Contacts of the strand formed by residues 232 - 237 (chain A) in PDB entry 1DY7
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 THR 232 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A HIS* 3.7 33.7 - - + +
150A VAL* 4.9 0.7 - - - +
193A LEU* 5.0 2.7 - - - +
194A ASP 4.0 9.2 + - - -
221A ASN* 2.9 33.6 + - - +
222A MET 3.4 7.0 - - - +
223A ILE* 3.9 9.0 - - - +
231A THR* 1.3 90.1 + - - +
233A VAL* 1.3 58.9 + - - +
234A ALA 3.4 25.6 - - - +
235A GLU* 4.4 3.8 - - + +
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Residues in contact with VAL 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A VAL* 3.5 2.1 - - - +
149A HIS* 2.7 28.8 + - - -
150A VAL* 3.1 27.3 + - + +
155A ARG* 3.7 33.9 - - - +
222A MET* 2.7 35.2 + - + +
224A ASP* 3.6 30.5 - - + +
227A MET* 3.7 20.2 - - - -
231A THR 3.3 3.8 + - - +
232A THR* 1.3 74.6 - - - +
234A ALA* 1.3 57.8 + - - +
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Residues in contact with ALA 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A LYS 3.2 11.4 - - - +
148A VAL* 4.3 6.3 - - + -
149A HIS* 4.3 1.1 - - - +
155A ARG* 4.8 0.9 - - - +
222A MET* 2.9 37.9 + - - -
232A THR* 3.4 9.5 - - - +
233A VAL* 1.3 82.4 - - + +
235A GLU* 1.3 61.3 + - - +
275A THR* 3.5 32.1 - - - +
276A LEU* 3.6 9.4 - - + +
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Residues in contact with GLU 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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145A SER 4.5 7.2 - - - +
146A TRP* 3.4 4.2 - - - -
147A LYS* 2.9 46.6 + - + +
149A HIS* 2.7 32.6 + - - +
219A LYS* 3.4 33.2 + - - -
220A VAL 3.1 15.3 - - - +
221A ASN* 4.5 3.3 - - - +
232A THR* 4.4 8.4 - - + +
234A ALA* 1.3 74.6 - - - +
236A ILE* 1.3 65.4 + - - +
276A LEU* 3.7 4.3 - - - -
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Residues in contact with ILE 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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142A MET* 3.5 22.0 - - + +
145A SER* 3.5 7.6 - - - +
146A TRP* 3.6 17.7 - - + -
219A LYS* 3.6 4.4 - - - +
220A VAL* 2.8 38.0 + - + +
235A GLU* 1.3 78.2 - - - +
237A LYS* 1.3 67.4 + - - +
238A ILE* 4.0 9.6 - - + -
271A MET* 3.8 26.2 - - - -
276A LEU* 3.6 19.7 - - + +
278A PRO* 3.5 40.8 - - + -
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Residues in contact with LYS 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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137A PHE* 3.3 38.4 - - + -
142A MET* 3.4 10.7 - - - +
145A SER* 2.8 27.3 + - - +
217A ASP* 2.7 36.2 + - - +
218A GLY 3.4 10.1 - - - +
219A LYS* 4.3 8.7 - - + +
236A ILE* 1.3 77.7 - - - +
238A ILE* 1.3 60.3 + - - +
239A GLY 3.0 20.9 + - - +
240A SER* 4.1 6.8 + - - +
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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