Contacts of the helix formed by residues 285 - 294 (chain D) in PDB entry 5YL4
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 THR 285 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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284D LEU* 1.3 79.2 - - - +
286D VAL* 1.3 59.5 + - - +
287D PRO* 3.7 13.4 - - - +
288D GLU* 2.8 38.7 + - - +
289D LEU* 3.0 27.9 + - - +
325D GLU* 5.8 0.9 - - - -
363D MET* 4.4 3.4 - - - -
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Residues in contact with VAL 286 (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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285D THR* 1.3 72.6 - - - +
287D PRO* 1.4 65.0 - - + +
289D LEU* 3.6 8.0 + - - +
290D THR* 2.7 40.5 + - - +
317D PHE* 4.7 6.1 - - + -
321D MET* 4.2 19.3 - - + -
322D SER 4.9 1.1 - - - +
325D GLU* 3.9 29.4 + - + +
326D VAL* 3.7 38.1 - - + +
329D GLN* 4.4 1.6 - - + -
363D MET* 3.9 19.1 - - + -
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Residues in contact with PRO 287 (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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285D THR* 3.5 14.4 - - - +
286D VAL* 1.4 95.9 - - + +
288D GLU* 1.3 57.6 + - + +
290D THR* 3.5 2.2 + - - +
291D GLN* 3.1 40.0 + - - +
325D GLU* 3.9 16.2 - - - +
329D GLN* 3.6 37.3 - - + +
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Residues in contact with GLU 288 (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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284D LEU* 3.4 24.7 - - + +
285D THR* 2.8 41.6 + - - +
287D PRO* 1.3 75.6 - - + +
289D LEU* 1.3 66.3 + - - +
291D GLN* 3.3 5.9 + - - +
292D GLN* 2.9 35.1 + - - +
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Residues in contact with LEU 289 (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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271D ALA* 3.6 34.3 - - + +
272D PRO* 4.2 2.0 - - + -
284D LEU* 4.0 20.5 - - + +
285D THR 3.0 13.1 + - - +
286D VAL* 3.6 11.4 - - - +
288D GLU* 1.3 77.1 - - - +
290D THR* 1.3 57.1 + - - +
292D GLN* 3.2 3.9 + - - +
293D MET* 3.0 32.5 + - - +
317D PHE* 4.4 18.2 - - + -
321D MET* 4.9 2.5 - - - -
363D MET* 3.5 40.2 - - + +
364D SER* 3.7 12.6 - - - +
365D ALA* 3.7 16.2 - - + +
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Residues in contact with THR 290 (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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286D VAL* 2.7 23.4 + - - +
287D PRO 3.8 4.3 - - - -
288D GLU 3.3 0.2 - - - -
289D LEU* 1.3 77.2 - - - +
291D GLN* 1.3 61.9 + - - +
293D MET* 3.6 8.2 - - - +
294D PHE* 3.3 26.9 + - + +
317D PHE* 3.7 14.3 - - + -
329D GLN* 3.8 32.3 - - - +
330D MET* 3.7 28.3 - - - -
333D VAL* 4.0 15.8 - - + +
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Residues in contact with GLN 291 (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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287D PRO* 3.1 27.5 + - - +
288D GLU* 3.9 5.5 - - - +
290D THR* 1.3 74.2 - - - +
292D GLN* 1.3 66.1 + - + +
294D PHE* 3.6 4.4 + - - +
295D ASP* 3.2 22.2 + - - +
329D GLN* 5.5 4.7 + - - +
332D ASN* 5.6 2.8 + - - +
333D VAL* 4.7 15.5 - - + -
336D LYS* 5.1 10.6 - - - +
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Residues in contact with GLN 292 (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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271D ALA* 3.9 4.7 - - + +
272D PRO* 3.9 21.0 - - - +
273D LEU* 4.6 1.9 + - - +
284D LEU* 3.7 32.9 - - - +
288D GLU* 2.9 21.6 + - - +
289D LEU 3.5 4.5 - - - +
291D GLN* 1.3 76.7 - - + +
293D MET* 1.3 61.6 + - - +
295D ASP* 3.1 18.5 + - - +
298D ASN* 3.2 40.7 + - - +
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Residues in contact with MET 293 (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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269D GLY* 5.3 0.7 - - - -
270D PHE 5.0 3.4 - - - +
271D ALA* 4.2 13.2 - - + +
289D LEU 3.0 11.0 + - - +
290D THR* 3.6 16.4 - - - +
292D GLN* 1.3 76.7 - - - +
294D PHE* 1.3 73.9 + - + +
295D ASP 4.2 0.7 - - - +
298D ASN* 4.7 6.3 - - - +
299D MET* 3.1 21.0 - - - +
315D ALA* 3.8 18.8 - - + -
316D ILE 4.3 1.3 - - - +
317D PHE* 3.9 26.0 - - + -
330D MET* 4.8 0.4 - - - +
365D ALA* 3.7 19.1 - - + +
366D THR 3.2 36.8 - - - +
367D PHE* 3.7 25.0 - - + +
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Residues in contact with PHE 294 (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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290D THR 3.3 22.6 + - - +
291D GLN* 3.6 5.5 + - - +
292D GLN 3.3 0.6 - - - -
293D MET* 1.3 91.6 - - + +
295D ASP* 1.3 59.4 + - - +
299D MET* 3.8 9.8 - - - +
305D PRO* 4.1 2.8 - - - +
306D ARG* 3.3 31.5 + - - +
310D TYR* 4.1 17.3 + + - -
313D VAL* 4.2 10.1 - - + -
315D ALA* 5.4 0.4 - - + -
330D MET* 3.6 36.1 - - + -
333D VAL* 3.9 23.1 - - + -
334D GLN* 6.0 0.2 - - + -
337D ASN* 6.2 5.2 - - + +
341D PHE* 3.7 30.3 - + - -
349D VAL* 4.5 1.8 - - + -
367D PHE* 3.9 23.6 - + - -
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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