Contacts of the strand formed by residues 1655 - 1663 (chain A) 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 LYS1655 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1562A PHE* 3.9 18.2 - - + -
1642A ALA 2.5 30.6 + - - -
1644A ASP* 2.8 27.7 + - - +
1647A SER* 2.8 36.5 + - - +
1648A ARG 4.5 0.9 - - - -
1649A PRO* 4.1 14.4 - - + -
1653A GLY 4.6 2.9 - - - +
1654A ARG* 1.3 76.9 - - - +
1656A HIS* 1.3 66.8 + - - +
1717A THR* 3.3 7.4 - - - +
1718A PHE* 2.8 66.4 + - + +
1719A ARG* 5.0 4.9 - - - -
1720A LYS* 5.0 7.2 - - + -
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Residues in contact with HIS1656 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1566A LYS* 6.2 0.2 - - - -
1602A GLY* 3.5 3.5 - - - -
1603A THR* 3.2 37.0 + - + +
1605A ALA* 3.8 28.3 + - + +
1608A VAL* 4.5 15.7 - - + -
1647A SER* 3.5 7.2 - - - -
1648A ARG 4.8 2.0 + - - -
1650A ASP* 3.6 17.6 + - - -
1654A ARG* 3.6 27.0 + - + +
1655A LYS* 1.3 76.3 - - - +
1657A VAL* 1.3 63.1 + - - +
1715A LEU* 4.1 23.3 - - + -
1716A ILE 3.4 3.1 - - - -
1717A THR* 3.5 31.4 - - - +
1609C PRO* 5.7 6.3 - - + +
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Residues in contact with VAL1657 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1555A PHE* 4.3 15.0 - - + -
1600A PHE* 3.7 27.6 - - + -
1601A HIS 3.4 8.5 - - - +
1602A GLY* 4.0 11.4 - - - -
1638A ALA* 5.1 0.7 - - + -
1641A SER* 4.0 19.5 - - - +
1642A ALA 4.5 0.4 - - - +
1647A SER* 4.0 1.3 - - - -
1656A HIS* 1.3 78.9 - - - +
1658A TYR* 1.3 75.9 + - - +
1715A LEU* 4.2 2.0 - - - +
1716A ILE* 2.8 39.0 + - + +
1718A PHE* 3.5 28.7 - - + -
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Residues in contact with TYR1658 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1570A ILE* 4.4 3.8 - - + -
1600A PHE* 3.2 6.9 - - - -
1601A HIS 2.8 40.1 + - - +
1603A THR* 4.0 24.9 - - + -
1608A VAL* 3.2 27.9 + - + +
1611A VAL* 3.6 15.2 - - + +
1612A ASN* 2.8 29.5 + - - -
1616A PHE* 4.4 10.5 - + + -
1656A HIS 5.6 0.2 - - - -
1657A VAL* 1.3 80.1 - - - +
1659A TYR* 1.3 59.2 + - - +
1660A VAL* 3.5 18.8 - - + -
1712A PRO* 3.6 25.1 - - + -
1714A TYR 3.1 18.4 - - - +
1715A LEU* 3.9 28.7 - - + -
1716A ILE* 5.1 0.2 - - - -
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Residues in contact with TYR1659 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1550A THR* 6.4 0.4 - - + -
1551A VAL* 4.1 18.8 - - + -
1554A LYS* 3.3 38.6 - - + +
1598A GLN* 3.3 63.7 + - + +
1599A LEU 3.5 9.4 - - - -
1600A PHE* 3.3 38.4 - + + -
1657A VAL 4.1 0.6 + - - -
1658A TYR* 1.3 71.8 - - - +
1660A VAL* 1.3 60.0 + - - +
1713A GLU* 3.5 9.7 + - - +
1714A TYR* 2.9 55.3 + + + -
1716A ILE* 4.5 3.6 - - + +
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Residues in contact with VAL1660 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1597A LYS 3.4 0.3 - - - +
1598A GLN* 3.3 5.5 - - - -
1599A LEU 2.6 40.4 + - - +
1601A HIS* 4.3 4.0 - - + -
1616A PHE* 3.7 23.3 - - + -
1634A PHE* 3.8 9.2 - - + -
1658A TYR* 3.5 31.4 - - + +
1659A TYR* 1.3 73.8 - - - +
1661A ARG* 1.3 76.4 + - - +
1662A VAL* 3.5 16.5 + - + +
1710A ALA* 3.7 14.4 - - + -
1711A TYR 3.3 15.0 - - - +
1712A PRO* 4.4 2.2 - - + -
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Residues in contact with ARG1661 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1576A TRP* 4.3 23.1 - - + -
1579A TYR* 3.4 20.3 + - + +
1580A GLN* 5.6 0.2 - - - +
1596A GLU* 2.5 41.3 + - - +
1597A LYS 3.6 5.4 - - - -
1598A GLN* 3.9 31.5 + - + +
1660A VAL* 1.3 72.9 - - - +
1662A VAL* 1.3 58.6 + - - +
1710A ALA* 3.1 4.9 - - - -
1711A TYR* 2.8 42.0 + - + +
1713A GLU* 2.7 38.1 + - + +
1714A TYR* 5.9 0.4 + - - -
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Residues in contact with VAL1662 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1579A TYR* 3.8 3.8 + - - -
1596A GLU* 3.2 0.7 - - - +
1597A LYS 2.7 40.0 + - - +
1599A LEU* 3.8 24.2 - - + -
1634A PHE* 4.0 26.5 - - + -
1660A VAL* 3.6 27.1 - - + +
1661A ARG* 1.3 77.9 - - - +
1663A LEU* 1.3 64.3 + - - +
1664A THR* 3.0 23.6 + - + +
1691A THR* 5.2 0.7 - - + -
1702A PHE* 5.6 1.1 - - + -
1704A ALA* 4.6 9.9 - - + -
1709A GLN 3.8 9.0 - - - +
1710A ALA* 4.0 4.7 - - + -
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Residues in contact with LEU1663 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1579A TYR* 3.5 34.3 - - + +
1582A LYS* 3.8 20.4 - - + +
1583A LYS* 3.5 54.3 - - + +
1586A MET* 3.7 20.3 - - + +
1595A ASN* 3.2 13.7 - - + +
1596A GLU* 4.1 13.9 - - + -
1662A VAL* 1.3 70.2 - - - +
1664A THR* 1.3 64.4 + - - +
1665A GLY 3.3 1.1 + - - -
1709A GLN* 3.1 39.3 + - + +
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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