Contacts of the strand formed by residues 233 - 237 (chain B) in PDB entry 1SOZ
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 GLY 233 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191B GLN* 3.4 6.1 - - - +
192B THR* 2.8 45.9 + - - +
194B ALA 5.4 0.4 + - - -
196B ILE* 4.4 15.5 - - - -
218B LEU 4.5 1.6 - - - -
219B SER* 4.3 8.3 - - - -
232B ILE* 1.3 74.4 - - - +
234B PHE* 1.3 65.5 + - - -
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Residues in contact with PHE 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A LEU* 4.6 8.1 - - + -
178B ARG* 4.4 4.5 - - + -
179B ILE* 4.1 29.2 - - + -
189B PHE* 3.8 28.7 - - + -
190B LEU 3.3 8.3 - - - +
191B GLN* 3.5 29.8 - - + -
192B THR* 5.3 1.6 - - - -
196B ILE* 5.1 2.9 - - - +
216B ASN* 3.6 5.5 + - - +
217B THR* 2.9 31.4 + - + +
218B LEU* 3.4 16.7 + - + +
220B PHE* 3.7 38.8 - + + -
232B ILE* 3.7 20.9 - - + -
233B GLY* 1.3 79.1 - - - -
235B ALA* 1.3 62.3 + - - +
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Residues in contact with ALA 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B PHE* 3.3 10.5 - - - -
190B LEU* 2.9 38.1 + - + +
192B THR* 5.6 1.1 - - + -
205B LEU* 4.5 11.4 - - + -
214B GLY* 4.2 7.2 - - - -
215B ILE 2.9 29.4 - - - +
216B ASN* 3.6 13.9 - - - +
217B THR* 4.0 1.8 - - - -
234B PHE* 1.3 75.8 - - - +
236B ILE* 1.3 61.3 + - - +
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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
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94B ASN* 5.0 2.5 - - - +
125B THR 3.8 19.1 - - - +
126B ASP* 5.7 0.2 - - + -
127B LEU* 4.1 32.8 - - + -
187B GLN* 5.3 4.3 - - + -
188B ASN 4.9 2.0 - - - +
189B PHE* 3.2 33.2 - - + -
214B GLY* 3.0 3.0 - - - -
215B ILE* 2.8 43.1 + - + +
217B THR* 4.4 9.9 - - - +
235B ALA* 1.3 71.2 - - - +
237B PRO* 1.3 74.8 - - + +
238B PHE* 4.3 0.2 - - - -
240B LEU* 3.2 36.6 - - + -
241B ALA* 4.2 3.6 - - + +
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Residues in contact with PRO 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B PRO* 6.5 0.7 - - + -
188B ASN* 3.3 42.6 - - - +
189B PHE 4.3 12.1 - - - -
190B LEU* 4.4 11.4 - - + +
213B MET 3.7 8.5 - - - +
214B GLY* 4.4 0.2 - - - -
235B ALA 3.7 2.9 - - - +
236B ILE* 1.3 91.1 - - + +
238B PHE* 1.3 68.2 + - + +
239B GLN* 4.6 5.6 - - + +
240B LEU* 3.0 23.1 + - + +
241B ALA* 3.0 9.7 + - - +
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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