Contacts of the strand formed by residues 1596 - 1603 (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 GLU1596 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1579C TYR* 2.6 42.2 + - - +
1580C GLN* 4.9 1.2 + - - -
1583C LYS* 3.9 28.5 - - - +
1594C MET* 3.4 8.2 - - - +
1595C ASN* 1.3 79.0 - - - +
1597C LYS* 1.3 75.4 + - - +
1598C GLN* 5.4 1.0 - - + +
1661C ARG* 2.7 41.7 + - + -
1662C VAL 3.3 5.4 - - - +
1663C LEU* 4.2 1.8 - - + -
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Residues in contact with LYS1597 (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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1594C MET* 4.8 11.0 + - - +
1596C GLU* 1.3 78.4 + - - +
1598C GLN* 1.3 64.6 + - - +
1599C LEU* 4.2 11.4 - - + -
1636C VAL* 5.9 0.9 - - + -
1660C VAL 3.5 0.7 - - - +
1661C ARG* 3.8 0.9 - - - -
1662C VAL* 2.8 34.3 + - - +
1664C THR* 3.4 28.5 + - + +
1667C TYR* 3.9 28.8 + - - -
1699C PRO* 5.6 1.3 - - - -
1702C PHE* 3.9 27.4 - - + -
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Residues in contact with GLN1598 (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* 6.0 2.2 - - - +
1554C LYS* 5.2 3.5 - - - -
1596C GLU* 5.4 1.1 - - + +
1597C LYS* 1.3 73.8 - - - +
1599C LEU* 1.3 67.5 + - - +
1636C VAL 4.7 4.7 - - - +
1659C TYR* 3.5 52.3 + - + +
1660C VAL 3.2 10.4 - - - +
1661C ARG* 3.9 33.4 + - + +
1713C GLU* 3.9 20.2 + - - -
1714C TYR* 4.6 5.1 - - - -
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Residues in contact with LEU1599 (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* 4.2 17.9 - - + +
1598C GLN* 1.3 83.9 - - - +
1600C PHE* 1.3 64.5 + - - +
1634C PHE* 3.6 28.7 - - + +
1635C ALA 3.4 14.6 - - - +
1636C VAL* 3.8 26.2 - - + -
1659C TYR* 3.5 3.3 - - - -
1660C VAL* 2.6 41.7 + - - +
1662C VAL* 3.9 15.5 - - + -
1664C THR* 3.8 19.7 - - + -
1702C PHE* 3.7 24.5 - - + -
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Residues in contact with PHE1600 (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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1551C VAL 5.0 0.7 - - - -
1554C LYS* 3.7 26.2 - - + -
1555C PHE* 3.8 15.9 - - + -
1599C LEU* 1.3 75.6 - - - +
1601C HIS* 1.3 59.7 + - - +
1634C PHE* 3.3 7.9 - - - -
1635C ALA 2.7 34.1 + - - +
1636C VAL 3.8 15.5 - - - -
1637C ASN* 3.5 22.7 - - - +
1638C ALA* 3.8 21.8 - - + -
1641C SER* 3.3 20.5 + - - +
1657C VAL* 3.8 18.4 - - + -
1658C TYR 3.3 6.3 - - - -
1659C TYR* 3.5 33.2 - + + -
1716C ILE* 4.0 19.1 - - + -
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Residues in contact with HIS1601 (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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4C 3AB 3.4 16.0 + - - -
1600C PHE* 1.3 75.7 - - - +
1602C GLY* 1.3 68.7 + - - +
1603C THR* 4.0 5.0 + - + -
1616C PHE* 3.4 29.4 - + + -
1620C TYR* 2.5 34.1 + + - -
1622C GLY 4.2 7.6 - - - -
1632C THR* 3.8 19.1 - - + +
1633C TYR* 2.7 28.5 + - + -
1634C PHE* 3.8 16.2 - + + -
1641C SER* 4.0 2.5 - - - -
1657C VAL* 3.3 1.6 - - - -
1658C TYR* 2.8 41.0 + + - +
1660C VAL* 4.4 1.8 - - + -
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Residues in contact with GLY1602 (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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4C 3AB 2.7 31.6 + - - -
1601C HIS* 1.3 78.2 + - - +
1603C THR* 1.3 61.9 + - - -
1620C TYR* 4.2 0.7 + - - -
1641C SER* 3.4 24.3 - - - -
1646C TYR* 3.8 10.0 - - - +
1647C SER* 4.0 1.1 - - - -
1656C HIS 3.5 9.6 - - - -
1657C VAL* 3.8 4.0 - - - -
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Residues in contact with THR1603 (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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1601C HIS* 4.1 2.0 - - + -
1602C GLY* 1.3 72.2 - - - -
1604C ASP* 1.3 74.8 + - - +
1605C ALA 4.1 0.2 + - - -
1607C SER* 3.1 24.3 + - - -
1608C VAL* 4.9 4.9 - - + -
1611C VAL* 5.2 0.7 - - + -
1620C TYR* 2.7 29.2 + - + +
1622C GLY* 5.0 2.3 - - - -
1646C TYR 3.2 15.8 + - - +
1647C SER* 3.3 11.8 - - - +
1648C ARG 3.7 1.0 + - - +
1656C HIS* 3.2 17.4 + - + +
1658C TYR* 4.0 31.0 - - + -
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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