Contacts of the strand formed by residues 236 - 241 (chain B) in PDB entry 1OBZ
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A ASP* 3.2 20.4 - - - -
195A PHE* 3.7 16.0 - + - -
197B ARG* 5.8 2.3 - - + +
217B LYS* 3.2 5.1 - - - +
218B ILE* 2.9 29.2 + - + +
233B LEU* 3.6 38.5 - - + +
234B THR 2.9 18.6 + - - -
235B GLU* 1.3 80.0 + - - +
237B ASN* 1.3 62.4 + - - +
238B ILE 3.7 0.5 + - - -
269B ILE* 3.5 33.9 - - + -
270B MET 3.4 6.3 - - - +
271B PRO* 3.3 39.4 - - + +
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Residues in contact with ASN 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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154B PHE* 4.0 33.3 - - + -
215B ASN 5.0 2.1 - - - +
216B GLY 3.6 6.6 - - - +
217B LYS* 4.0 13.3 - - - +
235B GLU 4.3 0.2 - - - -
236B HIS* 1.3 72.0 - - - +
238B ILE* 1.3 64.8 + - - +
239B CYS* 3.5 3.1 + - - -
247B ILE* 5.0 4.0 - - + -
269B ILE* 3.2 8.7 - - - -
270B MET* 2.8 34.6 + - + +
271B PRO 4.5 1.2 + - - -
272B ALA* 3.5 34.0 - - - +
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Residues in contact with ILE 238 (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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211B PHE* 4.2 11.4 - - + -
213B PHE* 4.0 36.3 - - + -
216B GLY* 3.0 20.1 + - - +
218B ILE* 3.9 27.1 - - + -
236B HIS 4.6 0.2 - - - +
237B ASN* 1.3 69.4 - - - +
239B CYS* 1.3 60.5 + - - +
240B GLU 4.5 0.7 - - - +
241B ILE* 3.8 24.7 - - + -
246B VAL* 3.4 30.8 - - + +
247B ILE* 3.5 13.5 - - - +
254B ILE* 4.3 11.0 - - + +
267B ILE* 3.9 12.8 - - + -
268B THR 4.0 2.9 - - - -
269B ILE* 4.5 1.8 - - - -
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Residues in contact with CYS 239 (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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154B PHE* 3.9 24.7 - - - -
193B ARG* 3.6 39.9 - - - +
237B ASN 3.9 12.1 - - - -
238B ILE* 1.3 73.9 - - - +
240B GLU* 1.3 61.7 + - - +
245B ASN* 3.6 10.7 - - - +
246B VAL* 3.0 25.8 + - - +
247B ILE* 3.8 7.3 + - + +
268B THR 2.8 17.2 + - - +
269B ILE 4.4 0.9 - - - -
270B MET* 4.0 19.7 - - - -
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Residues in contact with GLU 240 (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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153B ARG* 4.3 16.9 + - - +
193B ARG* 2.9 43.0 + - - -
196B GLU* 4.6 0.2 - - - +
239B CYS* 1.3 82.6 - - - +
241B ILE* 1.3 65.2 + - - +
242B ASN 4.2 0.4 - - - -
243B GLY* 4.1 19.1 - - - +
244B GLN 3.0 20.9 - - - +
245B ASN* 4.0 10.8 - - + +
246B VAL* 4.5 0.7 - - - +
247B ILE* 5.8 0.3 - - - +
266B THR 3.9 0.2 - - - +
267B ILE* 3.4 6.1 - - - +
268B THR* 2.9 46.5 + - - +
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Residues in contact with ILE 241 (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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238B ILE* 3.8 20.2 - - + -
240B GLU* 1.3 77.3 - - - +
242B ASN* 1.3 85.5 + - - +
243B GLY 3.1 0.2 - - - -
244B GLN* 3.0 24.2 + - - +
246B VAL* 4.2 11.4 - - + +
254B ILE* 3.9 28.7 - - + +
257B ILE* 3.8 28.2 - - + +
258B LEU* 4.0 22.2 - - + -
261B SER* 5.6 0.4 - - - +
265B VAL* 4.2 16.6 - - + -
266B THR 3.4 6.5 - - - +
267B ILE* 4.3 9.2 - - + -
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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