Contacts of the helix formed by residues 386 - 397 (chain C) in PDB entry 5Y3R
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 VAL 386 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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382C ASP 2.9 25.1 - - - +
383C PHE* 3.3 9.0 - - - +
384C MET 2.5 7.7 + - - +
385C TYR* 1.3 84.8 - - + +
387C GLU* 1.3 71.9 + - + +
388C LEU 2.9 1.3 - - - -
389C ILE* 3.1 5.0 + - - +
390C GLN* 2.8 25.3 + - - +
431C TYR* 2.9 24.6 - - + +
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Residues in contact with GLU 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350C ARG* 5.9 4.5 - - - +
383C PHE* 3.0 26.3 + - + +
384C MET* 5.5 0.4 - - - -
386C VAL* 1.3 90.2 - - + +
388C LEU* 1.3 57.4 + - - +
390C GLN* 2.9 33.1 + - - +
391C ARG* 2.8 29.6 + - - +
1722C PHE* 5.7 0.5 - - - -
1723C PRO* 5.8 5.0 - - - +
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Residues in contact with LEU 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368C LEU* 3.6 45.1 - - + +
372C PRO* 4.4 3.6 - - + -
383C PHE 4.0 0.6 + - - -
384C MET* 3.8 28.3 - - + -
385C TYR* 2.9 24.2 - - + +
386C VAL 2.9 1.0 - - - +
387C GLU* 1.3 77.7 - - - +
389C ILE* 1.3 65.0 + - + +
390C GLN 3.1 1.1 - - - -
391C ARG* 2.8 36.7 + - + +
392C CYS* 2.9 25.2 + - - -
416C SER* 6.0 6.3 - - - +
420C VAL* 6.0 4.3 - - + -
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Residues in contact with ILE 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385C TYR* 2.8 32.0 - - + +
386C VAL 3.1 1.9 + - - +
388C LEU* 1.3 77.2 - - + +
390C GLN* 1.3 70.2 + - - +
392C CYS* 2.9 34.5 - - + +
393C LYS* 2.9 5.7 + - - +
416C SER* 5.9 0.2 - - - +
417C VAL* 3.9 29.8 - - + -
420C VAL* 6.0 1.6 - - + -
431C TYR* 3.3 38.8 - - + -
434C VAL* 3.6 25.5 - - + +
438C LEU* 6.4 0.7 - - + -
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Residues in contact with GLN 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386C VAL 2.8 11.3 + - - +
387C GLU* 2.9 41.3 + - - +
389C ILE* 1.3 74.2 - - - +
391C ARG* 1.3 62.7 + - - +
393C LYS* 2.6 27.8 + - + +
394C GLN* 2.7 43.9 + - + +
1722C PHE* 3.0 41.0 - - + -
1723C PRO* 5.0 6.0 - - + +
1862C THR* 3.4 11.7 + - - +
1865C THR* 5.7 0.6 + - + -
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Residues in contact with ARG 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C TYR* 4.8 1.2 + - - -
349C ILE* 3.3 23.5 + - - +
350C ARG* 3.0 53.1 - - - +
352C VAL* 4.9 0.4 - - - +
353C ASP* 3.8 10.6 + - - +
364C ARG* 4.0 23.1 + - - +
368C LEU* 3.2 38.5 - - + +
387C GLU* 2.8 19.3 + - - +
388C LEU* 2.8 25.8 + - + +
390C GLN* 1.3 69.1 - - - +
392C CYS* 1.3 64.8 + - - +
394C GLN* 3.1 22.3 + - - +
395C MET* 2.9 24.9 + - - +
413C PHE* 4.6 0.9 - - - -
1858C LEU* 5.8 3.8 - - + +
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Residues in contact with CYS 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388C LEU* 2.9 28.5 + - - -
389C ILE* 2.9 32.3 - - + +
391C ARG* 1.3 72.8 - - - +
393C LYS* 1.3 55.9 + - - +
395C MET 2.7 23.4 + - - -
396C PHE* 2.8 8.8 + - - -
413C PHE* 2.9 58.4 - - + -
416C SER* 5.4 2.5 - - - -
417C VAL* 6.0 0.2 - - - -
434C VAL* 5.6 0.9 - - + -
438C LEU* 4.9 9.4 - - + -
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Residues in contact with LYS 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389C ILE 2.9 6.4 + - - +
390C GLN* 2.6 18.9 + - + +
392C CYS* 1.3 75.8 - - - +
394C GLN* 1.3 57.8 + - + +
396C PHE* 2.3 36.9 + - + -
397C LEU* 2.9 40.2 + - + +
434C VAL* 4.4 19.2 - - + +
437C HIS* 6.1 0.9 - - - +
438C LEU* 5.5 0.2 - - - -
1726C SER* 5.7 1.3 - - - -
1727C ARG* 5.7 4.0 - - - +
1813C SER* 5.0 7.9 - - - +
1865C THR* 3.1 35.6 + - - +
1869C LYS* 3.1 31.4 - - - +
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Residues in contact with GLN 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390C GLN* 2.7 43.3 + - + +
391C ARG* 3.3 26.9 - - - +
393C LYS* 1.3 73.1 - - + +
395C MET* 1.3 56.8 - - - +
397C LEU* 5.7 0.4 - - - -
398C THR* 2.2 38.4 + - - +
1858C LEU* 3.3 28.3 + - + +
1861C SER* 3.1 21.7 + - - +
1862C THR* 2.7 33.7 + - - +
1865C THR* 4.2 11.9 - - + +
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Residues in contact with MET 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361C ILE* 5.2 10.3 - - + -
364C ARG* 3.3 18.4 - - - +
391C ARG 2.9 13.4 + - - +
392C CYS 2.7 10.0 + - - +
393C LYS 2.9 2.5 - - - -
394C GLN* 1.3 83.0 - - - +
396C PHE* 1.3 62.8 + - - +
398C THR* 2.7 17.1 + - - +
399C GLN* 2.9 18.1 + - - +
405C ASP* 5.5 11.9 - - + -
406C ARG 6.2 0.4 - - - +
409C GLN* 3.2 39.5 - - + +
410C MET* 4.0 2.0 - - + -
413C PHE* 3.2 15.3 - - + -
1858C LEU* 4.4 17.7 - - - -
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Residues in contact with PHE 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392C CYS 2.8 6.2 + - - +
393C LYS* 2.3 31.5 + - + +
395C MET* 1.3 67.6 - - - +
397C LEU* 1.3 95.1 + - + +
399C GLN* 2.9 20.5 + - - +
410C MET* 3.8 14.1 - - + +
434C VAL* 6.2 1.1 - - + -
437C HIS* 3.4 27.1 - + - -
438C LEU* 3.6 30.5 - - + -
441C MET* 3.6 31.9 - - + -
1814C PHE* 3.2 37.2 - + + -
1817C GLN* 3.4 25.3 - - + +
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Residues in contact with LEU 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393C LYS* 2.9 42.9 + - - +
396C PHE* 1.3 102.6 - - + +
398C THR* 1.3 53.3 + - + +
400C THR* 2.2 36.8 + - + -
1813C SER* 4.5 10.1 - - - +
1817C GLN* 2.8 30.7 + - + +
1865C THR* 4.7 13.5 - - - +
1868C THR* 5.3 10.8 - - + -
1869C LYS* 3.2 32.3 - - + +
1873C TYR* 5.3 2.7 - - - +
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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