Contacts of the strand formed by residues 232 - 237 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B HIS* 3.7 30.7 - - + +
150B VAL* 5.1 0.5 - - - +
193B LEU* 5.2 3.1 - - - +
194B ASP 4.4 6.2 + - - -
221B ASN* 3.0 34.6 + - - +
222B MET 3.3 7.4 - - - +
223B ILE* 3.8 9.6 - - - +
231B THR* 1.3 91.9 + - - +
233B VAL* 1.3 58.8 + - - +
234B ALA 3.3 28.0 - - - +
235B GLU* 4.4 4.3 - - + +
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Residues in contact with VAL 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B VAL* 3.6 4.7 - - - +
149B HIS* 2.7 29.9 + - - -
150B VAL* 3.2 33.1 + - + +
155B ARG* 3.7 33.0 - - + +
210B TYR* 4.6 0.2 - - + -
222B MET* 2.8 31.9 + - + +
224B ASP* 3.7 32.1 - - + +
227B MET* 3.9 12.6 - - - -
231B THR 3.9 1.1 - - - +
232B THR* 1.3 75.5 - - - +
234B ALA* 1.3 59.8 + - - +
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Residues in contact with ALA 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B LYS 3.2 12.3 - - - +
148B VAL* 4.4 4.7 - - + -
149B HIS* 4.4 1.1 - - - -
155B ARG* 4.7 1.6 - - - +
222B MET* 2.9 35.4 + - - -
232B THR* 3.3 9.7 - - - +
233B VAL* 1.3 83.6 - - + +
235B GLU* 1.3 61.7 + - - +
275B THR* 3.4 30.7 - - - +
276B LEU* 3.6 11.2 - - + +
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Residues in contact with GLU 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B SER 4.3 0.4 - - - +
146B TRP* 3.4 3.8 - - - -
147B LYS* 3.0 71.5 + - + +
149B HIS* 2.8 27.0 + - - +
219B LYS* 3.3 34.1 + - - -
220B VAL 3.1 14.1 - - - +
221B ASN* 4.6 3.0 - - - +
232B THR* 4.4 8.8 - - + +
234B ALA* 1.3 75.6 - - - +
236B ILE* 1.3 66.3 + - - +
276B LEU* 3.7 4.3 - - - -
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Residues in contact with ILE 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B MET* 3.5 11.0 - - + +
145B SER* 3.4 19.1 - - - +
146B TRP* 3.7 16.2 - - + -
219B LYS* 3.7 4.3 - - - +
220B VAL* 2.8 41.2 + - + +
235B GLU* 1.3 78.1 - - - +
237B LYS* 1.3 64.4 - - - +
238B ILE* 4.1 6.3 - - + -
271B MET* 3.8 26.7 - - - -
276B LEU* 3.6 20.2 - - + +
278B PRO* 3.5 41.5 - - + -
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Residues in contact with LYS 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B PHE* 3.3 38.6 - - + -
142B MET* 3.5 10.7 - - - +
145B SER* 2.9 27.2 + - - +
217B ASP* 2.7 40.0 + - - +
218B GLY 3.4 9.6 - - - +
219B LYS* 4.4 5.8 - - + +
236B ILE* 1.3 75.8 - - - +
238B ILE* 1.3 65.6 + - - +
239B GLY 3.0 18.7 + - - +
240B SER* 4.2 6.0 - - - +
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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
------------------------------------------------------------
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