Contacts of the strand formed by residues 230 - 239 (chain D) in PDB entry 5E6J
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 ASP 230 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189D VAL 4.3 2.6 - - - +
191D LYS* 4.6 7.1 + - - +
222D SER* 6.1 3.1 - - - -
223D ILE 4.2 3.9 - - - +
224D PRO* 5.3 4.7 - - - +
225D CYS* 4.6 2.6 - - - +
228D GLY 4.5 4.3 - - - +
229D ARG* 1.3 100.8 + - + +
231D ALA* 1.3 64.2 + - - +
232D THR* 5.4 2.7 - - + -
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Residues in contact with ALA 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188D VAL* 3.9 16.6 - - + -
189D VAL* 3.0 22.4 - - - +
222D SER* 3.7 1.9 - - - -
223D ILE* 2.8 38.7 + - + +
224D PRO 4.6 0.4 - - - -
225D CYS* 3.4 26.0 - - + +
229D ARG 3.7 0.8 + - - -
230D ASP* 1.3 74.2 - - - +
232D THR* 1.3 69.3 + - - +
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Residues in contact with THR 232 (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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187D ASN 3.6 1.9 - - - +
188D VAL* 3.5 6.3 - - - -
189D VAL* 3.0 43.4 + - + +
220D GLY* 5.4 3.1 - - - -
221D VAL 3.0 17.0 - - - +
222D SER* 4.1 12.6 - - - +
223D ILE 4.3 1.3 - - - +
230D ASP* 5.4 3.8 - - + -
231D ALA* 1.3 84.3 - - - +
233D GLN* 1.3 63.8 + - - +
234D TYR* 4.6 2.6 - - - -
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Residues in contact with GLN 233 (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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186D LEU* 4.3 25.2 - - + +
187D ASN 3.5 4.9 - - - +
188D VAL* 3.7 28.1 - - + +
198D THR* 4.9 5.3 - - - +
208D TYR* 3.2 29.3 + - - -
217D LEU* 5.1 2.1 - - + +
220D GLY* 3.2 4.9 - - - -
221D VAL* 2.7 45.4 + - + +
223D ILE* 3.3 25.4 - - + +
232D THR* 1.3 74.7 - - - +
234D TYR* 1.3 60.7 + - - +
46E ALA* 3.3 31.0 + - - +
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Residues in contact with TYR 234 (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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186D LEU* 3.7 5.9 - - - -
187D ASN* 3.2 78.2 + - + +
189D VAL* 4.3 12.6 - - + -
195D GLN* 4.9 2.0 + - - -
217D LEU* 3.7 7.9 - - - -
218D LYS 4.0 2.9 - - - +
219D THR 3.4 22.2 - - - +
220D GLY* 4.1 0.7 - - - -
232D THR* 4.6 6.3 - - - -
233D GLN* 1.3 80.0 - - - +
235D LEU* 1.3 83.1 + - - +
236D VAL* 3.9 12.3 - - + +
313D THR* 4.2 15.9 - - + -
315D ILE* 4.1 31.7 + - + -
316D LYS* 4.3 11.8 - - - -
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Residues in contact with LEU 235 (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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184D ARG* 3.9 19.1 - - + +
185D VAL 3.5 6.1 - - - +
186D LEU* 3.9 13.7 - - + +
214D TYR* 4.0 21.1 - - + +
217D LEU* 3.3 22.4 + - + +
218D LYS* 3.9 14.3 + - + +
234D TYR* 1.3 81.8 - - - +
236D VAL* 1.3 60.4 + - - +
237D GLN 3.5 24.9 - - - +
238D GLN* 3.9 14.4 - - + +
311D TYR* 3.3 33.2 - - + -
313D THR* 2.2 28.3 + - - +
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Residues in contact with VAL 236 (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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185D VAL* 2.8 32.4 + - + +
186D LEU 3.8 6.1 - - - +
187D ASN* 3.6 30.7 - - + -
197D THR* 4.9 1.8 - - - +
234D TYR* 3.9 13.9 - - + +
235D LEU* 1.3 74.4 - - - +
237D GLN* 1.3 62.2 + - + +
312D THR* 3.7 2.8 + - - -
313D THR* 2.8 39.3 + - - +
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Residues in contact with GLN 237 (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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183D LYS* 4.1 3.7 - - - +
184D ARG* 3.5 2.3 - - - -
185D VAL* 2.9 42.8 + - + +
235D LEU* 3.5 8.5 - - - +
236D VAL* 1.3 84.8 - - + +
238D GLN* 1.3 62.1 + - - +
239D GLU* 4.2 9.7 + - + +
310D SER* 4.3 13.9 + - - -
311D TYR 3.0 22.4 - - - +
312D THR* 4.1 12.9 - - - +
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Residues in contact with GLN 238 (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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183D LYS 3.8 2.6 + - - -
184D ARG* 3.0 37.0 + - - +
205D ALA* 2.8 22.8 + - - +
206D VAL* 4.3 0.2 - - - +
214D TYR* 3.4 25.1 - - - +
235D LEU* 3.9 13.4 - - + +
237D GLN* 1.3 75.2 - - - +
239D GLU* 1.3 63.4 + - - +
240D SER* 2.9 26.6 + - - +
243D VAL* 3.6 17.8 - - + +
308D GLU* 3.8 9.9 - - + +
310D SER* 3.3 4.0 + - - -
311D TYR* 2.7 46.8 + - + +
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Residues in contact with GLU 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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181D SER* 4.2 16.5 + - - +
182D ALA* 3.2 5.6 - - - -
183D LYS* 2.7 54.5 + - + +
237D GLN* 4.5 11.3 + - - +
238D GLN* 1.3 72.8 - - - +
240D SER* 1.3 63.0 + - - +
309D THR 4.4 4.3 - - - +
310D SER* 2.4 37.8 + - - -
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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