Contacts of the strand formed by residues 236 - 242 (chain A) in PDB entry 1Z57
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 HIS 236 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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-2A SER* 4.5 4.2 - - - -
-1A MET* 3.9 38.4 + - + +
150A ILE* 4.1 17.1 - - + +
192A ILE* 4.1 17.5 - - + -
193A VAL 2.8 23.8 + - - +
194A LYS* 4.3 0.4 - - - -
195A ASN* 3.5 27.6 + - + +
200A CYS* 6.2 0.2 - - - -
232A GLU* 3.3 5.9 - - - -
233A HIS* 2.9 35.0 + - + +
234A HIS* 3.5 15.4 + - + -
235A GLY* 1.3 81.4 - - - +
237A ILE* 1.3 62.3 + - - +
238A CYS* 3.5 4.0 + - - -
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Residues in contact with ILE 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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193A VAL* 3.0 35.9 + - + +
200A CYS* 3.7 40.4 - - + +
203A ALA* 4.0 21.3 - - + -
204A ARG* 3.4 44.0 - - + +
207A ILE* 4.1 21.5 - - + -
230A TRP* 4.8 4.0 - - + -
231A PHE 3.7 7.9 - - - +
232A GLU* 4.6 5.8 - - + -
235A GLY 4.0 2.6 + - - +
236A HIS* 1.3 72.1 - - - +
238A CYS* 1.3 62.7 + - - +
239A ILE* 4.2 8.3 - - + -
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Residues in contact with CYS 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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157A LEU* 4.8 2.5 - - - -
190A VAL* 3.9 8.7 - - + -
191A LYS 3.2 4.3 - - - -
192A ILE* 4.2 27.4 - - - -
230A TRP* 3.2 5.9 - - - +
231A PHE* 2.8 76.6 + - + +
233A HIS* 3.8 12.8 - - - -
236A HIS* 3.7 11.4 - - - -
237A ILE* 1.3 79.4 - - - +
239A ILE* 1.3 62.5 + - - +
240A VAL 4.2 0.2 - - - -
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Residues in contact with ILE 239 (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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190A VAL* 3.3 2.6 - - - -
191A LYS* 2.8 44.6 + - + +
193A VAL* 4.9 2.9 - - + -
203A ALA* 4.1 19.1 - - + +
206A GLU* 3.6 26.7 - - + +
207A ILE* 3.8 30.5 - - + -
210A LEU* 4.7 0.2 - - + -
227A MET* 3.6 28.9 - - + -
229A GLU 3.8 3.4 - - - +
230A TRP* 4.2 0.9 - - + -
237A ILE* 4.2 4.9 - - + -
238A CYS* 1.3 77.9 - - - +
240A VAL* 1.3 63.7 + - - +
241A PHE* 3.4 32.9 - - + -
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Residues in contact with VAL 240 (chain A).
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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161A TYR* 3.8 24.7 - - + +
188A VAL* 3.8 32.8 - - + -
189A ALA 3.4 4.0 - - - +
190A VAL* 4.2 6.5 - - + +
227A MET* 3.5 7.3 - - - +
228A LEU* 2.8 42.0 + - + -
229A GLU* 2.8 26.5 + - + +
231A PHE* 3.7 31.0 - - + -
239A ILE* 1.3 73.9 - - - +
241A PHE* 1.3 58.7 + - - +
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Residues in contact with PHE 241 (chain A).
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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1A DBQ 3.4 43.5 - - + -
188A VAL* 3.5 9.0 - - - +
189A ALA 2.7 31.6 + - - +
191A LYS* 3.9 11.7 - - + -
206A GLU* 4.3 11.0 - - - -
210A LEU* 3.5 28.9 - - + -
225A VAL* 3.9 22.9 - - + -
226A GLN 3.4 14.6 - - - +
227A MET* 4.0 6.3 - - + -
228A LEU* 3.9 7.4 - - - -
239A ILE* 3.4 43.3 - - + -
240A VAL* 1.3 72.5 - - - +
242A GLU* 1.3 75.5 + - - +
243A LEU 3.5 0.2 + - - -
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Residues in contact with GLU 242 (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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1A DBQ 3.1 23.0 + - - -
186A ARG* 3.9 26.7 - - - +
188A VAL* 5.2 0.2 - - - +
189A ALA* 4.1 0.2 - - - +
225A VAL* 3.6 13.5 - - + -
226A GLN* 2.9 43.2 + - + +
228A LEU* 3.9 4.9 - - + +
241A PHE* 1.3 75.1 - - - +
243A LEU* 1.3 60.7 + - - +
244A LEU* 4.0 15.2 - - + +
322A LYS* 2.7 41.8 + - - +
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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