Contacts of the strand formed by residues 197 - 202 (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 ARG 197 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ASP 4.5 18.6 - - - +
191A ARG* 3.5 48.7 - - - +
192A ASP 4.5 4.0 + - - -
194A PRO* 4.0 27.6 + - + +
195A PHE* 6.2 3.1 - - + -
195B PHE 3.6 3.1 + - - +
196B GLU* 1.3 79.0 - - - +
198B THR* 1.3 71.7 + - - +
199B ILE* 4.2 20.2 - - + -
233B LEU* 6.5 1.3 - - + -
236B HIS* 5.8 2.2 - - + +
267B ILE 3.7 0.3 - - - +
268B THR* 3.4 1.6 - - - -
269B ILE* 2.9 50.7 + - + +
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Residues in contact with THR 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B GLU* 4.2 7.8 + - - -
197B ARG* 1.3 83.2 + - - +
199B ILE* 1.3 67.7 + - - +
200B THR* 4.3 3.4 + - - +
266B THR* 3.5 29.2 - - + -
267B ILE 3.3 3.4 - - - +
268B THR* 3.3 25.3 + - - +
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Residues in contact with ILE 199 (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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191A ARG* 3.7 25.1 - - - +
197B ARG* 4.2 11.0 - - + -
198B THR* 1.3 78.5 - - - +
200B THR* 1.3 63.0 + - - +
201B MET* 4.0 21.0 - - + +
230B ASN* 3.6 42.0 - - + +
231B GLY 3.9 9.0 - - - +
232B LEU* 3.9 24.9 - - + -
233B LEU* 6.0 0.2 - - + -
265B VAL 3.6 2.1 - - - +
266B THR* 3.5 1.5 - - - -
267B ILE* 2.8 35.1 + - - +
269B ILE* 4.2 13.9 - - + -
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Residues in contact with THR 200 (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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198B THR* 4.3 3.0 + - - +
199B ILE* 1.3 74.5 - - - +
201B MET* 1.3 62.9 + - - +
202B HIS* 4.2 17.4 + - + -
230B ASN* 3.4 24.8 + - - +
264B VAL* 3.6 29.6 - - + -
265B VAL 3.6 2.2 - - - -
266B THR* 3.7 17.8 + - - +
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Residues in contact with MET 201 (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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199B ILE* 4.0 23.8 - - + +
200B THR* 1.3 76.3 - - - +
202B HIS* 1.3 71.3 + - - +
209B VAL* 3.8 26.5 - - + -
211B PHE* 4.4 1.1 - - + -
226B SER* 3.3 25.8 - - - +
227B ALA* 3.6 28.9 - - - -
230B ASN* 4.1 0.2 - - - +
232B LEU* 4.2 13.0 - - + -
264B VAL* 3.6 4.7 - - - +
265B VAL* 2.9 37.9 + - + +
267B ILE* 3.4 42.0 - - + -
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Residues in contact with HIS 202 (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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200B THR* 4.2 18.7 + - + +
201B MET* 1.3 81.4 - - - +
203B LYS* 1.3 67.4 + - - +
204B ASP* 3.7 1.7 + - - +
208B HIS 4.1 1.9 - - - +
209B VAL* 3.7 4.9 - - - +
226B SER* 3.0 27.2 + - - +
229B ARG* 4.9 4.6 + - - +
230B ASN* 5.3 2.2 + - - -
263B THR* 3.4 14.1 - - + +
264B VAL* 3.8 30.9 - - + +
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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