Contacts of the strand formed by residues 1596 - 1603 (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 GLU1596 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1579A TYR* 2.6 39.5 + - - +
1580A GLN* 4.9 1.9 + - - -
1583A LYS* 3.9 24.5 - - - +
1594A MET* 3.4 8.2 - - - +
1595A ASN* 1.3 78.3 - - - +
1597A LYS* 1.3 76.9 + - - +
1598A GLN* 5.4 0.8 - - + +
1661A ARG* 2.5 40.9 + - + -
1662A VAL 3.2 7.9 - - - +
1663A LEU* 4.1 8.7 - - + +
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Residues in contact with LYS1597 (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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1594A MET* 4.7 11.4 + - - +
1596A GLU* 1.3 81.0 - - - +
1598A GLN* 1.3 64.4 + - - +
1599A LEU* 3.7 18.7 + - + -
1636A VAL* 6.2 0.2 - - + -
1660A VAL 3.4 1.0 - - - +
1661A ARG* 3.6 1.7 - - - -
1662A VAL* 2.7 35.7 + - - +
1664A THR* 3.3 25.4 - - + +
1665A GLY 5.7 0.2 - - - -
1667A TYR* 4.0 21.2 + - - -
1702A PHE* 3.9 33.2 - - + -
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Residues in contact with GLN1598 (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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1554A LYS* 5.9 1.2 - - - -
1596A GLU* 5.4 0.9 - - - +
1597A LYS* 1.3 74.9 - - - +
1599A LEU* 1.3 67.1 + - - +
1600A PHE* 5.1 0.5 - - - -
1636A VAL 4.9 4.3 - - - +
1659A TYR* 3.3 58.4 + - + +
1660A VAL 3.3 7.9 - - - +
1661A ARG* 3.9 42.7 + - + +
1713A GLU* 4.1 11.1 + - - -
1714A TYR* 4.7 4.0 - - - -
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Residues in contact with LEU1599 (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* 4.1 18.4 - - + +
1598A GLN* 1.3 82.3 - - - +
1600A PHE* 1.3 63.8 + - - +
1634A PHE* 3.7 27.6 - - + +
1635A ALA 3.4 15.5 - - - +
1636A VAL* 3.9 19.1 - - + +
1659A TYR* 3.5 3.5 - - - -
1660A VAL* 2.6 40.8 + - - +
1662A VAL* 3.8 14.8 - - + -
1664A THR* 3.7 29.4 - - + -
1702A PHE* 3.8 22.4 - - + -
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Residues in contact with PHE1600 (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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1A LDR 4.1 0.3 - - - +
1551A VAL 5.5 0.2 - - - -
1554A LYS* 3.6 29.6 - - + -
1555A PHE* 3.7 11.7 - - - -
1598A GLN 5.1 0.9 - - - -
1599A LEU* 1.3 75.2 - - - +
1601A HIS* 1.3 61.6 + - - +
1634A PHE* 3.3 10.5 - - - -
1635A ALA* 2.8 32.4 + - + +
1636A VAL 3.7 19.7 - - - -
1637A ASN* 4.6 0.7 - - - -
1638A ALA* 3.7 32.8 - - + -
1641A SER* 3.5 17.3 + - - +
1657A VAL* 3.7 17.0 - - + -
1658A TYR 3.2 14.4 - - - -
1659A TYR* 3.3 40.8 - + + -
1716A ILE* 4.3 8.3 - - + -
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Residues in contact with HIS1601 (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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1A LDR 3.3 21.2 + + - -
1600A PHE* 1.3 77.2 - - - +
1602A GLY* 1.3 66.5 + - - +
1603A THR* 4.1 5.4 - - + -
1616A PHE* 3.4 22.7 - + + -
1620A TYR* 2.6 37.3 + + - -
1624A ASN* 3.5 24.7 - - - -
1632A THR* 3.8 7.4 - - + +
1633A TYR 2.8 19.8 + - - -
1634A PHE* 3.9 13.5 - + + -
1657A VAL* 3.4 3.4 - - - +
1658A TYR* 2.8 39.4 + + - +
1660A VAL* 4.3 8.3 - - + -
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Residues in contact with GLY1602 (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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1A LDR 2.7 43.2 + - - -
1601A HIS* 1.3 74.4 + - - +
1603A THR* 1.3 60.8 + - - -
1641A SER* 3.6 21.5 - - - -
1646A TYR 3.4 7.4 - - - +
1647A SER* 4.0 1.3 - - - -
1656A HIS 3.5 11.4 - - - -
1657A VAL* 4.0 3.1 - - - -
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Residues in contact with THR1603 (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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1A LDR 5.2 1.0 - - - -
1601A HIS* 4.0 2.4 + - + -
1602A GLY* 1.3 73.0 - - - -
1604A ASP* 1.3 85.8 + - - +
1605A ALA 4.0 0.2 + - - -
1607A SER* 3.4 13.0 + - - -
1608A VAL* 4.5 6.1 - - + +
1611A VAL* 5.1 1.6 - - + -
1620A TYR* 2.7 30.3 + - - +
1623A LYS* 4.6 2.3 - - - +
1646A TYR 3.1 14.0 + - - -
1647A SER* 3.6 9.0 - - - -
1648A ARG 4.0 1.4 + - - +
1656A HIS* 3.2 23.5 + - + +
1658A TYR* 4.0 28.5 - - + -
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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