Contacts of the helix formed by residues 1566 - 1577 (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 THR1566 (chain C).
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Specific contacts
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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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Residues in contact with ILE1567 (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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1563C PHE 2.8 7.3 + - - +
1564C SER* 3.1 45.8 - - - +
1565C GLU 2.8 9.1 + - - +
1566C THR* 1.3 76.4 - - - +
1568C ASN* 1.3 75.2 + - - +
1569C THR 3.5 0.2 - - - -
1570C GLU* 3.1 17.4 + - - +
1571C LEU* 2.9 54.9 + - + +
1592C MET* 5.7 2.0 - - + -
1595C ALA 4.9 4.5 - - - +
1596C VAL* 4.8 15.7 - - + +
1599C GLY* 5.4 2.0 - - - -
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Residues in contact with ASN1568 (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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1565C GLU 4.1 13.1 + - - -
1566C THR 2.8 8.0 + - - +
1567C ILE* 1.3 83.1 - - - +
1569C THR* 1.3 66.7 + - + +
1571C LEU* 3.1 2.6 + - - +
1572C LEU* 2.9 25.9 + - + +
1603C GLN* 3.2 29.4 + - - +
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Residues in contact with THR1569 (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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1500C LEU* 5.6 1.1 - - + -
1501C PRO* 4.6 24.7 - - + +
1504C ASP* 3.6 30.6 + - + +
1505C LEU* 5.2 9.2 - - + +
1508C LYS* 4.9 2.4 - - - +
1566C THR 3.4 11.4 + - - +
1568C ASN* 1.3 74.9 - - + +
1570C GLU* 1.3 71.2 + - - +
1572C LEU* 2.9 29.7 + - + +
1573C LYS* 2.9 13.7 + - - +
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Residues in contact with GLU1570 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1483C LEU* 4.6 8.0 - - + +
1504C ASP* 5.3 2.9 - - - +
1508C LYS* 3.4 16.6 - - - +
1516C GLU* 2.7 32.0 - - + +
1520C ALA* 5.9 3.4 - - - +
1563C PHE* 2.7 36.2 - - - +
1564C SER* 4.6 0.2 - - - -
1566C THR* 2.1 37.5 + - - +
1567C ILE* 3.1 18.6 + - - +
1569C THR* 1.3 80.2 + - - +
1571C LEU* 1.3 65.9 + - + +
1573C LYS* 3.1 2.3 + - - +
1574C ASN* 2.8 14.8 + - - +
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Residues in contact with LEU1571 (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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1567C ILE* 2.9 47.8 + - + +
1568C ASN* 3.3 6.3 - - - +
1570C GLU* 1.3 75.1 - - + +
1572C LEU* 1.3 57.8 + - - +
1574C ASN* 2.8 14.4 + - - +
1575C LEU* 2.8 31.6 + - - +
1596C VAL* 3.0 33.7 - - + +
1599C GLY* 3.5 19.5 - - - -
1600C MET* 3.4 23.6 - - + +
1603C GLN* 3.0 26.2 - - - +
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Residues in contact with LEU1572 (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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1505C LEU* 6.6 0.2 - - + -
1568C ASN* 2.9 18.8 + - + +
1569C THR* 2.9 23.0 + - + +
1571C LEU* 1.3 74.8 - - - +
1573C LYS* 1.3 58.5 + - - +
1575C LEU* 2.8 28.6 + - + +
1576C ASP* 2.9 14.2 + - - +
1603C GLN* 3.2 21.5 - - + +
1606C ARG* 5.6 0.2 - - - +
1607C GLU* 3.1 28.3 - - - +
1632C TRP* 5.4 0.2 - - - -
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Residues in contact with LYS1573 (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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1508C LYS* 3.5 50.7 - - + +
1511C ALA 3.4 21.0 + - - -
1512C SER 3.6 0.8 - - - -
1513C GLY* 2.8 31.6 - - - +
1516C GLU* 3.4 16.8 - - - +
1569C THR 2.9 8.8 + - - +
1570C GLU 3.2 9.6 - - - +
1572C LEU* 1.3 74.1 - - - +
1574C ASN* 1.3 64.2 + - - +
1575C LEU 2.9 1.6 + - - -
1576C ASP* 3.1 18.8 + - + +
1577C LEU* 3.4 39.9 + - + +
1578C ALA* 4.5 3.2 + - - +
1581C GLU* 5.2 1.0 + - - -
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Residues in contact with ASN1574 (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* 3.4 7.1 + - - -
1516C GLU* 2.4 44.7 + - - +
1517C LEU* 3.4 17.6 - - - +
1570C GLU* 2.8 10.0 - - - +
1571C LEU* 2.8 16.6 + - - +
1573C LYS* 1.3 73.0 - - - +
1575C LEU* 1.3 60.9 + - - +
1578C ALA* 3.3 29.2 + - + +
1596C VAL* 5.1 1.0 - - - +
1600C MET* 3.5 34.6 - - + +
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Residues in contact with LEU1575 (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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1571C LEU 2.8 16.2 + - - +
1572C LEU* 2.8 25.9 + - + +
1574C ASN* 1.3 80.6 - - - +
1576C ASP* 1.3 66.6 + - - +
1578C ALA 4.7 0.9 + - - -
1600C MET* 3.5 36.6 - - + +
1603C GLN* 3.6 5.6 - - + -
1604C SER* 3.5 25.4 - - - +
1607C GLU* 3.4 35.2 - - - +
1632C TRP* 2.9 36.5 - - + -
1635C LYS* 4.8 2.4 - - - +
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Residues in contact with ASP1576 (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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1509C GLN* 5.5 2.8 - - - +
1572C LEU 2.9 10.8 + - - +
1573C LYS* 3.1 12.7 + - + +
1575C LEU* 1.3 82.0 - - - +
1577C LEU* 1.3 77.2 + - + +
1578C ALA 3.9 0.2 + - - -
1632C TRP* 3.5 30.5 + - + -
1635C LYS* 4.3 5.4 + - - -
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Residues in contact with LEU1577 (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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1508C LYS 5.0 3.4 - - - +
1509C GLN 6.0 2.5 - - - +
1510C LEU 5.5 4.0 - - - +
1511C ALA 4.9 5.4 - - - +
1512C SER* 5.7 1.8 - - - -
1513C GLY 5.2 0.9 - - - +
1573C LYS* 3.4 40.5 + - + +
1576C ASP* 1.3 91.8 - - + +
1578C ALA* 1.3 70.8 + - - +
1579C VAL* 3.6 6.9 + - - +
1581C GLU* 4.0 13.7 - - - +
1635C LYS* 5.1 4.1 - - - +
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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