Contacts of the strand formed by residues 213 - 222 (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 SER 213 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202B ALA 3.5 0.9 - - - +
203B GLN* 3.4 4.8 - - - -
204B PHE* 2.8 47.4 + - - +
206B MET* 4.3 8.8 - - - -
209B ASN* 3.8 21.0 + - - -
211B GLU 3.6 0.4 + - - -
212B GLU* 1.3 73.5 - - - +
214B THR* 1.3 62.8 + - - +
215B LEU* 3.5 11.4 + - - +
232B GLU* 3.6 28.8 + - - -
237B PRO* 5.3 2.2 - - - -
240B ASN* 4.2 4.3 + - - +
241B GLN 4.8 0.9 + - - -
243B PHE* 5.1 2.9 - - - -
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Residues in contact with THR 214 (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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159B ASP* 3.9 23.2 + - + +
161B LYS* 4.6 8.7 - - - +
164B TRP* 4.9 2.7 - - + -
201B PHE* 4.7 2.0 - - + -
202B ALA 3.5 4.7 - - - +
203B GLN* 3.0 32.1 + - - +
212B GLU 4.0 2.0 + - - -
213B SER* 1.3 70.8 - - - +
215B LEU* 1.3 64.9 + - - +
232B GLU* 3.5 8.4 + - - +
233B VAL* 3.0 49.8 + - + +
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Residues in contact with LEU 215 (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 4.0 0.2 - - - +
201B PHE* 3.3 8.8 - - - +
202B ALA* 2.6 45.5 + - + +
204B PHE* 3.7 24.7 - - + -
213B SER* 4.1 12.8 - - - +
214B THR* 1.3 75.1 - - - +
216B PHE* 1.3 61.5 + - - +
217B CYS* 4.0 0.9 - - + -
230B ILE* 4.1 18.6 - - + -
231B ILE 3.5 2.9 - - - +
232B GLU* 3.9 20.0 - - + -
233B VAL* 4.6 2.2 - - - -
243B PHE* 3.7 48.7 - - + -
287B LEU* 4.1 15.3 - - + -
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Residues in contact with PHE 216 (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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166B LEU* 3.7 31.0 - - + -
181B MET* 3.8 16.6 - - + -
183B LEU* 4.2 13.0 - - + -
194B ILE* 3.8 20.6 - - + -
199B ALA* 3.7 20.2 - - + -
200B SER 3.9 5.8 - - - -
201B PHE* 3.8 24.0 - + + -
214B THR 4.1 0.6 + - - -
215B LEU* 1.3 72.5 - - - +
217B CYS* 1.3 62.3 + - - +
218B PHE* 3.5 23.5 + + + -
229B HIS 3.6 0.9 - - - +
230B ILE* 4.7 0.4 - - - -
231B ILE* 2.6 50.9 + - + +
233B VAL* 3.6 23.3 - - + +
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Residues in contact with CYS 217 (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 ALA* 3.2 2.6 - - - +
200B SER 2.8 44.2 + - - +
215B LEU* 4.0 1.9 - - + -
216B PHE* 1.3 75.1 - - - +
218B PHE* 1.3 62.5 + - - +
228B LEU* 3.9 14.1 - - - -
229B HIS 3.1 11.4 - - - +
230B ILE* 4.0 18.8 - - + -
264B MET* 3.4 24.4 - - - +
266B ILE* 3.9 14.4 - - + -
273B VAL* 4.2 16.2 - - - -
287B LEU* 4.8 4.5 - - + -
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Residues in contact with PHE 218 (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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181B MET* 3.8 17.0 - - + -
194B ILE* 3.6 20.6 - - + -
195B GLU 3.6 20.0 - - - -
196B GLY* 4.1 8.1 - - - -
198B ALA 3.3 4.7 - - - +
199B ALA* 3.5 18.4 - - + -
216B PHE* 3.5 26.7 - + + -
217B CYS* 1.3 76.8 - - - +
219B ALA* 1.3 63.1 - - - +
220B VAL* 4.3 3.1 - - + -
227B LYS 4.0 0.5 - - - +
228B LEU* 3.6 1.8 - - - -
229B HIS* 2.8 81.9 + + + -
231B ILE* 4.8 5.6 - - + -
264B MET* 3.8 3.8 - - - -
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Residues in contact with ALA 219 (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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196B GLY* 3.8 1.6 - - - -
197B HIS* 2.9 22.3 + - - +
198B ALA 2.7 18.3 + - - +
218B PHE* 1.3 75.2 - - - +
220B VAL* 1.3 62.7 + - - +
227B LYS 3.4 8.3 - - - +
228B LEU* 3.7 20.6 - - + -
250B VAL* 4.8 2.0 - - + -
261B PRO* 3.8 9.4 - - + -
264B MET* 3.5 9.8 - - + +
275B LEU* 3.8 23.6 - - + -
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Residues in contact with VAL 220 (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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195B GLU* 3.4 35.9 - - + +
196B GLY* 3.7 8.5 - - - -
197B HIS* 3.5 18.4 - - + +
218B PHE* 4.3 10.5 - - + -
219B ALA* 1.3 78.5 - - - +
221B ARG* 1.3 64.0 + - - +
222B GLY* 3.7 20.0 - - - +
225B GLY 3.5 1.5 - - - +
226B GLY* 3.2 2.6 - - - -
227B LYS* 2.8 47.4 + - + +
229B HIS* 4.5 3.8 - - + -
250B VAL* 5.1 1.4 - - - +
252B PHE* 5.1 0.5 - - - -
261B PRO* 3.8 7.1 - - - +
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Residues in contact with ARG 221 (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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341A VAL 4.4 6.1 + - - -
342A LEU* 4.2 12.3 + - - +
343A GLN* 3.8 22.6 + - - +
176B ARG* 3.2 41.9 + - - +
197B HIS* 3.2 22.2 + - + -
220B VAL* 1.3 75.6 - - - +
222B GLY* 1.3 59.4 + - - +
225B GLY* 3.6 2.9 - - - -
226B GLY 4.0 11.1 - - - +
252B PHE* 3.4 52.3 + - + +
253B PRO 4.9 1.6 + - - -
256B ALA 3.2 22.8 + - - -
257B GLN* 4.5 2.6 - - - +
258B ASN 3.7 6.7 - - - +
259B ASP 2.9 33.7 + - - +
260B PHE* 4.4 1.6 - - + -
261B PRO* 4.1 8.7 - - + +
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Residues in contact with GLY 222 (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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343A GLN 3.6 11.8 - - - +
345A PRO* 4.0 2.3 - - - +
176B ARG* 3.6 13.2 + - - -
195B GLU* 3.4 23.8 - - - -
220B VAL* 3.6 8.7 - - - +
221B ARG* 1.3 75.2 - - - +
223B GLN* 1.3 65.9 + - - -
224B ALA 3.3 2.7 - - - -
225B GLY 3.1 18.6 + - - -
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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