Contacts of the helix formed by residues 1687 - 1696 (chain I) in PDB entry 2BT4
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 SER1687 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2407H TRS 3.6 7.0 - - - -
1659I GLU* 2.7 23.2 + - - -
1683I TYR* 2.9 28.5 + - - +
1685I HIS 3.9 0.6 - - - -
1686I THR* 1.3 74.3 + - - +
1688I VAL* 1.3 61.2 + - - +
1689I ALA 3.5 0.2 + - - -
1690I ILE* 2.9 35.3 + - - +
1691I LEU* 3.3 16.6 + - - +
1721I TYR* 3.9 11.3 - - - +
1722I VAL* 5.1 1.6 - - - +
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Residues in contact with VAL1688 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1482H ALA* 3.6 17.0 - - + +
1485H HIS* 4.1 10.5 - - + -
1486H THR* 3.6 27.6 - - + +
1516H PHE* 3.6 28.7 - - + -
1517H ARG* 3.8 7.9 - - - +
1686I THR 3.4 1.8 + - - -
1687I SER* 1.3 69.6 - - - +
1689I ALA* 1.3 59.3 + - - +
1691I LEU* 3.2 8.4 + - + +
1692I ASP* 2.8 36.4 + - - +
1721I TYR* 3.9 33.7 - - + +
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Residues in contact with ALA1689 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1415H PRO* 3.9 15.7 - - + -
1416H ASN* 3.3 10.8 + - - +
1482H ALA* 3.4 20.4 - - + +
1483H TYR* 3.9 29.6 - - + +
1486H THR* 5.6 0.8 + - - +
1659I GLU* 3.9 2.2 + - - +
1663I VAL* 3.9 9.3 - - + +
1687I SER* 3.1 7.1 - - - +
1688I VAL* 1.3 78.5 - - - +
1690I ILE* 1.3 57.4 + - - +
1692I ASP 3.3 0.2 + - - -
1693I ALA* 3.0 25.6 + - - +
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Residues in contact with ILE1690 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1659I GLU* 4.2 6.7 - - + +
1662I LEU* 3.9 31.0 - - + -
1663I VAL* 4.0 15.9 - - + -
1666I ILE* 4.0 16.6 - - + -
1678I ILE* 4.1 14.1 - - + -
1680I PRO* 5.1 2.9 - - + -
1683I TYR* 3.9 25.8 - - + -
1687I SER* 2.9 26.1 + - - +
1689I ALA* 1.3 72.1 - - - +
1691I LEU* 1.3 67.8 + - - +
1693I ALA* 3.1 7.8 + - - +
1694I LEU* 2.9 25.0 + - + +
1722I VAL* 3.9 21.8 - - + -
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Residues in contact with LEU1691 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1516H PHE* 3.9 29.6 - - + -
1517H ARG* 4.5 4.9 - - - +
1687I SER 3.3 10.7 + - - +
1688I VAL* 3.2 9.8 + - - +
1690I ILE* 1.3 80.7 - - - +
1692I ASP* 1.3 59.2 + - - +
1694I LEU* 3.1 9.5 + - - +
1695I ASN* 2.9 40.9 + - - +
1721I TYR* 3.4 41.7 - - + +
1722I VAL* 4.7 3.7 - - - +
1724I GLN* 4.0 12.3 - - + +
1725I ARG* 3.7 29.4 - - + +
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Residues in contact with ASP1692 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1416H ASN* 3.4 22.2 - - + +
1482H ALA* 3.3 15.1 - - - +
1513H ARG* 5.1 0.7 + - - -
1517H ARG* 2.7 34.7 + - - -
1560H CA2 2.6 40.3 + - + +
1688I VAL* 2.8 18.8 + - - +
1689I ALA 4.3 0.2 - - - -
1691I LEU* 1.3 73.1 - - - +
1693I ALA* 1.3 61.2 + - - +
1695I ASN* 3.3 18.3 + - - +
1696I THR* 3.3 18.4 + - - +
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Residues in contact with ALA1693 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1416H ASN* 3.2 22.4 - - - +
1663I VAL* 4.0 13.9 - - + -
1666I ILE* 3.6 26.5 - - + +
1667I HIS* 4.3 2.0 - - - +
1689I ALA 3.0 12.6 + - - +
1690I ILE* 3.4 9.2 - - - +
1692I ASP* 1.3 72.0 - - - +
1694I LEU* 1.3 64.5 + - - +
1696I THR* 2.6 26.8 + - - -
1697I CYS* 3.6 5.9 - - - -
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Residues in contact with LEU1694 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1666I ILE* 4.0 17.9 - - + -
1676I ILE* 3.9 32.1 - - + -
1678I ILE* 4.4 6.5 - - + -
1690I ILE* 2.9 27.2 + - + +
1691I LEU* 3.6 8.5 - - - +
1693I ALA* 1.3 75.0 - - - +
1695I ASN* 1.3 58.3 + - - +
1697I CYS* 2.9 28.3 + - - +
1702I VAL* 4.1 24.7 - - + -
1722I VAL* 3.7 32.8 - - + +
1725I ARG* 3.4 29.0 + - + -
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Residues in contact with ASN1695 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1423H ARG* 3.0 37.2 + - - +
1517H ARG* 4.0 11.9 - - - +
1691I LEU* 2.9 25.6 + - - +
1692I ASP* 3.4 25.4 + - - +
1693I ALA 3.2 0.2 - - - -
1694I LEU* 1.3 76.8 - - - +
1696I THR* 1.3 59.4 + - - +
1697I CYS 3.2 1.6 + - - -
1698I ASP* 4.2 3.6 + - - +
1724I GLN 5.2 0.7 - - - +
1725I ARG* 3.5 32.2 + - - +
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Residues in contact with THR1696 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1416H ASN* 4.6 7.2 - - + +
1419H LEU* 3.8 26.3 - - + +
1423H ARG* 3.5 20.7 - - - +
1560H CA2 4.3 17.7 - - + -
1667I HIS* 4.1 4.0 - - - -
1670I ARG* 2.9 32.9 + - - -
1692I ASP 3.3 15.9 - - - +
1693I ALA* 2.6 20.7 + - - +
1694I LEU 3.0 1.2 + - - -
1695I ASN* 1.3 73.6 - - - +
1697I CYS* 1.3 57.1 + - - +
1698I ASP* 3.0 20.1 + - - +
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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