Contacts of the strand formed by residues 304 - 314 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226D GLU* 4.1 7.2 - - - +
227D PRO* 3.4 7.4 - - - +
300D GLU* 3.2 5.1 - - - +
301D ASN* 3.1 32.2 + - - +
302D SER 3.5 1.0 + - - -
303D ARG* 1.3 81.8 - - - +
305D LYS* 1.3 62.8 + - - -
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Residues in contact with LYS 305 (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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229C LYS* 4.7 1.9 + - - -
226D GLU* 4.1 6.7 - - - +
227D PRO* 4.8 1.6 - - - -
262D ARG* 5.2 9.5 - - - +
298D ILE* 4.5 17.8 - - + +
299D ALA 3.3 7.4 - - - +
300D GLU* 3.4 35.9 - - + +
304D GLY* 1.3 73.0 - - - -
306D ASN* 1.3 78.2 + - - +
307D VAL* 5.4 4.9 - - + -
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Residues in contact with ASN 306 (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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226C HIS* 4.0 8.5 - - - -
229C LYS* 2.9 36.9 + - - +
226D GLU* 3.3 20.6 + - - +
227D PRO* 2.4 36.8 + - + +
228D LYS* 4.5 1.0 - - - +
229D ILE* 3.6 17.8 - - + +
298D ILE* 3.7 1.2 - - - +
299D ALA* 2.9 33.6 + - - +
305D LYS* 1.3 78.7 + - - +
307D VAL* 1.3 64.6 + - - +
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Residues in contact with VAL 307 (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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229D ILE* 3.7 4.4 - - - +
262D ARG* 5.7 2.9 - - - +
296D GLU* 5.3 4.9 - - - +
297D CYS 3.2 9.0 - - - +
298D ILE* 3.9 23.8 - - + -
305D LYS* 5.4 5.8 - - + -
306D ASN* 1.3 82.7 + - - +
308D ALA* 1.3 61.2 + - - +
309D ARG* 3.5 46.0 - - + +
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Residues in contact with ALA 308 (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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229D ILE* 3.6 16.9 - - + +
232D GLN* 3.2 42.8 - - + +
233D PHE* 4.0 7.2 - - + +
249D CYS* 4.5 7.0 - - - -
296D GLU* 3.4 3.5 - - - +
297D CYS* 2.9 32.4 + - + +
307D VAL* 1.3 75.1 - - - +
309D ARG* 1.3 61.6 + - - +
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Residues in contact with ARG 309 (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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232D GLN* 4.6 6.0 + - - +
233D PHE* 3.9 5.0 - - - +
234D PRO 4.4 1.2 - - - +
235D GLU* 3.9 14.2 + - - +
264D SER* 5.1 1.8 - - - -
294D SER* 4.6 7.2 - - - +
295D TYR 3.5 6.3 - - - +
296D GLU* 3.4 34.1 + - + -
307D VAL* 3.5 32.5 - - + +
308D ALA* 1.3 77.2 - - - +
310D GLY* 1.3 59.6 + - - +
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Residues in contact with GLY 310 (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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233D PHE* 3.2 18.5 - - - -
234D PRO 3.6 6.5 - - - -
235D GLU 3.1 13.2 - - - -
294D SER* 3.4 2.3 - - - -
295D TYR* 2.7 37.7 + - - +
309D ARG* 1.3 75.5 - - - +
311D ARG* 1.3 62.2 + - - -
312D LEU* 4.0 1.6 + - - +
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Residues in contact with ARG 311 (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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235D GLU 2.8 12.2 + - - +
236D THR* 3.2 36.0 - - - +
237D LEU 2.8 24.8 + - - -
293D GLY* 3.5 12.8 - - - +
294D SER* 4.5 14.6 - - - +
310D GLY* 1.3 75.6 - - - +
312D LEU* 1.3 65.1 + - - +
313D THR* 3.8 25.3 + - + +
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Residues in contact with LEU 312 (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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233D PHE* 4.8 3.8 - - + -
237D LEU* 3.6 21.3 - - + +
239D ALA* 6.2 0.9 - - + -
245D VAL* 4.0 11.9 - - + -
247D LEU* 3.8 24.5 - - + -
284D ILE* 3.6 24.7 - - + -
287D PHE* 3.9 23.3 - - + -
291D ASP 4.4 0.7 - - - +
292D THR* 3.3 7.9 - - - -
293D GLY* 3.0 31.7 + - - +
295D TYR* 3.5 33.2 - - + -
310D GLY 4.4 6.7 - - - +
311D ARG* 1.3 77.0 - - - +
313D THR* 1.3 63.9 + - - +
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Residues in contact with THR 313 (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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236D THR* 5.4 3.6 - - - -
237D LEU 3.2 6.3 + - - +
238D PRO* 3.5 24.1 - - - +
239D ALA 3.1 17.3 + - - -
287D PHE* 3.3 14.5 - - - -
292D THR* 4.1 5.2 - - - -
311D ARG* 3.9 35.7 - - + +
312D LEU* 1.3 79.8 - - - +
314D TYR* 1.3 67.2 + - - +
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Residues in contact with TYR 314 (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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238D PRO* 5.3 1.8 - - - -
239D ALA 3.1 19.3 - - - +
241D LYS* 3.4 40.1 - - + -
287D PHE* 4.0 8.5 - + + -
289D GLN* 2.4 43.9 + - - -
292D THR* 3.5 18.4 - - + -
313D THR* 1.3 80.0 + - - +
315D TYR* 1.3 88.1 + - - +
316D ALA* 3.9 7.8 + - + -
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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