Contacts of the helix formed by residues 1572 - 1591 (chain C) in PDB entry 3SE2
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 ASN1572 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1534C GLN* 3.3 20.7 + - - +
1535C ASN 3.7 9.9 - - - +
1536C PHE* 3.7 9.1 - - + +
1570C ILE* 4.8 2.7 - - + -
1571C GLN* 1.3 75.8 - - - +
1573C PRO* 1.3 53.9 - - - +
1574C ASP 3.3 4.2 + - - -
1575C LEU* 2.9 25.5 + - + +
1576C TRP* 2.8 31.5 + - - +
1612C ASN 3.1 17.4 + - - +
1613C ARG* 3.1 26.5 + - - +
1711C TYR* 3.0 16.5 + - + +
1721C GOL 3.2 3.4 + - - -
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Residues in contact with PRO1573 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1535C ASN 3.7 13.9 - - - +
1536C PHE* 5.0 0.4 - - - -
1571C GLN* 3.8 7.4 - - + +
1572C ASN* 1.3 85.6 - - - +
1574C ASP* 1.3 64.5 + - - +
1576C TRP* 3.7 7.5 - - + +
1577C ASN* 2.8 41.5 + - - +
1721C GOL 4.5 2.9 - - - +
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Residues in contact with ASP1574 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1532C LYS 3.7 15.1 + - - +
1533C GLN 2.5 34.1 + - - +
1534C GLN* 3.3 23.6 - - + +
1535C ASN 5.2 1.1 + - - -
1572C ASN* 3.3 2.4 + - - -
1573C PRO* 1.3 79.8 - - - +
1575C LEU* 1.3 61.1 + - - +
1577C ASN* 3.3 12.8 + - - +
1578C SER* 2.9 33.9 + - - -
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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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1534C GLN* 3.3 24.8 - - + +
1570C ILE* 6.3 0.2 - - + -
1572C ASN* 2.9 24.7 + - + +
1574C ASP* 1.3 77.5 - - - +
1576C TRP* 1.3 57.6 + - - +
1578C SER* 3.6 1.6 + - - -
1579C TYR* 3.0 27.1 + - + +
1611C VAL 4.1 4.9 - - - +
1612C ASN 4.2 7.0 - - - +
1613C ARG 4.1 6.1 - - - +
1614C ASN 3.8 14.8 - - - +
1615C GLY* 3.5 28.0 - - - +
1707C ASP 5.3 1.8 - - - +
1708C TYR* 3.9 20.8 - - + -
1710C ALA 5.4 3.8 - - - +
1711C TYR* 3.9 11.6 - - + -
1712C PRO* 3.9 19.1 - - + -
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Residues in contact with TRP1576 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1572C ASN 2.8 18.0 + - - +
1573C PRO* 3.7 6.7 - - + +
1575C LEU* 1.3 75.4 - - - +
1577C ASN* 1.3 70.4 + - - +
1579C TYR* 3.4 12.5 + + - +
1580C GLN* 2.9 72.3 + - + +
1661C ARG* 4.1 25.1 - - - -
1711C TYR* 3.6 43.7 - + + -
1713C GLU* 5.6 0.4 - - - -
1721C GOL 4.0 37.6 - - - +
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Residues in contact with ASN1577 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1573C PRO* 2.8 32.9 + - - +
1574C ASP* 3.3 13.6 + - - +
1576C TRP* 1.3 88.1 - - - +
1578C SER* 1.3 57.2 + - - +
1580C GLN* 3.3 6.7 + - - +
1581C ALA* 3.0 28.4 + - - +
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Residues in contact with SER1578 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1544B SER* 5.9 1.8 - - - -
1534C GLN* 4.1 7.6 + - - -
1574C ASP 2.9 18.4 + - - -
1575C LEU 3.9 1.8 - - - -
1577C ASN* 1.3 74.9 - - - +
1579C TYR* 1.3 64.5 + - - +
1581C ALA* 3.4 6.4 + - - +
1582C LYS* 3.3 23.7 + - - +
1708C TYR* 3.5 38.4 - - - +
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Residues in contact with TYR1579 (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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1575C LEU* 3.0 19.8 + - + +
1576C TRP* 3.6 15.3 - + - +
1578C SER* 1.3 75.4 - - - +
1580C GLN* 1.3 81.3 + - - +
1582C LYS* 3.3 5.2 + - - +
1583C LYS* 3.0 27.0 + - + +
1596C GLU* 2.6 42.9 + - - +
1661C ARG* 3.4 27.6 - - + +
1662C VAL 3.7 0.2 + - - -
1663C LEU* 3.5 20.0 - - + +
1708C TYR* 3.4 25.5 - - - +
1709C GLN 3.5 20.0 - - - -
1710C ALA 3.8 7.2 - - - +
1711C TYR* 3.8 17.3 - - + -
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Residues in contact with GLN1580 (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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1576C TRP* 2.9 73.5 + - + +
1577C ASN* 3.8 7.6 - - - +
1578C SER 3.3 0.4 - - - -
1579C TYR* 1.3 90.9 - - - +
1581C ALA* 1.3 56.1 + - - +
1583C LYS* 3.7 19.2 - - - +
1584C LYS* 3.0 27.9 + - - +
1596C GLU* 4.9 1.2 + - - -
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Residues in contact with ALA1581 (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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1577C ASN 3.0 16.6 + - - +
1578C SER* 3.9 6.7 - - - +
1579C TYR 3.3 0.4 - - - -
1580C GLN* 1.3 75.9 - - - +
