Contacts of the strand formed by residues 234 - 240 (chain A) in PDB entry 1Z8G
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 234 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212A LEU* 4.0 34.3 + - + +
213A SER* 5.7 0.2 - - - -
215A TRP* 3.9 27.0 + - + +
217A VAL* 3.9 15.3 - - + -
233A GLY* 1.3 79.4 - - - +
235A GLN* 1.3 63.3 + - - +
236A ALA 3.6 24.2 - - - +
237A VAL* 3.9 14.4 - - + -
261A VAL* 3.8 25.6 - - + -
262A HIS 3.8 2.0 - - - -
264A SER* 4.1 4.2 + - - -
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Residues in contact with GLN 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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212A LEU* 3.6 4.9 - - - +
234A VAL* 1.3 73.7 - - - +
236A ALA* 1.3 56.1 + - - +
262A HIS* 2.7 33.2 + - - +
263A LEU 4.0 10.7 - - - +
264A SER* 3.8 18.8 - - - +
409A GLU* 3.2 39.3 + - - +
410A ALA 3.0 22.6 + - - +
411A SER* 3.3 14.0 + - - +
412A GLY 3.0 19.6 + - - -
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Residues in contact with ALA 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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197A TRP* 5.8 0.4 - - + -
212A LEU* 3.6 2.7 - - - -
234A VAL* 3.6 3.9 - - - +
235A GLN* 1.3 82.7 - - - +
237A VAL* 1.3 69.9 - - - +
238A VAL* 4.2 6.7 - - + -
260A LEU 3.9 0.2 - - - +
261A VAL* 3.5 0.7 - - - -
262A HIS* 2.8 37.2 + - + +
407A HIS 5.6 1.3 - - - +
410A ALA* 3.3 29.6 - - + +
411A SER 4.0 0.2 - - - -
412A GLY 3.3 13.7 - - - +
414A VAL* 5.0 2.2 - - + -
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Residues in contact with VAL 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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205A PHE* 3.8 47.8 - - + -
212A LEU* 3.7 24.0 - - + -
215A TRP* 5.6 0.4 - - + -
234A VAL* 3.9 9.2 - - + -
236A ALA* 1.3 78.9 - - - +
238A VAL* 1.3 67.1 + - - +
239A TYR* 3.7 4.3 + - + +
259A ALA* 4.5 4.3 - - + -
260A LEU 3.3 9.2 - - - +
261A VAL* 4.5 5.4 - - + -
412A GLY 3.0 6.3 + - - +
413A MET* 3.5 20.5 - - + -
414A VAL 2.8 27.4 + - - +
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Residues in contact with VAL 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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197A TRP* 4.4 19.1 - - + -
236A ALA* 5.1 4.5 - - + -
237A VAL* 1.3 74.0 - - - +
239A TYR* 1.3 56.7 + - - +
259A ALA* 3.3 3.4 - - - -
260A LEU* 2.7 45.4 + - + +
399A TRP* 3.6 6.8 - - + -
403A ALA* 4.1 14.8 - - + +
407A HIS* 3.9 36.8 - - + +
414A VAL* 3.2 14.6 - - + +
416A GLN* 3.7 29.6 - - + -
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Residues in contact with TYR 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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202A ALA* 4.3 11.9 - - + +
205A PHE* 5.6 0.9 - - + -
237A VAL* 4.1 5.4 - - + -
238A VAL* 1.3 75.3 - - - +
240A HIS* 1.3 72.1 + - - +
246A PHE* 3.4 61.8 - + + -
247A ARG* 4.2 10.8 + - - -
259A ALA* 3.9 16.6 - - + -
399A TRP* 3.9 2.7 - - - -
413A MET* 4.0 16.9 + - + +
414A VAL* 2.9 33.0 + - - -
415A THR* 3.4 28.8 + - - +
416A GLN* 3.0 25.3 + - - +
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Residues in contact with HIS 240 (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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202A ALA* 4.7 0.4 - - - +
239A TYR* 1.3 79.9 - - - +
241A GLY* 1.3 63.5 + - - +
242A GLY* 2.9 33.4 + - - -
243A TYR* 3.1 18.2 + - + +
256A ASN* 3.5 39.1 + - + +
258A ILE* 3.2 19.4 + - + +
335A LYS* 5.8 1.4 + - - -
396A PHE* 3.6 29.7 - + - -
399A TRP* 3.4 35.8 - + + +
416A GLN 3.4 4.5 - - - -
417A LEU* 3.9 19.0 + - + -
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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