Contacts of the strand formed by residues 261 - 267 (chain B) in PDB entry 5ODS
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 PRO 261 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197B HIS* 3.2 41.8 - - + +
198B ALA* 4.1 6.3 - - + -
219B ALA* 3.8 23.8 - - + +
220B VAL 3.8 3.6 - - - +
221B ARG 4.1 10.3 - - - +
250B VAL* 5.9 0.9 - - + -
252B PHE* 3.7 17.5 - - + -
260B PHE* 1.3 94.2 - - + +
262B VAL* 1.3 59.0 + - - +
275B LEU* 3.9 29.8 - - + -
276B ILE 3.8 4.9 - - - +
277B THR* 4.2 5.2 - - + -
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Residues in contact with VAL 262 (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 ILE* 4.9 18.4 - - + +
197B HIS 4.8 3.4 - - - +
198B ALA* 4.1 6.9 - - - +
260B PHE* 3.3 11.8 + - + -
261B PRO* 1.3 75.3 - - - +
263B ALA* 1.3 65.3 + - + +
276B ILE* 2.7 20.8 + - + +
277B THR 4.0 1.6 - - - +
278B LYS* 3.7 44.6 - - + +
302B THR* 5.1 4.7 - - + -
303B ILE 4.0 22.0 - - - +
304B PHE* 5.4 5.2 - - - +
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Residues in contact with ALA 263 (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 ALA* 4.0 5.6 - - - +
262B VAL* 1.3 86.4 - - + +
264B MET* 1.3 61.8 + - - +
275B LEU* 3.4 9.4 - - - +
276B ILE* 2.9 37.9 + - + -
306B THR* 3.4 38.4 - - + +
315B ILE* 4.8 3.8 - - + -
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Residues in contact with MET 264 (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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157B ARG* 2.9 26.0 + - - -
198B ALA* 3.6 12.4 - - + +
199B ALA 4.0 8.6 + - - +
200B SER* 3.8 18.0 - - - -
217B CYS* 3.4 43.7 - - - +
218B PHE* 3.8 1.1 - - - -
219B ALA* 3.5 33.7 - - + +
228B LEU* 3.7 13.7 - - + -
263B ALA* 1.3 77.6 - - - +
265B GLN* 1.3 66.0 + - - +
266B ILE* 4.6 0.7 - - - -
273B VAL* 3.6 12.6 - - + -
274B PHE 3.2 16.4 - - - +
275B LEU* 3.9 6.7 - - + -
315B ILE* 5.3 0.2 - - - -
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Residues in contact with GLN 265 (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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157B ARG* 3.0 29.0 + - - +
200B SER* 5.1 0.2 + - - -
264B MET* 1.3 75.0 + - - +
266B ILE* 1.3 65.1 + - - +
274B PHE* 2.8 42.4 + - + +
306B THR* 4.7 8.6 + - - +
307B ALA* 4.2 12.0 - - - +
308B PRO* 3.5 37.1 - - + +
314B GLY 4.7 5.4 - - - +
315B ILE* 3.5 41.2 - - + +
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Residues in contact with ILE 266 (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 SER* 3.5 35.0 + - - +
201B PHE 4.0 2.2 - - - +
202B ALA* 3.7 35.0 - - + +
217B CYS* 3.9 24.5 - - + -
265B GLN* 1.3 78.6 + - - +
267B SER* 1.3 70.3 + - - +
268B GLU* 3.5 11.8 + - - +
272B VAL 3.6 10.8 - - - +
273B VAL* 4.0 18.4 - - + -
274B PHE* 5.0 0.4 - - - -
287B LEU* 3.9 22.4 - - + -
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Residues in contact with SER 267 (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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265B GLN 4.0 1.2 + - - -
266B ILE* 1.3 72.4 - - - +
268B GLU* 1.3 54.4 + - - +
269B LYS* 3.6 4.3 + - - +
270B HIS* 2.9 28.9 + - - -
271B ASP* 2.7 37.1 + - - -
272B VAL* 2.9 21.1 + - - -
274B PHE* 3.8 15.7 - - - -
313B ALA* 3.3 24.4 + - - +
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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