Contacts of the helix formed by residues 1560 - 1566 (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 TYR1560 (chain C).
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Specific contacts
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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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Residues in contact with SER1561 (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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472C GLY 3.9 4.7 + - - -
473C PRO* 3.2 20.3 + - - +
474C VAL* 3.1 27.6 - - - +
1556C GLY 3.8 1.2 + - - -
1557C GLU* 3.5 26.3 + - - +
1560C TYR* 1.3 76.5 - - - +
1562C LEU* 1.3 57.6 + - - +
1563C PHE 2.7 0.6 + - - -
1564C SER* 2.3 41.4 + - - -
1565C GLU* 2.8 12.5 + - - +
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Residues in contact with LEU1562 (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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1483C LEU* 4.2 9.6 - - + +
1484C LEU 5.2 0.4 - - - +
1486C LEU* 5.8 9.2 - - + -
1487C VAL* 3.6 40.2 - - + +
1523C GLY 5.8 0.9 - - - +
1524C LEU* 4.3 3.4 - - + +
1526C GLU* 6.3 1.6 - - + -
1557C GLU* 3.5 43.7 + - + +
1558C TYR* 5.0 1.3 - - - -
1560C TYR 3.6 0.8 + - - -
1561C SER* 1.3 73.9 - - - +
1563C PHE* 1.3 112.8 + - + +
1565C GLU* 2.9 16.9 - - - +
1566C THR* 2.9 31.7 + - + +
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Residues in contact with PHE1563 (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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1483C LEU* 3.3 53.2 - - + -
1484C LEU* 4.0 19.1 - - + -
1519C PHE* 4.9 7.2 - + - -
1520C ALA* 4.1 17.0 - - + +
1523C GLY* 3.6 11.9 - - - -
1524C LEU* 3.3 52.5 - - + +
1561C SER 2.7 4.6 + - - -
1562C LEU* 1.3 93.7 - - + +
1564C SER* 1.3 56.6 + - - +
1565C GLU 2.9 4.9 - - - -
1566C THR* 2.8 11.2 + - - -
1567C ILE 2.8 8.7 + - - -
1570C GLU* 2.7 33.9 - - - +
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Residues in contact with SER1564 (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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1524C LEU* 3.9 3.6 - - - +
1560C TYR* 3.6 9.7 + - - -
1561C SER* 2.3 26.6 + - - -
1563C PHE* 1.3 69.7 - - - +
1565C GLU* 1.3 54.4 - - - -
1567C ILE* 3.1 40.9 - - - +
1592C MET* 3.4 30.5 - - - +
1596C VAL* 5.2 4.2 - - - +
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Residues in contact with GLU1565 (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* 5.0 2.0 - - - +
476C ARG* 4.3 20.4 + - - +
1486C LEU* 6.5 0.2 - - - -
1491C ILE* 4.9 1.6 - - - +
1497C ARG* 2.6 43.8 + - - +
1557C GLU* 2.8 27.4 - - - +
1561C SER* 2.8 10.7 + - - +
1562C LEU* 2.9 24.7 + - - +
1563C PHE 2.9 0.8 - - - -
1564C SER* 1.3 78.3 - - - +
1566C THR* 1.3 51.8 + - - +
1567C ILE* 2.8 17.4 + - - +
1568C ASN* 4.1 8.8 + - - -
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Residues in contact with THR1566 (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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1483C LEU* 3.6 27.3 - - + +
1486C LEU* 5.7 5.6 - - + -
1497C ARG* 4.8 8.3 - - - +
1500C LEU* 3.9 23.6 - - + -
1504C ASP* 4.7 6.5 - - - -
1562C LEU* 2.9 11.6 + - + +
1563C PHE* 2.8 12.0 + - - -
1565C GLU* 1.3 71.6 - - + +
1567C ILE* 1.3 52.1 + - - +
1568C ASN* 2.8 17.1 + - - +
1569C THR* 3.4 17.8 + - - +
1570C GLU* 2.1 30.9 + - - +
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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