Contacts of the helix formed by residues 1627 - 1638 (chain B) in PDB entry 4BHW
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 ARG1627 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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700B 01K 4.5 8.7 + - - -
1377B HIS* 4.0 20.6 + - + +
1397B TYR* 3.5 52.9 + - + -
1444B ASP* 4.7 13.3 + - - -
1445B ASP 2.9 19.2 + - - -
1446B TYR* 2.9 33.6 + - - +
1447B ILE* 4.6 5.2 - - + +
1626B GLY* 1.3 72.3 - - - -
1628B ASP* 1.3 79.1 + - - +
1629B ALA 3.4 1.6 - - - -
1630B PHE* 3.6 7.5 + - - +
1631B LEU* 3.3 36.4 + - + +
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Residues in contact with ASP1628 (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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1625B ASP 5.1 0.8 + - - +
1626B GLY 3.6 1.4 - - - -
1627B ARG* 1.3 97.0 + - - +
1629B ALA* 1.3 61.1 + - - +
1631B LEU* 3.4 9.3 + - - +
1632B THR* 2.8 36.3 + - - +
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Residues in contact with ALA1629 (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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1622B ASP 3.7 16.2 - - - +
1623B LEU* 3.2 28.3 - - + +
1625B ASP 5.0 5.8 + - - +
1626B GLY 4.7 1.0 + - - +
1627B ARG 3.4 0.6 - - - -
1628B ASP* 1.3 80.9 - - - +
1630B PHE* 1.3 55.5 + - - +
1632B THR* 3.9 5.9 - - - +
1633B LEU* 3.0 28.1 + - - +
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Residues in contact with PHE1630 (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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1361B PHE* 4.2 9.4 - + - -
1447B ILE* 4.2 18.4 - - + +
1448B PHE* 4.3 18.8 - + - -
1623B LEU* 3.5 11.0 + - + +
1624B MET* 3.9 28.9 - - + -
1627B ARG* 3.6 9.6 + - - +
1628B ASP 3.3 0.4 - - - -
1629B ALA* 1.3 76.6 - - - +
1631B LEU* 1.3 66.1 + - - +
1633B LEU* 3.4 21.0 + - + -
1634B ALA* 3.0 26.1 + - + +
1639B LEU* 5.0 7.6 - - + -
1641B PHE* 4.1 17.9 - + - -
1650B SER 5.3 0.4 - - - -
1654B MET* 3.5 51.1 - - + -
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Residues in contact with LEU1631 (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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1445B ASP* 3.7 14.8 - - + +
1446B TYR 3.7 2.7 - - - +
1447B ILE 3.1 30.1 - - - +
1449B HIS* 3.8 24.2 - - + +
1627B ARG* 3.3 48.5 + - + +
1628B ASP* 3.8 12.1 - - - +
1630B PHE* 1.3 77.0 - - - +
1632B THR* 1.3 64.5 + - - +
1634B ALA* 3.2 6.0 + - - +
1635B ARG* 2.9 50.3 + - - +
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Residues in contact with THR1632 (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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1628B ASP* 2.8 23.6 + - - +
1629B ALA* 3.9 5.6 - - - +
1631B LEU* 1.3 76.3 - - - +
1633B LEU* 1.3 64.5 + - - +
1635B ARG* 3.2 19.3 + - - +
1636B ASP* 2.9 46.8 + - - +
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Residues in contact with LEU1633 (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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1623B LEU* 4.1 13.9 - - + -
1629B ALA 3.0 19.1 + - - +
1630B PHE* 3.6 25.1 - - + +
1632B THR* 1.3 76.4 - - - +
1634B ALA* 1.3 57.1 + - - +
1636B ASP* 3.1 8.7 + - + +
1637B LYS* 2.9 53.0 + - + +
1639B LEU* 4.5 12.6 - - + -
1653B CYS* 5.8 0.9 - - + -
1654B MET* 5.4 2.9 - - - +
1657B GLU* 4.1 39.5 - - + +
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Residues in contact with ALA1634 (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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1449B HIS* 3.6 24.2 - - + +
1630B PHE* 3.0 23.1 + - + +
1631B LEU 3.5 3.8 - - - +
1633B LEU* 1.3 77.6 - - - +
1635B ARG* 1.3 61.8 - - - +
1636B ASP 3.1 0.3 + - - -
1637B LYS 3.1 0.3 + - - -
1638B HIS* 2.9 7.6 + - - -
1639B LEU* 2.9 53.8 + - + +
1641B PHE* 5.4 4.3 - - + -
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Residues in contact with ARG1635 (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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1173B GLN* 5.3 10.3 - - + +
1449B HIS* 3.8 36.3 + - + +
1631B LEU* 2.9 43.7 + - - +
1632B THR* 3.6 29.3 + - - +
1634B ALA* 1.3 75.5 - - - +
1636B ASP* 1.3 65.0 + - - +
1638B HIS* 4.0 9.3 + - - +
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Residues in contact with ASP1636 (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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1632B THR* 2.9 36.5 + - - +
1633B LEU* 3.4 7.9 - - + +
1635B ARG* 1.3 84.7 - - - +
1637B LYS* 1.3 66.0 + - + +
1638B HIS* 3.3 4.5 + - - +
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Residues in contact with LYS1637 (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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1633B LEU* 2.9 41.5 + - + +
1636B ASP* 1.3 82.3 - - + +
1638B HIS* 1.3 71.3 + - - +
1639B LEU* 3.2 24.1 + - + +
1649B TRP* 5.1 1.9 + - - -
1653B CYS* 5.9 4.5 - - + -
1657B GLU* 4.2 17.9 - - - +
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Residues in contact with HIS1638 (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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1170B PHE* 3.7 64.4 - + + +
1171B SER 6.0 0.4 - - - -
1173B GLN* 5.2 11.5 + - + +
1240B ASP* 2.9 32.2 + - + +
1257B ILE* 5.7 0.3 - - - +
1449B HIS* 6.3 0.2 - - - -
1634B ALA 2.9 5.3 + - - -
1635B ARG* 4.0 7.4 + - - +
1636B ASP 3.3 6.2 - - - -
1637B LYS* 1.3 81.7 - - - +
1639B LEU* 1.3 64.3 + - - +
1640B GLU* 3.6 8.7 + - - +
1649B TRP* 5.3 4.2 + - - -
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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