Contacts of the strand formed by residues 1654 - 1663 (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 ARG1654 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1610A HIS* 4.0 30.8 + - - +
1619A SER* 5.3 6.1 + - - -
1565C GLU* 3.1 26.9 + - - +
1566C LYS* 6.4 0.2 - - - +
1649C PRO* 3.5 1.2 - - - +
1650C ASP* 2.9 44.0 + - - +
1652C ASN* 3.9 29.8 - - - +
1653C GLY* 1.3 77.6 - - - +
1655C LYS* 1.3 61.3 + - - +
1656C HIS* 3.3 21.0 + - + +
1717C THR* 4.0 15.9 - - + -
1718C PHE 3.5 7.2 - - - +
1719C ARG* 4.0 14.8 - - - +
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Residues in contact with LYS1655 (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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1562C PHE* 3.8 9.2 - - + -
1642C ALA 2.9 20.3 + - - -
1644C ASP* 2.8 21.8 + - - +
1647C SER* 2.4 49.7 + - - +
1648C ARG 4.5 0.4 - - - -
1649C PRO* 4.1 10.5 - - + -
1653C GLY 4.2 5.2 - - - +
1654C ARG* 1.3 75.9 - - - +
1656C HIS* 1.3 67.8 + - - +
1717C THR* 3.4 6.4 - - - +
1718C PHE* 2.8 69.6 + - + +
1720C LYS* 3.7 27.4 - - + +
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Residues in contact with HIS1656 (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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1606A GLY 5.7 2.2 - - - -
1601C HIS 4.2 0.2 - - - +
1603C THR* 3.2 37.0 + - + +
1605C ALA* 3.7 33.6 - - + +
1608C VAL* 4.4 16.3 - - + +
1647C SER* 3.5 4.7 - - - +
1648C ARG 4.6 3.1 - - - -
1650C ASP* 3.6 13.4 + - - -
1654C ARG* 3.3 25.3 + - + -
1655C LYS* 1.3 78.9 + - - +
1657C VAL* 1.3 66.2 + - - +
1658C TYR 4.3 0.4 - - - -
1715C LEU* 4.2 15.5 - - + +
1716C ILE 3.6 3.6 - - - -
1717C THR* 3.8 32.4 + - + -
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Residues in contact with VAL1657 (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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1555C PHE* 4.7 7.2 - - + -
1600C PHE* 3.8 28.5 - - + -
1601C HIS 3.3 6.5 - - - +
1602C GLY* 3.8 8.5 - - - -
1638C ALA 5.3 0.9 - - - +
1641C SER* 3.9 15.5 - - - +
1642C ALA* 4.3 0.9 - - - +
1647C SER* 3.7 14.6 - - - -
1656C HIS* 1.3 79.8 - - - +
1658C TYR* 1.3 68.2 + - - +
1715C LEU* 4.1 3.0 - - - +
1716C ILE* 2.8 47.4 + - + +
1718C PHE* 3.5 27.1 - - + -
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Residues in contact with TYR1658 (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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1570C ILE* 4.4 4.7 - - + -
1599C LEU 3.8 0.2 - - - +
1600C PHE* 3.3 4.5 - - - -
1601C HIS* 2.8 42.0 + + - +
1603C THR* 4.0 24.9 - - + -
1608C VAL* 3.3 25.7 + - + +
1611C VAL* 3.4 23.4 - - + +
1612C ASN* 2.6 28.6 + - - -
1616C PHE* 4.1 13.5 - + + -
1657C VAL* 1.3 77.8 - - - +
1659C TYR* 1.3 59.5 + - - +
1660C VAL* 3.4 18.3 - - + +
1712C PRO* 3.5 19.1 - - + -
1714C TYR 3.1 20.6 - - - +
1715C LEU* 3.7 28.3 - - + -
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Residues in contact with TYR1659 (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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1550C THR* 5.2 9.4 - - + +
1551C VAL* 3.9 39.5 - - + -
1554C LYS* 3.5 31.8 - - + +
1598C GLN* 3.5 55.5 + - + +
1599C LEU 3.5 10.5 - - - -
1600C PHE* 3.5 37.9 - + + -
1657C VAL 4.0 0.8 + - - -
1658C TYR* 1.3 71.0 - - - +
1660C VAL* 1.3 59.9 + - - +
1713C GLU* 3.6 6.6 + - - +
1714C TYR* 2.9 48.5 + + + +
1716C ILE* 4.6 1.8 - - + -
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Residues in contact with VAL1660 (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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1597C LYS 3.5 0.7 - - - +
1598C GLN* 3.2 7.2 - - - -
1599C LEU 2.6 41.5 + - - +
1601C HIS* 4.4 2.2 - - + -
1616C PHE* 3.7 16.8 - - + -
1634C PHE* 3.8 11.4 - - + -
1658C TYR* 3.4 35.7 - - + +
1659C TYR* 1.3 74.4 - - - +
1661C ARG* 1.3 77.6 + - - +
1662C VAL* 3.5 15.2 + - + +
1710C ALA* 3.8 8.3 - - + -
1711C TYR 3.2 22.4 - - - +
1712C PRO* 4.1 3.8 - - + -
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Residues in contact with ARG1661 (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* 4.1 25.8 - - - -
1579C TYR* 3.4 20.1 - - + +
1596C GLU* 2.7 40.6 + - - +
1597C LYS 3.8 3.8 - - - -
1598C GLN* 3.9 31.0 + - + +
1659C TYR 4.4 0.2 + - - -
1660C VAL* 1.3 73.9 - - - +
1662C VAL* 1.3 57.0 + - - +
1710C ALA* 3.0 4.9 - - - -
1711C TYR* 2.7 44.1 + - + +
1713C GLU* 2.9 38.0 + - + +
1714C TYR* 5.7 0.6 + - - -
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Residues in contact with VAL1662 (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* 3.7 4.9 + - - -
1596C GLU* 3.3 3.3 - - - +
1597C LYS 2.8 40.4 + - - +
1599C LEU* 3.9 16.6 - - + -
1634C PHE* 3.9 37.2 - - + -
1660C VAL* 3.6 25.4 - - + +
1661C ARG* 1.3 80.2 - - - +
1663C LEU* 1.3 62.7 + - - +
1664C THR* 3.0 20.6 + - + +
1691C THR* 5.2 1.8 - - + -
1702C PHE* 5.6 1.3 - - + -
1704C ALA* 4.5 9.9 - - + -
1709C GLN* 3.6 7.9 - - + +
1710C ALA* 4.1 2.5 - - + -
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Residues in contact with LEU1663 (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* 3.5 33.4 - - + +
1582C LYS* 3.7 16.6 - - + +
1583C LYS* 3.4 56.1 - - + +
1586C MET* 3.9 19.7 - - + +
1595C ASN* 3.2 18.2 - - + +
1596C GLU* 4.2 7.0 - - + -
1662C VAL* 1.3 70.8 - - - +
1664C THR* 1.3 62.3 + - - +
1665C GLY 3.3 2.4 + - - -
1709C GLN* 2.9 51.5 + - + +
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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