Contacts of the strand formed by residues 238 - 248 (chain D) in PDB entry 5J63
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 GLN 238 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33C THR* 4.5 15.3 + - - +
35C ASN* 4.7 7.9 - - - +
60C ASP* 2.8 49.9 + - + +
234D TYR* 3.3 3.3 - - - -
235D VAL* 2.6 45.2 + - - +
237D ASN* 1.3 69.8 - - - +
239D LYS* 1.3 66.2 + - - +
240D PHE* 3.7 1.6 + - - -
281D ALA* 4.7 5.3 - - + +
282D GLY* 3.5 28.5 + - - +
296D LEU* 3.8 16.6 - - + -
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Residues in contact with LYS 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C ASN* 5.5 2.8 + - - +
232D PHE* 3.9 54.1 - - + -
233D SER 3.4 6.3 - - - +
234D TYR* 3.8 23.6 + - + -
237D ASN 3.5 5.6 + - - +
238D GLN* 1.3 77.0 + - - +
240D PHE* 1.3 61.8 + - - +
241D THR* 5.0 7.4 - - - +
282D GLY* 2.9 32.4 + - - +
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Residues in contact with PHE 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210D TRP* 5.1 0.4 - + - -
232D PHE* 3.1 5.1 - - - +
233D SER* 2.8 64.9 + - - +
234D TYR 4.0 3.6 - - - -
235D VAL* 4.0 10.3 - - + -
238D GLN 4.5 0.7 - - - -
239D LYS* 1.3 74.8 - - - +
241D THR* 1.3 69.6 + - - +
242D VAL* 4.1 10.8 - - + -
276D ILE* 3.7 27.8 - - + -
280D GLN 3.2 13.2 - - - +
281D ALA* 4.1 6.3 - - - -
282D GLY 4.3 0.7 - - - +
292D LEU* 4.2 11.9 - - + -
296D LEU* 3.4 36.1 - - + -
298D LEU* 5.2 2.9 - - + -
304D LEU* 3.7 32.8 - - + -
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Residues in contact with THR 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229D PRO 4.2 4.1 + - - +
230D GLY* 3.7 24.5 - - - -
231D ALA 3.2 16.2 - - - +
232D PHE* 4.0 7.3 - - - +
239D LYS* 5.0 8.5 - - - +
240D PHE* 1.3 78.3 - - - +
242D VAL* 1.3 60.1 + - - +
243D TRP* 3.7 26.8 - - + -
276D ILE* 5.4 0.2 - - - +
279D GLY* 3.1 24.8 - - - -
280D GLN* 2.8 32.5 + - - +
282D GLY 5.0 2.6 + - - -
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Residues in contact with VAL 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208D LEU* 3.4 30.7 - - + -
210D TRP* 5.2 0.9 - - + -
221D VAL* 3.7 28.5 - - + +
225D ALA* 5.8 0.3 - - - -
231D ALA* 2.5 28.4 + - - +
232D PHE* 4.9 0.9 - - - -
240D PHE* 4.1 9.4 - - + -
241D THR* 1.3 73.9 - - - +
243D TRP* 1.3 63.2 + - - +
244D SER 3.8 17.9 - - - +
245D SER* 4.3 4.5 - - - -
274D LEU* 5.3 2.0 - - + -
276D ILE* 3.9 38.4 - - + -
278D THR 3.8 3.4 - - - +
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Residues in contact with TRP 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D LYS* 5.6 4.7 - - - -
157D ILE* 5.9 0.3 - - - +
221D VAL* 3.5 9.9 - - - +
225D ALA* 3.7 22.5 - - - +
226D ASP* 3.5 47.8 - - + +
228D TRP 3.7 8.3 - - - -
229D PRO 3.6 16.2 - - - -
230D GLY* 3.3 24.7 - - - -
241D THR* 3.7 18.4 + - + -
242D VAL* 1.3 75.2 - - - +
244D SER* 1.3 56.9 + - - +
278D THR* 2.7 23.8 + - - +
279D GLY* 3.5 21.8 - - - -
280D GLN* 3.0 40.4 + - - +
286D THR* 3.2 25.6 + - + -
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Residues in contact with SER 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B GLU* 6.0 1.0 - - - +
157D ILE* 6.6 0.2 - - - -
221D VAL* 3.7 5.6 - - - -
242D VAL* 3.8 3.7 - - - +
243D TRP* 1.3 79.7 - - - +
245D SER* 1.3 64.2 + - - +
276D ILE 3.7 0.7 - - - -
277D VAL* 2.8 37.7 + - - +
278D THR* 2.8 36.6 + - - +
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Residues in contact with SER 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218D HIS* 3.2 30.4 + - - -
221D VAL* 3.2 32.2 - - - +
222D ARG* 5.7 0.2 - - - +
242D VAL* 4.3 2.9 - - - -
244D SER* 1.3 76.8 - - - +
246D ARG* 1.3 64.8 + - - +
274D LEU* 3.6 16.6 - - - -
275D GLU 3.2 17.0 - - - -
277D VAL* 3.7 8.2 - - - +
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Residues in contact with ARG 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218D HIS* 3.7 8.7 - - + -
245D SER* 1.3 78.7 + - - +
247D VAL* 1.3 69.7 + - - +
248D HIS* 3.8 9.5 + - + -
274D LEU* 3.5 6.1 - - - +
275D GLU* 2.9 70.3 + - + +
277D VAL* 3.8 29.3 - - + +
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Residues in contact with VAL 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214D ALA* 4.1 10.1 - - + +
215D SER* 4.3 21.5 - - - +
218D HIS* 3.8 35.4 - - + +
246D ARG* 1.3 80.6 - - - +
248D HIS* 1.3 76.1 + - - +
272D GLY* 6.2 0.2 - - - -
273D ALA 4.1 2.7 - - - -
274D LEU* 4.8 1.6 - - - -
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Residues in contact with HIS 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246D ARG* 3.9 13.0 + - + -
247D VAL* 1.3 88.0 + - - +
249D PRO* 1.4 79.0 - - + +
264D PRO* 5.7 5.4 - - + -
266D LEU* 3.8 27.3 - - + +
272D GLY* 4.0 2.4 - - - -
273D ALA* 3.1 34.9 + - + +
275D GLU* 2.7 44.8 + - + -
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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