Contacts of the strand formed by residues 233 - 242 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A ARG* 6.4 0.2 - - - +
225C LYS* 3.5 41.6 + - - +
226C ILE 3.5 8.1 - - - -
227C ARG* 4.2 25.1 - - + +
231C GLY 4.2 6.4 + - - -
232C GLU* 1.3 79.7 - - - +
234C GLU* 1.3 60.5 + - - +
235C LYS 4.1 0.5 + - - -
263C ARG 3.8 10.3 - - - -
264C LYS* 3.0 39.5 - - - -
265C VAL 3.6 5.8 - - - -
266C LYS* 3.4 52.1 - - + +
42E SER 5.3 2.0 - - - -
44E PRO 5.6 0.7 - - - -
45E ALA 5.4 2.7 - - - -
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Residues in contact with GLU 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225C LYS* 3.2 21.7 - - - -
226C ILE* 3.0 26.7 + - + +
228C ILE* 4.6 21.7 - - + +
232C GLU* 4.0 0.4 + - + -
233C TRP* 1.3 73.0 - - - +
235C LYS* 1.3 73.6 + - - +
237C TRP* 3.6 28.7 + - - +
251C ASN* 5.2 4.0 + - - -
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Residues in contact with LYS 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A GLU* 3.9 15.9 + - - +
224C VAL 4.4 1.3 - - - -
225C LYS* 3.8 33.7 - - + +
233C TRP 4.1 1.0 + - - +
234C GLU* 1.3 91.4 - - - +
236C GLY* 1.3 62.1 + - - +
237C TRP* 3.7 3.9 + - - -
251C ASN* 5.8 0.2 + - - -
268C ASP* 3.3 35.5 + - - +
269C ILE* 5.2 3.2 - - - +
38E PRO* 4.2 14.0 + - - +
39E HIS* 3.8 28.1 + - - +
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Residues in contact with GLY 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224C VAL 4.3 1.6 + - - -
235C LYS* 1.3 79.0 - - - +
237C TRP* 1.3 65.8 + - - +
251C ASN* 4.0 6.8 + - - -
252C ARG* 3.2 51.6 + - - +
253C ASP 5.1 0.2 + - - -
268C ASP* 4.7 2.0 + - - -
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Residues in contact with TRP 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223C PRO* 3.4 4.7 - - - +
224C VAL* 3.0 42.1 + - + +
226C ILE* 3.4 34.5 - - + +
234C GLU* 3.6 41.3 + - - -
235C LYS 3.8 3.1 + - - -
236C GLY* 1.3 82.1 - - - +
238C ASN* 1.3 68.3 + - - +
249C VAL* 3.7 17.5 - - + -
250C LYS 3.4 7.9 - - - -
251C ASN* 3.4 53.7 - - + +
252C ARG* 3.4 2.8 + - - +
256C LYS* 4.0 21.8 - - - -
258C ILE* 3.5 33.7 - - + -
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Residues in contact with ASN 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220C GLU* 4.4 12.4 - - - +
221C GLY 2.4 39.6 + - - +
222C PRO 3.3 11.2 - - - -
223C PRO* 3.9 3.8 - - - +
224C VAL* 4.3 0.9 - - - -
237C TRP* 1.3 75.1 - - - +
239C VAL* 1.3 61.2 + - - +
240C LEU* 5.0 0.4 - - + -
249C VAL* 3.1 4.1 - - - -
250C LYS* 2.6 51.7 + - + +
252C ARG* 2.7 47.9 + - - +
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Residues in contact with VAL 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C LEU* 5.1 1.9 - - - +
221C GLY* 3.2 18.9 - - - -
222C PRO* 3.2 35.1 + - + +
224C VAL* 4.0 16.9 - - + +
238C ASN* 1.3 72.3 - - - +
240C LEU* 1.3 58.2 + - - +
241C VAL 3.2 23.3 - - - +
242C TRP* 4.1 10.8 - - + -
247C ALA* 3.8 17.7 - - + -
248C ALA 3.1 16.2 - - - +
249C VAL* 3.9 9.4 - - + -
265C VAL* 6.1 0.2 - - + -
241D VAL* 5.3 4.9 - - + -
259D TRP* 5.5 1.1 - - + -
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Residues in contact with LEU 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217C VAL* 5.7 6.7 - - + -
218C LEU* 3.2 58.6 - - + +
221C GLY* 4.1 13.7 - - - +
238C ASN 4.8 1.3 - - - +
239C VAL* 1.3 78.8 - - - +
241C VAL* 1.3 65.1 + - + +
248C ALA* 2.6 18.6 + - + +
250C LYS* 3.7 44.0 - - + -
257C VAL* 3.9 18.4 - - + -
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Residues in contact with VAL 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214C ARG* 5.3 11.4 - - - +
239C VAL* 3.2 5.7 - - - +
240C LEU* 1.3 86.5 - - + +
242C TRP* 1.3 65.7 + - - +
243C GLY* 4.0 7.0 - - - +
247C ALA* 3.0 2.1 - - - -
248C ALA* 2.5 47.6 + - + -
259C TRP* 4.0 24.2 - - + -
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Residues in contact with TRP 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239C VAL* 4.1 14.4 - - + -
241C VAL* 1.3 77.2 - - - +
243C GLY* 1.3 83.1 + - - +
244C ARG* 4.7 4.9 - - - -
246C TYR 3.9 4.3 - - - -
247C ALA* 4.1 9.4 - - + +
262C SER* 3.3 28.3 - - - -
240D LEU 5.4 1.3 - - - -
241D VAL* 4.3 35.3 - - + +
242D TRP 5.9 1.0 + - - -
243D GLY* 6.2 3.1 - - - -
46E LEU* 4.4 26.5 - - + -
47E GLU 6.3 0.2 - - - -
48E ALA* 4.9 9.6 - - + -
229E GLU* 4.8 13.1 + - + +
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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