1582C LYS* 1.3 60.0 + - + +
1584C LYS* 3.4 8.3 + - - +
1585C THR* 2.9 31.5 + - - -
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Residues in contact with LYS1582 (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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1544B SER* 3.0 43.1 + - - +
1546B PRO* 4.5 9.3 - - - +
1549B ASN* 4.8 11.0 - - - +
1578C SER 3.3 9.4 + - - +
1579C TYR 3.3 7.8 + - - +
1581C ALA* 1.3 77.8 - - + +
1583C LYS* 1.3 59.7 + - - +
1585C THR* 3.3 12.5 + - - +
1586C MET* 3.0 33.7 + - + +
1663C LEU* 3.7 12.6 - - + +
1706C TYR* 5.7 7.0 - - + -
1708C TYR* 4.1 29.6 - - + +
1709C GLN* 5.2 3.1 - - + +
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Residues in contact with LYS1583 (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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1579C TYR* 3.0 15.9 + - + +
1580C GLN* 3.7 28.3 - - - +
1582C LYS* 1.3 72.4 - - - +
1584C LYS* 1.3 61.0 + - - +
1586C MET* 3.8 1.5 - - - +
1587C ASP* 2.8 68.0 + - - +
1595C ASN* 5.6 0.9 - - - +
1596C GLU* 3.9 42.0 - - - +
1663C LEU* 3.4 25.2 - - + +
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Residues in contact with LYS1584 (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 GLN 3.0 17.4 + - - +
1581C ALA* 3.6 9.2 - - - +
1582C LYS 3.3 0.2 - - - -
1583C LYS* 1.3 78.5 - - - +
1585C THR* 1.3 62.1 + - - +
1587C ASP* 3.6 8.0 - - + +
1588C ALA* 3.2 23.5 + - + +
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Residues in contact with THR1585 (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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1581C ALA 2.9 18.1 + - - -
1582C LYS* 3.7 13.9 + - - +
1583C LYS 3.2 0.4 - - - -
1584C LYS* 1.3 78.7 - - - +
1586C MET* 1.3 61.8 + - - +
1588C ALA* 3.7 6.2 + - - +
1589C LYS* 3.2 23.3 + - + +
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Residues in contact with MET1586 (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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1582C LYS* 3.0 19.9 + - + +
1583C LYS* 3.9 5.8 - - - +
1585C THR* 1.3 75.6 - - - +
1587C ASP* 1.3 64.6 + - - +
1589C LYS* 3.0 11.7 + - - +
1590C ASN* 3.0 30.3 + - - +
1595C ASN* 3.5 21.8 + - + +
1663C LEU* 3.9 33.0 - - + +
1665C GLY* 3.8 27.1 - - - -
1690C ASP* 3.7 25.8 - - + +
1706C TYR* 6.4 1.3 - - + -
1709C GLN* 4.5 8.1 - - + +
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Residues in contact with ASP1587 (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 LYS* 2.8 57.7 + - - +
1584C LYS* 3.6 8.3 - - + +
1586C MET* 1.3 75.7 - - - +
1588C ALA* 1.3 61.7 + - - +
1589C LYS 3.2 0.7 + - - -
1590C ASN 3.5 0.5 + - - -
1591C GLY* 3.4 27.1 + - - +
1593C THR 4.8 1.5 - - - +
1595C ASN* 2.9 29.1 + - - +
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Residues in contact with ALA1588 (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 LYS* 3.2 14.4 + - + +
1585C THR* 3.9 6.3 - - - +
1586C MET 3.4 0.2 - - - -
1587C ASP* 1.3 78.6 - - - +
1589C LYS* 1.3 61.4 + - - +
1591C GLY* 4.1 5.9 + - - -
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Residues in contact with LYS1589 (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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1585C THR* 3.2 17.3 + - + +
1586C MET* 3.0 16.0 + - - +
1588C ALA* 1.3 78.7 - - - +
1590C ASN* 1.3 83.5 + - - +
1591C GLY 3.3 3.6 + - - -
1680C LYS* 5.4 2.5 - - - +
1687C ASP* 4.9 14.3 + - - +
1688C LEU 4.4 12.1 + - - +
1690C ASP* 2.7 27.5 + - - -
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Residues in contact with ASN1590 (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 MET* 3.0 18.7 + - - +
1587C ASP 4.1 0.7 - - - -
1589C LYS* 1.3 100.7 - - - +
1591C GLY* 1.3 58.6 + - - +
1592C GLN 2.9 10.7 + - - -
1593C THR* 3.2 24.7 + - - +
1595C ASN* 2.8 28.9 + - - +
1666C ILE* 3.4 25.8 - - + +
1680C LYS* 4.7 1.9 + - - -
1690C ASP* 3.0 23.4 + - - -
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Residues in contact with GLY1591 (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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1587C ASP* 3.4 17.0 + - - +
1588C ALA 4.1 5.0 + - - -
1589C LYS 3.3 5.5 + - - -
1590C ASN* 1.3 72.8 - - - +
1592C GLN* 1.3 72.1 + - - +
1593C THR 3.6 2.9 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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