Contacts of the helix formed by residues 1549 - 1560 (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 SER1549 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1548C GLY* 1.3 72.0 - - - +
1550C VAL* 1.3 59.4 + - - +
1553C PHE* 2.4 63.6 + - - +
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Residues in contact with VAL1550 (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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1488C TYR 4.9 10.6 - - - +
1489C LYS* 5.9 3.4 - - - +
1548C GLY 3.3 3.1 - - - +
1549C SER* 1.3 78.6 - - - +
1551C ILE* 1.3 68.7 + - + +
1553C PHE* 3.6 1.3 - - - +
1554C SER* 2.5 40.6 + - - +
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Residues in contact with ILE1551 (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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1548C GLY* 3.3 29.6 - - - +
1550C VAL* 1.3 89.1 - - + +
1552C HIS* 1.3 62.4 + - + +
1554C SER* 3.2 9.6 + - - +
1555C HIS* 2.9 25.8 + - - +
1558C TYR* 4.8 1.2 - - - -
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Residues in contact with HIS1552 (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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425C ASP* 5.0 5.2 + - - -
469C ALA* 2.9 32.1 + - + -
470C ALA* 3.5 24.0 + - + +
472C GLY* 4.7 8.2 - - - -
473C PRO* 5.1 6.4 - - + +
1548C GLY* 2.3 36.2 + - - +
1551C ILE* 1.3 67.3 - - + +
1553C PHE* 1.3 62.2 + - + +
1554C SER 3.0 4.7 - - - -
1555C HIS* 2.9 38.1 + + + +
1556C GLY 3.9 4.3 + - - -
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Residues in contact with PHE1553 (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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473C PRO* 5.6 12.1 - - + +
1489C LYS 4.9 2.7 - - - +
1490C GLY* 3.6 20.7 - - - -
1491C ILE* 3.5 50.8 + - + +
1548C GLY 4.5 0.2 - - - -
1549C SER* 2.4 58.2 + - - +
1550C VAL 3.6 1.6 - - - +
1552C HIS* 1.3 83.5 - - + +
1554C SER* 1.3 57.2 + - - +
1557C GLU* 3.8 13.7 - - - +
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Residues in contact with SER1554 (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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1487C VAL* 4.0 17.6 + - - +
1488C TYR 4.5 5.0 + - - -
1490C GLY 5.4 0.5 + - - -
1550C VAL* 2.5 29.4 + - - +
1551C ILE* 3.2 12.6 - - - -
1552C HIS 3.0 0.2 - - - -
1553C PHE* 1.3 79.5 - - - +
1555C HIS* 1.3 61.5 + - - +
1556C GLY 3.5 1.5 + - - -
1557C GLU* 3.8 2.6 + - - +
1558C TYR* 3.0 57.4 + - - -
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Residues in contact with HIS1555 (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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425C ASP* 4.5 24.4 + - + +
470C ALA 5.9 0.4 - - - -
1551C ILE 2.9 14.6 + - - +
1552C HIS* 2.9 29.9 + + + +
1554C SER* 1.3 77.0 - - - +
1556C GLY* 1.3 58.4 + - - +
1558C TYR* 3.0 29.0 - - - +
1559C PHE* 3.0 51.9 - + - -
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Residues in contact with GLY1556 (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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471C LYS 5.1 1.8 - - - -
472C GLY* 4.3 23.3 - - - -
473C PRO* 5.4 1.0 - - - +
1552C HIS* 3.9 5.9 + - - -
1555C HIS* 1.3 75.7 - - - +
1557C GLU* 1.3 57.0 + - - +
1558C TYR 3.0 2.0 - - - -
1559C PHE* 2.5 37.2 + - - +
1560C TYR* 2.9 11.4 + - - +
1561C SER* 3.8 6.5 + - - -
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Residues in contact with GLU1557 (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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473C PRO* 4.0 20.4 - - + +
1486C LEU* 5.6 1.2 - - - +
1487C VAL* 5.0 2.7 - - + +
1490C GLY* 3.5 28.8 - - - +
1491C ILE* 4.2 13.0 + - - +
1497C ARG* 4.7 0.2 + - - -
1524C LEU* 3.6 14.2 - - - +
1553C PHE* 3.8 10.0 + - - +
1554C SER 3.8 6.4 + - - +
1555C HIS 3.6 0.2 - - - -
1556C GLY* 1.3 70.7 - - - +
1558C TYR* 1.3 67.0 + - - +
1559C PHE 3.2 0.2 + - - -
1561C SER* 3.5 28.0 + - - -
1562C LEU* 3.5 40.5 + - + +
1565C GLU* 2.8 27.3 - - - +
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Residues in contact with TYR1558 (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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1487C VAL* 3.8 23.7 + - + -
1524C LEU* 2.6 26.3 - - - +
1525C CYS* 4.3 0.7 - - - -
1526C GLU* 3.2 43.6 - - + +
1551C ILE 4.8 1.1 - - - -
1554C SER* 3.0 48.1 + - - -
1555C HIS* 3.0 22.7 - - - +
1556C GLY 3.0 0.2 - - - -
1557C GLU* 1.3 76.9 - - - +
1559C PHE* 1.3 75.0 + + + +
1562C LEU* 4.5 2.0 - - - +
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Residues in contact with PHE1559 (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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425C ASP* 5.3 10.1 - - + -
427C VAL* 5.7 8.1 - - + -
1524C LEU* 3.4 9.1 - - - +
1525C CYS* 6.1 0.2 - - - -
1526C GLU 4.3 6.5 - - - -
1555C HIS* 3.0 67.3 - + - -
1556C GLY* 2.5 20.0 + - - +
1558C TYR* 1.3 89.8 - + + +
1560C TYR* 1.3 83.2 + - + +
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Residues in contact with TYR1560 (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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427C VAL* 4.1 34.7 - - + +
429C GLU* 5.5 7.1 - - + +
474C VAL* 5.1 8.5 - - + -
1524C LEU* 2.9 23.5 - - - +
1556C GLY 2.9 6.8 + - - +
1559C PHE* 1.3 99.7 - - + +
1561C SER* 1.3 71.1 + - - +
1564C SER* 3.6 10.2 + - - -
1591C LYS* 2.8 40.0 + - - -
1592C MET* 3.6 40.5 - - + +
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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