Contacts of the helix formed by residues 285 - 294 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282B ARG* 5.0 4.5 - - - +
283B ALA 4.9 3.8 - - - +
284B LEU* 1.3 77.9 - - - +
286B VAL* 1.3 64.9 + - - +
287B PRO* 3.6 15.3 - - - +
288B GLU* 3.0 39.3 + - - +
289B LEU* 3.2 11.6 + - - +
325B GLU* 5.3 1.6 - - - -
363B MET* 4.5 2.7 - - - -
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Residues in contact with VAL 286 (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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284B LEU 4.2 0.2 + - - -
285B THR* 1.3 72.1 - - - +
287B PRO* 1.4 69.7 - - + +
289B LEU* 3.5 5.9 + - - +
290B THR* 2.9 32.3 + - - +
317B PHE* 4.7 4.3 - - + -
321B MET* 4.1 21.8 - - + -
325B GLU* 3.9 27.5 + - + +
326B VAL* 3.9 29.8 - - + +
329B GLN* 3.8 18.4 - - + -
363B MET* 3.8 22.6 - - + +
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Residues in contact with PRO 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B THR* 3.4 15.0 - - - +
286B VAL* 1.4 94.0 - - + +
288B GLU* 1.3 56.5 + - + +
290B THR* 3.9 2.6 - - - -
291B GLN* 3.0 29.5 + - - +
325B GLU* 3.7 14.6 - - - +
329B GLN* 3.5 39.3 - - + +
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Residues in contact with GLU 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B ARG* 3.2 36.6 + - - -
284B LEU* 3.4 18.4 - - + +
285B THR* 3.0 38.2 + - - +
287B PRO* 1.3 76.0 - - + +
289B LEU* 1.3 57.7 + - - +
291B GLN* 3.3 6.9 + - + +
292B GLN* 2.7 49.8 + - - +
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Residues in contact with LEU 289 (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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271B ALA* 3.6 36.3 - - + +
284B LEU* 4.0 17.7 - - + +
285B THR 3.2 10.8 + - - +
286B VAL* 3.7 8.3 - - - +
288B GLU* 1.3 75.8 - - - +
290B THR* 1.3 58.1 + - - +
293B MET* 3.0 36.7 + - - +
317B PHE* 3.9 22.7 - - + -
321B MET* 4.8 0.9 - - - -
363B MET* 3.7 42.6 - - + +
364B SER* 3.8 23.8 - - - +
365B ALA* 4.1 2.9 - - + +
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Residues in contact with THR 290 (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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286B VAL* 2.9 18.1 + - - +
287B PRO 3.9 3.6 - - - -
289B LEU* 1.3 78.7 - - - +
291B GLN* 1.3 62.1 + - - +
293B MET* 3.7 7.8 - - - +
294B PHE* 3.4 27.0 + - + +
317B PHE* 3.7 16.3 - - - -
329B GLN* 3.5 40.3 - - + +
330B MET* 4.0 17.4 - - - -
333B VAL* 3.9 18.8 - - + -
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Residues in contact with GLN 291 (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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287B PRO 3.0 18.5 + - - +
288B GLU* 4.0 9.4 - - + +
290B THR* 1.3 77.6 - - - +
292B GLN* 1.3 77.2 + - + +
294B PHE* 3.5 5.0 + - - +
295B ASP* 3.1 38.0 + - - +
333B VAL* 5.3 6.5 - - + -
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Residues in contact with GLN 292 (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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271B ALA* 3.7 7.6 - - + -
272B PRO* 3.7 18.0 - - - +
273B LEU 4.6 1.2 + - - -
282B ARG* 6.1 0.2 - - - +
284B LEU* 3.2 34.1 - - - +
288B GLU* 2.7 31.2 + - - +
291B GLN* 1.3 87.3 - - + +
293B MET* 1.3 58.3 + - - +
295B ASP* 2.9 25.0 + - - +
298B ASN* 3.2 32.6 + - - +
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Residues in contact with MET 293 (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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269B GLY* 5.1 1.9 - - - -
270B PHE 5.0 3.1 - - - +
271B ALA* 4.0 12.9 - - + +
289B LEU 3.0 18.0 + - - +
290B THR* 3.7 8.7 - - - +
292B GLN* 1.3 76.3 - - - +
294B PHE* 1.3 71.2 + - + +
295B ASP 4.3 0.7 - - - +
298B ASN* 4.7 6.9 - - - +
299B MET* 3.3 18.5 - - - +
315B ALA* 3.7 18.2 - - + -
316B ILE 4.7 0.7 - - - +
317B PHE* 4.0 18.6 - - + -
330B MET* 5.0 0.4 - - - +
365B ALA* 3.4 28.9 - - + +
366B THR 3.2 36.6 - - - +
367B PHE* 3.6 27.4 - - + +
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Residues in contact with PHE 294 (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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290B THR* 3.4 22.6 + - + +
291B GLN* 3.7 5.2 - - - +
292B GLN 3.2 0.6 - - - -
293B MET* 1.3 86.5 - - + +
295B ASP* 1.3 59.6 + - - +
299B MET* 3.7 10.1 - - - +
305B PRO* 4.6 1.7 - - - +
310B TYR* 4.5 9.6 + + - -
313B VAL* 4.1 9.4 - - + -
315B ALA* 5.7 0.2 - - + -
330B MET* 3.7 32.3 - - + -
333B VAL* 3.7 25.1 - - + -
341B PHE* 3.7 28.9 - + - -
349B VAL* 4.7 2.2 - - + -
367B PHE* 3.7 28.0 - + - -
505B MES 2.8 50.6 + - - -
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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