Contacts of the strand formed by residues 233 - 242 (chain D) in PDB entry 5EJK
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 TRP 233 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225D LYS* 3.5 55.6 - - + +
226D ILE 3.6 3.8 - - - -
227D ARG* 3.0 56.6 - - + +
231D GLY 4.3 0.9 - - - -
232D GLU* 1.3 77.3 - - - +
234D GLU* 1.3 60.0 + - - +
235D LYS* 4.1 2.8 + - - +
263D ARG 4.0 8.3 - - - -
264D LYS 3.1 35.2 - - - -
265D VAL 3.9 0.4 - - - -
266D LYS* 3.7 33.7 - - + -
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Residues in contact with GLU 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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225D LYS* 3.4 21.4 - - - +
226D ILE 3.1 17.3 + - - +
228D ILE* 3.4 33.2 - - + +
233D TRP* 1.3 72.7 - - - +
235D LYS* 1.3 74.7 + - - +
237D TRP* 3.5 27.2 + - - +
251D ASN* 4.4 9.4 + - - -
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Residues in contact with LYS 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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225D LYS* 4.5 12.8 - - + +
233D TRP 4.1 3.0 + - - +
234D GLU* 1.3 92.9 - - - +
236D GLY* 1.3 63.0 + - - +
237D TRP* 3.7 2.4 + - - -
251D ASN* 5.5 0.3 + - - -
268D ASP* 3.6 35.4 + - - +
269D ILE* 4.5 16.4 - - - +
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Residues in contact with GLY 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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224D VAL 4.4 0.4 + - - -
235D LYS* 1.3 79.8 - - - +
237D TRP* 1.3 63.9 + - - +
251D ASN* 3.9 6.0 + - - -
252D ARG* 3.0 52.6 + - - +
253D ASP 4.9 0.2 + - - -
268D ASP* 4.2 6.1 + - - -
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Residues in contact with TRP 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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223D PRO* 3.3 4.9 - - - +
224D VAL* 2.7 36.4 + - + +
226D ILE* 3.4 37.3 - - + +
228D ILE* 5.7 0.7 - - + -
234D GLU* 3.5 50.0 + - - -
235D LYS 3.7 2.4 + - - -
236D GLY* 1.3 81.8 - - - +
238D ASN* 1.3 69.5 + - - +
249D VAL* 4.0 15.5 - - + -
250D LYS 3.3 7.4 - - - -
251D ASN* 3.3 52.1 - - + +
252D ARG* 3.9 0.4 - - - +
256D LYS* 3.9 10.5 - - + -
258D ILE* 3.8 34.3 - - + -
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Residues in contact with ASN 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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220D GLU* 4.8 13.9 + - + +
221D GLY* 3.3 34.7 + - - +
223D PRO* 3.4 18.8 - - - +
224D VAL* 4.2 6.3 - - - +
237D TRP* 1.3 75.8 - - - +
239D VAL* 1.3 60.6 + - - +
240D LEU* 5.0 1.6 - - + -
249D VAL* 3.3 1.0 - - - -
250D LYS* 2.5 51.8 + - + +
252D ARG* 2.8 40.3 + - - +
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Residues in contact with VAL 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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220D GLU 4.1 4.2 - - - +
221D GLY* 3.7 16.7 + - - -
222D PRO* 3.5 26.2 - - + -
224D VAL* 3.8 12.1 - - + +
238D ASN* 1.3 72.5 - - - +
240D LEU* 1.3 60.7 + - - +
241D VAL 3.6 8.5 - - - +
242D TRP* 3.1 46.9 - - + +
247D ALA* 4.1 1.8 - - + -
248D ALA 3.1 17.5 - - - +
249D VAL* 3.7 18.2 - - + -
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Residues in contact with LEU 240 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218C LEU* 6.2 4.9 - - + -
220C GLU 6.0 1.8 - - - +
221C GLY* 6.2 0.4 - - - -
222C PRO* 5.1 10.1 - - + -
242C TRP* 5.4 1.6 - - - -
214D ARG* 6.1 1.1 - - - +
220D GLU* 4.6 20.6 - - + -
221D GLY 4.9 0.4 - - - +
238D ASN* 4.9 2.0 - - + +
239D VAL* 1.3 79.1 - - - +
241D VAL* 1.3 66.3 + - + +
242D TRP* 5.9 0.4 - - - -
248D ALA* 2.8 15.8 + - + +
250D LYS* 3.7 54.5 - - + +
257D VAL* 4.2 15.0 - - + -
229E GLU* 4.4 5.1 - - - +
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Residues in contact with VAL 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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222C PRO* 4.4 15.9 - - + -
239C VAL* 5.3 4.3 - - + -
242C TRP* 4.3 33.9 - - + +
239D VAL* 3.6 1.0 - - - +
240D LEU* 1.3 84.4 - - + +
242D TRP* 1.3 64.7 + - - +
243D GLY* 4.2 8.7 - - - +
247D ALA* 3.2 4.9 - - - +
248D ALA* 2.6 47.7 + - + +
259D TRP* 3.5 24.2 - - + -
46E LEU* 5.8 3.8 - - + -
229E GLU* 3.7 4.5 - - - -
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Residues in contact with TRP 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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242C TRP* 5.9 0.7 + - - -
224D VAL* 5.4 2.2 - - + +
239D VAL* 3.1 40.6 - - + +
240D LEU 5.9 0.4 - - - -
241D VAL* 1.3 74.2 - - - +
243D GLY* 1.3 61.8 + - - +
246D TYR 3.8 5.2 - - - -
247D ALA* 3.5 16.8 - - + -
262D SER* 3.1 44.0 - - - -
265D VAL* 3.7 40.4 - - + -
229E GLU* 2.9 55.9 + - + +
230E THR* 4.0 31.9 - - + +
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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