Contacts of the helix formed by residues 1653 - 1661 (chain B) in PDB entry 3LQJ
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 ASN1653 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1649B THR* 2.8 22.7 + - - +
1650B ALA* 3.0 9.1 + - - +
1651B LEU 2.8 3.0 + - - -
1652B LEU* 1.3 86.3 - - - +
1654B SER* 1.3 63.7 + - - +
1655B ARG* 3.5 6.8 + - - +
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Residues in contact with SER1654 (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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1650B ALA 3.2 4.2 + - - -
1651B LEU 3.0 2.3 + - - -
1652B LEU 4.5 1.2 - - - +
1653B ASN* 1.3 77.8 + - - +
1655B ARG* 1.3 63.0 + - - +
1656B THR* 2.4 39.4 + - - +
1657B THR* 3.3 18.4 + - - +
1658B SER 4.1 1.0 + - - -
1757B PHE* 3.3 35.9 - - - -
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Residues in contact with ARG1655 (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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1653B ASN 3.5 5.1 + - - +
1654B SER* 1.3 71.7 - - - +
1656B THR* 1.3 58.1 + - + +
1657B THR 3.0 1.3 - - - -
1658B SER* 2.9 38.2 + - - +
1659B HIS* 4.8 0.5 + - - -
1750B ALA* 5.7 1.4 - - - +
1753B MET* 6.5 0.2 - - + -
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Residues in contact with THR1656 (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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1654B SER* 2.4 29.9 + - - +
1655B ARG* 1.3 79.7 - - + +
1657B THR* 1.3 58.4 + - - +
1658B SER 3.5 0.2 - - - -
1659B HIS* 2.9 25.0 - - - -
1750B ALA* 3.6 7.6 - - - +
1753B MET* 3.7 51.1 + - + +
1754B VAL* 3.1 21.3 - - - +
1757B PHE* 3.7 14.6 - - + -
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Residues in contact with THR1657 (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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1651B LEU* 2.9 47.2 + - + +
1652B LEU* 4.0 5.2 - - - -
1654B SER* 3.3 6.4 + - - +
1655B ARG 3.0 0.6 + - - -
1656B THR* 1.3 89.5 - - - +
1658B SER* 1.3 56.3 + - - +
1659B HIS* 3.0 5.4 - - - -
1660B LEU* 2.6 30.9 + - + +
1661B LEU* 3.3 12.5 + - - +
1708B LEU* 3.5 24.1 - - + +
1754B VAL* 3.7 14.6 - - + -
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Residues in contact with SER1658 (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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1654B SER 4.1 0.8 + - - -
1655B ARG* 2.9 26.7 + - - +
1656B THR 3.5 0.2 - - - -
1657B THR* 1.3 78.2 + - - +
1659B HIS* 1.3 65.3 + - - +
1660B LEU 3.5 0.5 + - - -
1661B LEU* 3.9 27.4 + - - +
1662B ARG 5.2 0.7 + - - -
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Residues in contact with HIS1659 (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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1656B THR 2.9 28.4 + - - -
1657B THR 4.1 0.4 - - - -
1658B SER* 1.3 83.8 + - - +
1660B LEU* 1.3 86.6 + - + +
1661B LEU 3.5 0.7 - - - -
1662B ARG 4.5 9.6 - - - +
1663B TYR* 5.8 0.5 - - - -
1737B ALA* 4.4 8.7 - - + +
1747B ILE* 4.9 7.6 + - + -
1750B ALA* 3.7 31.6 + - + +
1751B ASN* 4.2 18.2 + - - -
1754B VAL* 4.7 1.9 - - + +
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Residues in contact with LEU1660 (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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1657B THR* 2.6 19.4 + - + +
1659B HIS* 1.3 90.2 - - + +
1661B LEU* 1.3 58.6 + - - +
1662B ARG 3.5 2.9 - - - -
1663B TYR* 6.2 0.4 - - - +
1707B ASP* 3.2 9.5 - - - +
1708B LEU* 2.9 41.8 + - + +
1733B ILE* 3.8 18.8 - - + +
1734B ILE* 3.9 29.2 - - + -
1737B ALA* 3.3 34.8 - - + -
1754B VAL* 4.0 25.8 - - + -
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Residues in contact with LEU1661 (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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1652B LEU* 3.5 40.4 - - + +
1657B THR* 3.3 19.0 + - - +
1658B SER* 4.0 20.2 - - - +
1659B HIS 3.5 1.4 - - - -
1660B LEU* 1.3 77.8 - - - +
1662B ARG* 1.3 62.3 + - + +
1707B ASP* 3.2 3.6 - - - +
1708B LEU* 4.3 5.6 - - + -
1709B GLU* 3.1 45.4 + - + +
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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