Contacts of the strand formed by residues 243 - 253 (chain C) in PDB entry 3IKR
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 LYS 243 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239C SER* 3.6 1.4 + - - -
240C VAL* 2.9 38.5 + - + +
242C GLU* 1.3 79.0 - - - +
244C ILE* 1.3 71.0 + - - +
245C PHE* 3.6 21.3 - - + -
270C SER 3.0 11.7 + - - -
272C ARG* 4.2 11.9 - - - +
276C GLU* 2.8 37.6 + - - +
354C GLU* 3.0 45.7 + - + +
355C PHE 3.6 10.5 - - - +
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Residues in contact with ILE 244 (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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227B GLN* 3.6 25.1 - - + +
228B TYR* 3.5 44.4 - - + +
231B VAL* 4.2 25.8 - - + -
233C LEU* 3.9 18.6 - - + -
238C GLN 3.4 4.3 - - - +
239C SER* 4.3 12.3 - - - +
242C GLU 4.8 1.3 - - - +
243C LYS* 1.3 80.5 - - - +
245C PHE* 1.3 75.3 + - - +
246C LYS* 4.0 1.5 + - + -
353C CYS 3.7 0.3 - - - +
354C GLU* 3.1 4.3 - - - -
355C PHE* 2.8 39.7 + - - +
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Residues in contact with PHE 245 (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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237C GLY* 3.2 3.1 - - - -
238C GLN* 2.8 36.3 + - + +
240C VAL* 3.9 24.9 - - + -
243C LYS* 3.6 15.7 - - + -
244C ILE* 1.3 76.0 - - - +
246C LYS* 1.3 61.8 + - - +
269C ALA* 3.8 27.8 - - + -
270C SER 4.0 0.9 - - - -
271C PRO* 4.4 9.9 - - + -
276C GLU* 3.3 32.1 - - + -
279C ALA* 4.2 3.6 - - + -
280C LEU* 4.0 24.0 - - + -
283C LEU* 3.8 19.0 - - + +
352C VAL* 4.2 2.0 - - + -
353C CYS 3.3 3.4 - - - +
354C GLU* 3.6 31.4 - - + -
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Residues in contact with LYS 246 (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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404A CA 4.3 3.6 - - - -
231B VAL* 2.9 36.0 + - + +
232B GLU 3.8 6.5 + - - -
234B PHE* 2.8 42.0 + - + +
235B PRO* 4.7 3.3 - - - +
232C GLU* 2.9 26.9 + - - +
236C ASN* 3.4 25.4 - - - +
237C GLY* 4.6 2.9 - - - +
244C ILE* 4.0 1.1 + - + -
245C PHE* 1.3 76.8 - - - +
247C THR* 1.3 71.0 + - - +
352C VAL* 4.0 4.2 - - - +
353C CYS 2.9 30.9 + - - +
355C PHE* 4.3 13.9 - - + -
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Residues in contact with THR 247 (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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234B PHE* 4.0 3.0 - - - -
235B PRO* 4.9 1.4 - - - +
236C ASN* 3.0 44.9 + - + +
246C LYS* 1.3 81.1 - - - +
248C ALA* 1.3 63.4 + - - +
249C GLY 3.1 10.2 + - - +
283C LEU* 4.2 8.8 - - + +
287C LYS* 3.9 23.1 - - + +
350C LEU* 3.4 18.8 - - - +
351C VAL 3.0 14.8 + - - -
352C VAL* 3.9 13.0 - - - +
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Residues in contact with ALA 248 (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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234B PHE* 3.7 23.3 - - + -
235B PRO* 4.0 20.0 - - + +
236C ASN* 5.9 1.1 - - - -
247C THR* 1.3 74.2 + - - +
249C GLY* 1.3 60.8 + - - +
250C PHE* 3.3 44.5 - - + -
351C VAL* 3.0 17.0 + - + +
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Residues in contact with GLY 249 (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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236C ASN* 5.2 2.7 - - - -
247C THR* 3.1 19.5 + - - -
248C ALA* 1.3 78.1 - - - +
250C PHE* 1.3 58.9 + - - +
287C LYS* 4.9 11.9 - - - +
350C LEU* 4.1 9.4 - - - -
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Residues in contact with PHE 250 (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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235B PRO* 4.5 9.6 - - + -
287B LYS* 4.3 21.1 - - - -
248C ALA* 3.3 38.6 - - + -
249C GLY* 1.3 80.0 - - - +
251C VAL* 1.3 66.2 + - - +
252C LYS* 3.6 39.9 - - + -
260C LEU* 3.8 20.9 - - + -
350C LEU* 3.7 3.6 - - - +
351C VAL* 3.0 26.5 + - + +
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Residues in contact with VAL 251 (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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250C PHE* 1.3 77.4 - - - +
252C LYS* 1.3 79.2 + - - +
289C GLU* 4.1 24.0 - - + +
348C LYS* 3.9 25.2 - - + +
349C ARG* 3.1 16.4 - - - +
350C LEU* 3.6 22.2 - - + +
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Residues in contact with LYS 252 (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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286B ALA 5.3 7.4 + - - -
250C PHE* 3.6 33.7 - - + -
251C VAL* 1.3 85.7 - - - +
253C PRO* 1.3 85.0 - - + +
256C GLU* 4.0 15.0 - - + +
257C ALA* 4.0 3.8 - - - +
260C LEU* 4.3 10.3 - - + -
292C PHE* 3.5 5.9 - - - -
348C LYS* 3.8 7.2 - - - -
349C ARG 3.0 24.2 + - - +
351C VAL* 3.7 13.6 - - + +
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Residues in contact with PRO 253 (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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252C LYS* 1.3 92.8 - - + +
254C PHE* 1.3 66.1 + - - +
255C THR* 3.4 1.6 - - - +
256C GLU* 3.0 33.5 + - + +
257C ALA* 2.9 18.5 + - - +
345C CYS 4.0 4.3 - - - +
346C GLY* 3.8 17.0 - - - +
347C GLU 3.3 10.8 - - - +
348C LYS* 3.5 32.3 - - + +
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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