3.9 4.3 - - + +
273B ILE* 4.5 0.7 - - - -
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Residues in contact with ARG 250 (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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232B GLU* 2.8 38.0 + - - +
233B VAL 4.1 4.7 - - - +
248B ALA 4.0 1.8 + - - -
249B HIS* 1.3 71.5 - - - +
251B GLY* 1.3 52.7 + - - +
252B THR* 2.6 28.3 + - - +
253B LYS* 3.0 19.0 + - + +
254B VAL* 2.8 14.6 - - - +
267B SER* 4.8 2.2 + - - -
270B ASP* 4.1 5.8 + - + -
271B VAL 5.3 2.2 + - - +
272B PRO* 5.1 1.0 - - - +
273B ILE* 4.1 18.5 - - + +
286B ARG* 3.5 37.6 - - - +
288B ASP* 3.0 28.3 + - - -
289B TYR* 3.8 4.9 - - - +
424B ALA* 6.0 0.2 - - + -
425B GLY* 3.3 33.2 - - - +
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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