Contacts of the strand formed by residues 225 - 232 (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 GLY 225 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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342A LEU* 5.0 4.5 - - - -
343A GLN 3.5 20.8 + - - -
344A ASN* 3.6 13.7 - - - -
220B VAL* 3.5 1.7 - - - +
221B ARG* 4.0 3.4 - - - -
222B GLY* 3.1 30.1 + - - -
223B GLN 3.3 2.4 + - - -
224B ALA* 1.3 82.5 + - - +
226B GLY* 1.3 62.4 + - - -
227B LYS* 3.4 5.2 + - - +
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Residues in contact with GLY 226 (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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342A LEU 5.7 0.4 + - - -
220B VAL 3.2 8.7 - - - -
221B ARG* 4.0 15.7 - - - +
225B GLY* 1.3 69.3 - - - -
227B LYS* 1.3 66.9 + - - +
249B ASP* 3.4 8.8 - - - +
250B VAL* 2.9 40.7 + - - +
252B PHE* 4.2 2.8 - - - -
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Residues in contact with LYS 227 (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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291A THR* 4.9 8.0 + - - +
344A ASN* 4.7 6.5 - - - +
218B PHE 4.0 0.5 - - - +
219B ALA* 3.4 2.8 - - - -
220B VAL* 2.8 38.3 + - + +
224B ALA* 3.2 38.4 + - + +
225B GLY 3.4 3.1 + - - +
226B GLY* 1.3 73.6 + - - +
228B LEU* 1.3 60.2 + - - +
229B HIS* 3.6 27.5 + - + +
247B ALA* 4.9 8.1 - - + -
248B VAL 3.2 21.8 - - - +
249B ASP* 2.9 32.0 + - - +
250B VAL* 3.5 6.6 - - - +
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Residues in contact with LEU 228 (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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217B CYS* 3.9 12.3 - - - -
218B PHE 3.6 1.8 - - - +
219B ALA* 3.7 23.3 - - + -
227B LYS* 1.3 73.2 - - - +
229B HIS* 1.3 61.9 + - - +
230B ILE* 4.2 19.5 + - + +
246B LYS 3.9 0.3 - - - +
247B ALA* 3.4 3.6 + - - -
248B VAL* 2.7 55.6 + - + +
250B VAL* 3.7 10.5 - - + -
264B MET* 3.7 18.4 - - + -
273B VAL* 4.9 4.0 - - + -
275B LEU* 4.6 9.4 - - + -
285B TYR* 3.7 37.2 - - + -
290B GLY* 4.6 0.7 - - - -
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Residues in contact with HIS 229 (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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216B PHE 3.6 1.3 - - - +
217B CYS* 3.1 7.3 - - - -
218B PHE* 2.8 81.9 + + + +
220B VAL* 4.5 5.2 - - + -
227B LYS* 3.6 32.1 + - + +
228B LEU* 1.3 72.2 - - - +
230B ILE* 1.3 64.7 + - - +
231B ILE* 4.0 6.5 - - + -
246B LYS 3.4 5.4 - - - +
247B ALA* 3.8 26.2 - - + +
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Residues in contact with ILE 230 (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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215B LEU* 4.1 17.5 - - + -
216B PHE 3.8 3.1 - - - +
217B CYS* 4.0 17.7 - - + +
228B LEU* 4.2 14.1 - - + +
229B HIS* 1.3 77.7 - - - +
231B ILE* 1.3 60.9 + - - +
243B PHE* 3.4 27.5 - - + -
245B LYS* 3.6 0.3 - - - -
246B LYS* 2.9 47.2 + - + -
248B VAL* 5.6 0.7 - - + -
273B VAL* 5.3 1.1 - - + -
286B ASP 4.1 2.9 - - - +
287B LEU* 3.5 33.4 - - + +
289B THR 4.6 0.2 - - - -
290B GLY* 3.7 29.6 - - - +
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Residues in contact with ILE 231 (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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215B LEU* 3.5 6.2 - - - -
216B PHE* 2.6 64.6 + - + +
218B PHE* 4.8 5.2 - - + -
229B HIS* 4.7 10.3 - - + -
230B ILE* 1.3 79.3 - - - +
232B GLU* 1.3 73.0 + - - +
233B VAL* 5.3 4.9 - - + -
243B PHE* 4.7 0.7 - - - -
245B LYS* 3.4 46.2 - - + +
246B LYS 5.8 0.4 - - - +
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Residues in contact with GLU 232 (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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213B SER* 3.6 27.6 + - - -
214B THR 3.5 15.5 + - - +
215B LEU* 3.9 7.5 - - + +
231B ILE* 1.3 86.9 - - - +
233B VAL* 1.3 69.2 + - - +
234B GLY 3.8 7.3 + - - +
236B PRO* 3.7 31.5 - - - +
237B PRO* 4.4 2.6 - - - +
241B GLN 5.3 0.2 - - - +
242B PRO* 3.8 7.8 - - - +
243B PHE* 2.9 47.4 + - + +
245B LYS* 5.3 1.5 + - - +
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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