Contacts of the strand formed by residues 1596 - 1603 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1579B TYR* 2.6 38.1 + - - +
1580B GLN* 4.8 1.4 + - - -
1583B LYS* 3.6 29.4 - - - +
1594B MET* 3.2 11.0 - - - +
1595B ASN* 1.3 78.9 - - - +
1597B LYS* 1.3 71.6 + - - +
1598B GLN* 5.0 5.9 + - + +
1661B ARG* 3.5 41.3 + - + +
1662B VAL 3.4 4.5 - - - +
1663B LEU* 4.3 1.6 - - + -
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Residues in contact with LYS1597 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1594B MET* 5.0 8.0 + - + +
1595B ASN 4.0 0.4 + - - -
1596B GLU* 1.3 79.5 - - - +
1598B GLN* 1.3 61.3 + - - +
1599B LEU* 3.7 20.7 + - + -
1636B VAL* 5.9 0.4 - - + -
1660B VAL 3.4 1.6 - - - +
1661B ARG* 3.6 0.7 - - - -
1662B VAL* 2.8 36.1 + - - +
1664B THR* 3.5 22.4 - - + +
1667B TYR* 3.8 26.2 + - - -
1699B PRO* 5.9 1.1 - - - +
1702B PHE* 3.8 26.9 - - + -
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Residues in contact with GLN1598 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1554B LYS* 4.7 8.3 + - - +
1596B GLU* 5.0 6.0 + - + +
1597B LYS* 1.3 72.2 - - - +
1599B LEU* 1.3 67.5 + - - +
1600B PHE* 5.3 0.2 - - - -
1636B VAL 5.0 3.5 - - - +
1659B TYR* 3.4 54.5 + - + +
1660B VAL 3.2 10.1 - - - +
1661B ARG* 3.9 39.7 + - + +
1713B GLU* 4.0 5.2 - - - +
1714B TYR* 4.8 3.6 - - - -
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Residues in contact with LEU1599 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1597B LYS* 3.9 22.7 - - + +
1598B GLN* 1.3 82.9 - - - +
1600B PHE* 1.3 68.3 + - - +
1634B PHE* 3.7 26.2 - - + +
1635B ALA 3.4 13.9 - - - +
1636B VAL* 4.0 24.2 - - + -
1659B TYR* 3.4 4.5 - - - -
1660B VAL* 2.7 36.4 + - - +
1662B VAL* 4.0 13.7 - - + -
1664B THR* 3.8 28.7 - - + -
1702B PHE* 3.9 12.6 - - + -
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Residues in contact with PHE1600 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B LDR 4.0 0.2 - - - +
1554B LYS* 3.8 9.0 - - + -
1555B PHE* 3.7 37.0 - + + -
1598B GLN 5.3 0.2 - - - -
1599B LEU* 1.3 75.7 - - - +
1601B HIS* 1.3 60.7 + - - +
1634B PHE* 3.2 10.3 - - - -
1635B ALA 2.9 32.9 + - - +
1636B VAL 3.7 19.1 - - - -
1637B ASN* 3.8 2.0 - - - +
1638B ALA* 3.5 36.3 - - + -
1641B SER* 3.4 18.0 + - - +
1657B VAL* 3.8 14.6 - - + -
1658B TYR 3.2 13.9 - - - -
1659B TYR* 3.4 39.5 - + + -
1716B ILE* 4.4 2.9 - - + -
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Residues in contact with HIS1601 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B LDR 3.4 27.6 + + - -
1600B PHE* 1.3 76.6 - - - +
1602B GLY* 1.3 68.8 + - - +
1603B THR* 3.7 9.4 + - + -
1616B PHE* 3.6 20.0 - + + -
1620B TYR* 2.8 39.9 + + - -
1632B THR* 3.9 11.2 - - + +
1633B TYR 2.7 26.5 + - - -
1634B PHE* 3.8 14.1 - + + -
1657B VAL* 3.4 4.6 - - - -
1658B TYR* 2.8 36.1 + + + +
1660B VAL* 4.3 8.5 - - + -
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Residues in contact with GLY1602 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B LDR 2.9 40.6 + - - -
1601B HIS* 1.3 73.5 + - - +
1603B THR* 1.3 60.6 + - - -
1641B SER* 3.4 24.0 - - - -
1646B TYR* 3.6 8.4 - - - +
1647B SER* 4.0 1.8 - - - -
1656B HIS 3.5 10.3 - - - -
1657B VAL* 3.8 4.9 - - - -
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Residues in contact with THR1603 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B LDR 5.2 2.5 - - - -
1601B HIS* 3.7 5.4 - - + -
1602B GLY* 1.3 75.4 - - - -
1604B ASP* 1.3 77.5 + - - +
1605B ALA 4.1 0.2 + - - -
1607B SER* 3.3 18.7 + - - -
1608B VAL* 4.5 6.3 - - + -
1611B VAL* 5.3 0.9 - - + -
1620B TYR* 2.6 29.3 + - - +
1646B TYR 3.2 14.1 + - - +
1647B SER* 3.5 6.6 - - - -
1648B ARG 4.1 0.5 + - - -
1656B HIS* 3.1 23.8 + - + +
1658B TYR* 4.0 27.6 - - + -
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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