Contacts of the strand formed by residues 233 - 238 (chain A) 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 VAL 233 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A ALA* 4.3 4.9 - - + +
188A LEU* 3.9 22.2 - - + +
189A SER* 3.5 38.5 + - - +
192A LEU* 4.5 1.8 - - + -
195A LEU* 4.1 18.8 - - + -
199A VAL* 3.5 26.2 - - + -
201A LEU* 3.9 17.7 - - + -
232A GLU* 1.3 77.7 - - - +
234A MSE 1.3 63.0 + - - +
250A ARG* 4.0 3.6 - - - +
251A GLY* 3.0 21.0 + - - -
290A ARG* 5.7 2.7 - - - +
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Residues in contact with MSE 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A PRO* 4.9 3.4 - - + -
199A VAL 2.9 6.4 + - - +
200A VAL* 3.4 23.6 - - + -
201A LEU* 2.9 28.1 + - - +
225A MSE 3.2 59.5 - - + +
230A VAL* 3.5 24.0 - - + -
232A GLU* 3.4 13.2 - - + +
233A VAL* 1.3 80.5 - - - +
235A VAL* 1.3 69.9 + - - +
236A VAL* 4.5 3.8 - - + -
248A ALA* 4.2 7.6 - - + -
249A HIS 3.1 16.2 - - - +
251A GLY 4.1 1.1 - - - +
273A ILE* 4.3 13.7 - - + -
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Residues in contact with VAL 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A MSE 3.5 34.8 - - + +
182A GLY* 5.6 0.7 - - - -
185A ALA* 3.7 30.5 - - + -
201A LEU* 3.5 10.1 - - + +
234A MSE 1.3 77.7 - - - +
236A VAL* 1.3 63.0 - - - +
237A MSE 4.1 14.4 - - + -
247A LEU 3.3 1.6 - - - +
248A ALA* 3.3 3.1 - - - -
249A HIS* 2.8 34.6 + - + +
251A GLY* 4.6 0.9 - - - -
254A VAL* 4.2 25.1 - - + -
265A PHE* 4.7 10.8 - - + -
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Residues in contact with VAL 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A VAL* 3.7 25.6 - - + -
201A LEU 3.3 7.5 + - - +
202A VAL* 3.6 16.3 - - + +
218A ASN* 4.0 4.2 - - - +
221A CYS* 3.8 2.0 - - + -
222A SER* 3.7 17.3 - - - +
225A MSE 4.1 15.9 - - + -
234A MSE 4.2 4.2 - - + -
235A VAL* 1.3 77.4 - - - +
237A MSE 1.3 75.0 + - - +
246A CYS* 3.8 11.9 - - + -
247A LEU 3.3 3.6 - - - +
248A ALA* 4.0 20.2 - - + -
276A ILE* 3.5 23.3 - - + -
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Residues in contact with MSE 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A THR* 3.8 9.9 - - + +
181A MSE 3.6 13.7 - - - -
202A VAL* 4.7 0.7 - - - -
203A GLY* 3.0 48.5 - - - +
204A ALA* 5.1 1.3 - - - -
205A GLN* 5.5 2.0 - - + +
214A ASP* 5.2 1.1 - - - +
218A ASN* 3.4 11.7 - - - +
235A VAL* 4.1 12.3 - - + -
236A VAL* 1.3 84.0 - - - +
238A HIS* 1.3 72.9 + - - +
246A CYS* 3.2 7.3 - - - -
247A LEU* 2.9 24.4 + - - +
249A HIS* 4.9 3.0 + - - +
262A ARG 4.6 4.5 - - - +
265A PHE* 3.5 50.0 - - + -
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Residues in contact with HIS 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A ASP* 3.4 32.8 + - + +
217A MSE 3.8 23.6 - - + -
218A ASN* 3.0 27.7 + - - +
237A MSE 1.3 81.8 - - - +
239A GLY* 1.3 60.8 + - - +
240A GLU 3.4 16.4 - - - +
242A GLY 3.2 26.5 - - - -
243A ASP* 3.0 25.9 + - - -
244A THR 4.7 0.2 - - - -
245A TYR 3.9 6.1 - - - -
246A CYS* 4.0 2.9 - - - -
247A LEU* 4.6 1.7 + - - +
249A HIS* 5.0 0.3 + - - -
262A ARG* 3.6 37.6 + - + +
265A PHE 4.7 4.3 - - - +
266A ARG* 4.3 4.9 + - - -
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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