Contacts of the helix formed by residues 1616 - 1623 (chain B) in PDB entry 4LX0
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 MET1616 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1612B VAL* 3.8 18.6 - - - +
1613B LEU* 2.8 30.3 + - - +
1615B PRO* 1.3 83.2 - - + +
1617B ILE* 1.3 64.4 + - - +
1618B VAL 3.5 0.8 + - - -
1619B SER 3.8 1.4 + - - -
1620B ALA* 3.1 23.9 + - - +
1652B TYR* 3.5 39.8 - - + +
1656B ALA* 3.3 50.0 - - + +
1657B ILE* 3.8 15.3 - - + +
1660B GLN* 4.5 9.2 - - + +
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Residues in contact with ILE1617 (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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1613B LEU* 3.4 20.4 - - + +
1614B GLN* 3.2 11.2 + - - +
1616B MET* 1.3 78.0 - - - +
1618B VAL* 1.3 59.5 + - - +
1620B ALA* 3.3 0.9 + - - -
1621B MET* 2.8 41.5 + - + +
1657B ILE* 4.1 11.4 - - + -
1688B MET* 4.0 26.0 - - - -
1689B ILE* 4.0 28.9 - - + +
1692B VAL* 3.9 33.0 - - + -
1693B THR* 3.2 25.6 - - - +
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Residues in contact with VAL1618 (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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1614B GLN 4.7 1.7 + - - +
1615B PRO 5.1 1.2 + - - +
1617B ILE* 1.3 75.6 - - - +
1619B SER* 1.3 59.6 + - - +
1621B MET* 4.9 1.8 - - - -
1622B LEU* 2.8 40.6 + - + +
1623B GLU* 3.5 22.1 + - + +
1692B VAL* 4.1 21.8 - - + +
1693B THR* 5.2 1.1 - - - -
1696B ASN* 3.4 47.8 - - + +
1700B ARG* 3.6 3.4 - - - +
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Residues in contact with SER1619 (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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1615B PRO 4.9 3.3 + - - -
1616B MET 4.0 6.0 - - - -
1618B VAL* 1.3 80.6 - - - +
1620B ALA* 1.3 61.7 + - - +
1623B GLU* 3.2 47.0 + - - +
1624B ASN* 3.8 1.2 + - - +
1650B ASN 4.5 6.1 - - - -
1651B SER* 3.3 15.1 - - - -
1652B TYR* 2.7 40.2 + - - +
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Residues in contact with ALA1620 (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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1616B MET 3.1 17.5 + - - +
1619B SER* 1.3 80.7 - - - +
1621B MET* 1.3 62.4 + - - +
1624B ASN* 4.3 12.2 + - - +
1652B TYR* 3.4 11.2 - - + +
1653B CYS* 3.6 28.0 - - - +
1654B LEU* 3.9 13.1 + - + +
1657B ILE* 3.7 20.2 - - + -
1715B ASN* 3.5 11.8 + - - -
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Residues in contact with MET1621 (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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1617B ILE* 2.8 27.2 + - + +
1618B VAL 4.2 0.4 - - - +
1620B ALA* 1.3 82.8 - - + +
1622B LEU* 1.3 57.2 + - + +
1624B ASN 5.4 0.9 - - - -
1654B LEU* 3.6 27.4 - - - -
1657B ILE* 4.9 2.2 - - + -
1689B ILE* 4.1 9.9 - - + -
1693B THR* 3.7 25.8 - - + +
1708B THR* 5.7 0.3 - - - +
1711B GLN* 5.0 2.8 - - - +
1712B LEU* 3.5 19.1 + - + +
1715B ASN* 2.9 31.5 + - + +
1716B ILE* 4.0 18.6 - - + -
1719B LEU* 4.1 17.7 - - + -
1737B MET* 5.4 0.2 - - + -
1740B LEU* 4.0 25.6 - - + -
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Residues in contact with LEU1622 (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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1618B VAL* 2.8 21.2 + - + +
1621B MET* 1.3 80.8 - - - +
1623B GLU* 1.3 65.3 + - + +
1624B ASN 3.5 3.2 + - - -
1693B THR* 3.8 32.3 - - + +
1696B ASN* 3.5 26.7 - - + +
1697B LEU* 4.2 14.6 - - + +
1700B ARG* 4.8 0.2 - - - +
1703B VAL* 4.1 27.2 - - + +
1708B THR* 3.8 30.9 + - + +
1711B GLN* 6.2 3.1 - - - -
1712B LEU* 3.8 19.3 - - + -
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Residues in contact with GLU1623 (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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1618B VAL* 3.5 17.9 - - - +
1619B SER* 3.2 27.7 + - - +
1622B LEU* 1.3 82.6 - - - +
1624B ASN* 1.3 62.1 + - - +
1625B GLU 4.2 0.2 - - - -
1651B SER* 5.8 3.7 - - - -
1700B ARG* 2.8 42.6 + - - +
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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