Contacts of the strand formed by residues 297 - 307 (chain D) in PDB entry 5E6J
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 TYR 297 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252D TYR 4.4 0.4 - - - -
253D LYS* 3.1 5.9 - - - +
254D LEU* 2.5 53.2 + - + +
264D GLU* 2.8 33.1 + - - +
277D ILE* 3.3 35.0 - - + -
283D LEU* 3.9 17.9 - - + +
285D ARG* 3.6 25.2 + - - -
294D MET* 3.9 20.9 - - - -
296D GLU* 1.3 75.7 - - - +
298D LYS* 1.3 65.0 + - - +
299D GLY* 3.4 28.9 - - - -
300D PRO* 3.9 0.5 - - - +
301D VAL* 4.0 12.6 - - + -
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Residues in contact with LYS 298 (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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251D GLU* 4.3 5.5 - - - +
252D TYR 3.3 7.4 - - - +
253D LYS* 4.3 11.7 - - + -
297D TYR* 1.3 89.0 - - - +
299D GLY* 1.3 57.8 + - - +
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Residues in contact with GLY 299 (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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251D GLU* 3.3 17.2 + - - -
252D TYR 2.7 35.5 + - - +
297D TYR* 3.4 13.8 - - - -
298D LYS* 1.3 74.8 - - - +
300D PRO* 1.3 70.7 - - - +
301D VAL* 3.0 6.8 + - - +
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Residues in contact with PRO 300 (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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249D PRO* 5.0 5.4 - - + +
250D ALA 3.3 16.8 - - - +
251D GLU* 3.9 13.7 - - + +
264D GLU* 3.1 25.0 - - - +
265D TYR 2.8 45.0 + - - +
266D THR* 3.7 19.5 - - + -
297D TYR* 3.9 0.4 - - - +
299D GLY* 1.3 79.3 - - - +
301D VAL* 1.3 57.8 + - - +
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Residues in contact with VAL 301 (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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212D LEU* 3.4 23.4 - - + +
248D PRO 4.1 1.2 - - - +
249D PRO* 3.5 1.5 - - - +
250D ALA 2.8 25.2 + - - -
252D TYR* 3.7 19.3 - - + +
254D LEU* 4.1 13.7 - - + -
262D ALA* 4.6 4.0 - - + -
263D ASN 3.5 12.8 - - - +
264D GLU* 4.5 2.9 - - + -
297D TYR* 4.0 17.5 - - + -
299D GLY 3.5 12.6 - - - +
300D PRO* 1.3 74.6 - - - +
302D THR* 1.3 63.8 + - - +
303D ASP 3.8 2.9 - - - +
304D VAL* 3.5 31.9 - - + -
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Residues in contact with THR 302 (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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165D ASP* 5.4 0.2 + - - -
212D LEU* 3.2 7.6 - - - +
246D SER* 3.3 0.3 - - - -
247D ALA 3.0 39.5 + - - -
249D PRO* 4.3 6.8 - - - -
263D ASN 2.9 17.3 + - - +
265D TYR* 3.7 17.7 - - + -
274D TYR* 3.6 30.7 - - + +
301D VAL* 1.3 73.7 - - - +
303D ASP* 1.3 81.6 + - - +
73E LEU* 3.5 19.0 - - - +
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Residues in contact with ASP 303 (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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165D ASP* 5.0 0.4 - - - +
166D VAL* 3.6 26.7 - - - +
167D ARG* 4.2 8.5 + - - +
244D MET* 3.5 21.2 - - + +
245D MET 3.6 3.6 - - - -
246D SER* 2.5 27.0 + - - +
262D ALA* 3.1 5.7 - - - +
263D ASN* 2.6 44.4 + - + +
274D TYR* 4.3 1.7 + - - -
301D VAL 3.9 0.2 - - - -
302D THR* 1.3 104.3 + - - +
304D VAL* 1.3 65.0 + - - +
305D PHE* 4.5 4.3 - - + -
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Residues in contact with VAL 304 (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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212D LEU* 3.8 24.5 - - + +
244D MET* 4.6 0.4 - - - +
245D MET 2.8 39.7 + - - +
252D TYR* 4.7 2.5 - - + -
254D LEU* 4.4 10.3 - - + -
259D PHE* 4.0 19.1 - - + -
261D CYS 3.8 2.7 - - - -
262D ALA* 3.9 11.2 - - + -
301D VAL* 3.5 21.5 - - + -
303D ASP* 1.3 82.2 - - - +
305D PHE* 1.3 61.9 + - - +
306D TYR* 3.2 36.7 - - + +
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Residues in contact with PHE 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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120D ALA* 3.9 24.0 - - + -
124D LEU* 4.1 37.0 - - + -
166D VAL* 5.2 0.7 - - + -
170D MET* 4.2 10.8 - - + -
242D PHE* 4.4 2.0 - + - -
243D VAL 3.3 6.3 - - - +
244D MET* 3.3 55.2 - - + -
259D PHE* 3.6 5.2 - - - +
260D LEU* 3.3 21.7 + - + -
261D CYS* 2.8 44.3 + - - +
262D ALA* 4.5 1.8 - - - -
263D ASN* 4.2 16.2 - - - -
303D ASP* 4.5 8.1 - - + -
304D VAL* 1.3 72.3 - - - +
306D TYR* 1.3 70.0 + - - +
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Residues in contact with TYR 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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212D LEU 2.5 29.5 + - - -
213D SER* 3.6 2.8 - - - -
214D TYR* 3.4 52.1 + + + -
215D ASP* 5.9 2.7 - - - -
242D PHE* 3.2 4.5 - - - +
243D VAL* 2.7 43.3 + - + +
245D MET* 3.5 16.2 - - + -
252D TYR* 4.3 6.1 + - - -
258D THR 3.4 26.0 - - - -
259D PHE* 3.9 9.0 - - + +
260D LEU* 4.6 4.9 - - - +
304D VAL* 3.2 36.2 - - + +
305D PHE* 1.3 78.1 - - - +
307D LYS* 1.3 64.4 + - - +
308D GLU* 4.3 0.3 - - - +
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Residues in contact with LYS 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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125D GLU* 4.4 19.3 + - + +
214D TYR* 5.2 1.9 - - - -
241D SER* 3.4 13.9 - - - +
242D PHE* 4.4 2.0 - - - +
260D LEU* 4.4 25.7 - - + +
306D TYR* 1.3 74.9 - - - +
308D GLU* 1.3 83.9 + - - +
309D THR* 4.4 8.5 - - - +
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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