Contacts of the helix formed by residues 1580 - 1590 (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 LEU1580 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1579C VAL* 1.3 79.4 - - + +
1581C GLU* 1.3 55.7 + - - +
1582C LEU* 2.9 5.9 - - - +
1583C MET* 2.7 70.2 + - + -
1584C GLN* 3.0 21.0 + - - +
1635C LYS 5.2 0.2 + - - -
1639C LEU* 3.5 42.0 - - + +
1642C LYS* 3.8 17.9 - - + -
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Residues in contact with GLU1581 (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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1513C GLY 5.3 4.2 + - - -
1514C LEU* 3.0 48.2 + - + +
1517C LEU* 3.9 4.3 - - + +
1573C LYS* 5.2 1.9 + - - -
1577C LEU* 4.0 16.4 - - - +
1578C ALA* 3.1 25.1 - - + +
1579C VAL* 2.5 40.9 + - - +
1580C LEU* 1.3 72.0 - - - +
1582C LEU* 1.3 63.0 + - - +
1584C GLN* 3.0 20.7 + - - +
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Residues in contact with LEU1582 (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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1517C LEU* 4.3 12.7 - - - +
1578C ALA* 5.3 4.9 - - + +
1579C VAL 4.7 0.2 - - - -
1580C LEU 4.1 2.2 - - - +
1581C GLU* 1.3 77.5 - - - +
1583C MET* 1.3 63.0 - - - +
1584C GLN 2.7 12.5 + - - -
1585C SER 3.4 1.0 + - - -
1586C SER* 2.2 43.5 + - - +
1597C LEU* 3.7 35.7 - - + -
1600C MET* 4.3 15.7 - - + -
1636C ASP* 5.9 0.4 - - - -
1639C LEU* 3.4 39.9 - - + -
1643C MET* 3.4 26.5 - - + -
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Residues in contact with MET1583 (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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1580C LEU* 2.7 58.6 + - + +
1582C LEU* 1.3 78.6 - - + +
1584C GLN* 1.3 75.8 + - - +
1586C SER* 3.5 9.6 - - - -
1587C VAL* 2.8 37.7 + - + +
1639C LEU 4.5 0.2 - - - +
1642C LYS* 4.4 6.7 - - + -
1643C MET* 3.6 31.2 - - + -
1646C LEU* 3.4 28.5 - - + -
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Residues in contact with GLN1584 (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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1514C LEU* 4.1 16.4 - - + -
1580C LEU* 3.0 27.1 + - - +
1581C GLU* 3.0 24.5 - - - +
1582C LEU 2.7 5.3 + - - -
1583C MET* 1.3 96.8 - - - +
1585C SER* 1.3 64.2 + - - +
1587C VAL* 3.9 0.9 - - - +
1588C ASP* 3.0 28.9 + - - +
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Residues in contact with SER1585 (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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1514C LEU* 4.3 3.6 + - - +
1517C LEU* 3.3 38.0 - - - +
1518C ALA* 3.5 15.2 + - - +
1581C GLU 4.1 0.6 + - - -
1582C LEU 3.4 1.6 + - - -
1584C GLN* 1.3 80.0 - - - +
1586C SER* 1.3 68.5 + - - +
1588C ASP* 3.9 10.3 + - - -
1589C ASN* 2.9 39.5 + - - +
1593C VAL* 3.8 4.2 - - - +
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Residues in contact with SER1586 (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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1517C LEU* 5.5 1.3 - - - +
1582C LEU* 2.2 43.1 + - - +
1583C MET* 3.4 5.8 - - - -
1585C SER* 1.3 79.8 - - - +
1587C VAL* 1.3 65.4 + - - +
1590C THR* 2.9 22.2 + - - -
1593C VAL* 3.8 22.0 - - - +
1643C MET* 3.4 24.0 - - - -
1647C ALA* 4.5 3.3 - - - +
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Residues in contact with VAL1587 (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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1583C MET* 2.8 42.0 + - + +
1584C GLN 4.0 1.1 - - - +
1586C SER* 1.3 75.3 - - - +
1588C ASP* 1.3 68.6 + - - +
1590C THR* 3.7 12.0 - - - +
1643C MET* 4.0 1.1 - - + -
1646C LEU* 3.7 14.8 - - + +
1647C ALA* 3.5 40.6 - - + +
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Residues in contact with ASP1588 (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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1584C GLN* 3.0 22.1 + - - +
1585C SER* 3.5 12.2 + - - +
1586C SER 3.1 0.2 - - - -
1587C VAL* 1.3 84.2 - - - +
1589C ASN* 1.3 69.5 - - - +
1590C THR* 4.0 5.5 - - - +
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Residues in contact with ASN1589 (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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1517C LEU 4.4 1.8 + - - -
1518C ALA* 5.1 1.8 + - - +
1521C PHE* 3.1 67.3 - - + +
1585C SER* 2.9 33.6 + - - +
1588C ASP* 1.3 83.0 - - - +
1590C THR* 1.3 68.7 + - - +
1591C LYS* 2.9 15.8 + - - +
1593C VAL* 4.0 14.0 - - + +
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Residues in contact with THR1590 (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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1586C SER 2.9 15.5 + - - -
1587C VAL 3.7 13.5 - - - +
1588C ASP 4.0 6.7 - - - +
1589C ASN* 1.3 87.3 - - - +
1591C LYS* 1.3 58.1 + - + +
1593C VAL* 3.9 3.9 - - - +
1647C ALA* 5.0 0.6 - - - -
1650C ALA* 5.7 2.8 - - - +
1651C LYS* 2.5 38.5 + - - +
1679C LEU* 5.5 3.1 - - - +
1683C LYS* 3.4 16.4 - - - -
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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