Contacts of the strand formed by residues 304 - 315 (chain B) in PDB entry 5E5R
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 GLY 304 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B GLU* 4.2 9.6 - - - -
227B PRO* 3.2 19.1 - - - +
300B GLU* 3.4 2.3 - - - -
301B ASN 3.2 22.2 + - - +
302B SER 3.5 1.4 + - - -
303B ARG* 1.3 79.2 - - - +
305B LYS* 1.3 59.7 + - - -
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Residues in contact with LYS 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A LYS* 4.9 2.6 + - - -
226B GLU* 5.1 3.2 - - - +
227B PRO* 4.3 0.9 - - - -
262B ARG* 5.5 7.6 - - - +
298B ILE* 3.9 21.8 - - + -
299B ALA 3.2 12.6 - - - +
300B GLU* 3.5 23.3 - - + +
304B GLY* 1.3 73.5 - - - -
306B ASN* 1.3 72.2 + - - +
307B VAL* 4.5 13.9 - - + +
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Residues in contact with ASN 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A HIS* 4.4 5.7 - - - -
229A LYS* 3.0 34.0 + - - +
226B GLU* 3.3 23.2 + - - +
227B PRO* 2.7 28.9 + - - +
228B LYS* 4.9 0.9 - - - +
229B ILE* 4.1 17.8 - - + +
298B ILE* 3.7 1.9 - - - +
299B ALA* 3.0 32.0 + - - +
305B LYS* 1.3 76.9 + - - +
307B VAL* 1.3 68.3 + - - +
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Residues in contact with VAL 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B ILE* 3.7 4.7 - - - +
232B GLN* 5.1 1.2 + - - -
262B ARG* 5.6 2.2 - - - +
296B GLU* 4.3 11.0 - - + +
297B CYS 3.3 9.0 - - - +
298B ILE* 4.4 15.7 - - + -
305B LYS* 4.5 18.4 - - + +
306B ASN* 1.3 85.4 + - - +
308B ALA* 1.3 69.4 + - - +
309B ARG* 3.6 39.7 + - - +
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Residues in contact with ALA 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B ILE* 3.5 17.4 - - + +
232B GLN* 3.4 39.0 - - + +
233B PHE* 4.0 6.8 - - + -
249B CYS* 4.2 0.2 - - - -
295B TYR 3.8 0.9 - - - +
296B GLU* 3.3 3.6 - - - -
297B CYS* 2.7 50.6 + - + +
307B VAL* 1.3 75.0 - - - +
309B ARG* 1.3 60.1 + - - +
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Residues in contact with ARG 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232B GLN* 4.8 5.0 + - - +
233B PHE* 3.9 9.2 - - - +
234B PRO 4.2 1.4 - - - +
235B GLU* 4.1 13.0 + - - +
264B SER* 4.2 11.4 - - - +
294B SER* 5.0 6.1 - - - -
295B TYR 3.5 6.3 - - - +
296B GLU* 2.8 52.0 + - + +
307B VAL* 3.6 24.1 + - - +
308B ALA* 1.3 74.9 - - - +
310B GLY* 1.3 61.3 + - - +
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Residues in contact with GLY 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B PHE* 3.5 16.8 - - - -
234B PRO 3.7 4.5 - - - -
235B GLU* 3.1 14.6 - - - -
294B SER* 4.3 3.4 - - - -
295B TYR* 2.8 31.9 + - - +
309B ARG* 1.3 81.2 - - - +
311B ARG* 1.3 62.5 + - - -
312B LEU* 3.8 1.3 + - - +
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Residues in contact with ARG 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B GLU 2.8 12.7 + - - +
236B THR* 3.3 14.5 + - - +
237B LEU 3.0 23.9 + - - -
293B GLY* 3.5 18.2 - - - +
294B SER* 4.1 14.5 + - - +
310B GLY* 1.3 72.3 - - - -
312B LEU* 1.3 72.6 + - - +
313B THR* 3.8 18.4 + - - +
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Residues in contact with LEU 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B PHE* 4.4 7.2 - - + -
237B LEU* 3.5 23.6 - - + +
239B ALA* 5.7 1.1 - - + -
245B VAL* 3.8 16.4 - - + -
247B LEU* 3.9 28.9 - - + -
284B ILE* 3.7 30.5 - - + -
287B PHE* 4.1 17.0 - - + -
291B ASP 4.5 0.7 - - - +
292B THR* 3.4 6.4 - - - -
293B GLY 2.9 32.9 + - - +
295B TYR* 4.0 16.6 - - + -
310B GLY 4.3 8.1 - - - +
311B ARG* 1.3 78.1 - - - +
313B THR* 1.3 63.5 + - - +
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Residues in contact with THR 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B THR* 4.7 8.0 + - - +
237B LEU 3.0 5.4 + - - -
238B PRO* 3.2 26.0 - - - +
239B ALA* 2.9 24.2 + - - +
287B PHE* 3.2 11.8 - - - -
292B THR* 3.9 4.3 - - - -
311B ARG* 4.0 25.1 - - + +
312B LEU* 1.3 79.2 - - - +
314B TYR* 1.3 63.6 + - - +
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Residues in contact with TYR 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B ALA 3.6 3.1 - - - -
241B LYS* 2.9 51.8 - - + +
287B PHE* 3.7 10.5 - + + -
288B GLN* 3.5 11.8 + - - -
289B GLN* 3.3 40.2 - - + -
292B THR* 3.4 22.6 - - + +
313B THR* 1.3 77.1 - - - +
315B TYR* 1.3 76.6 + - - +
316B ALA* 3.9 11.2 - - + +
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Residues in contact with TYR 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238B PRO* 3.6 20.9 - - + -
239B ALA* 3.2 34.7 + - - -
240B ALA* 3.2 25.8 + - + +
241B LYS 2.9 23.0 + - - -
313B THR* 5.7 0.2 - - - -
314B TYR* 1.3 86.7 - - - +
316B ALA* 1.3 71.2 + - - +
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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