Contacts of the helix formed by residues 1629 - 1641 (chain B) in PDB entry 5WBY
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 ILE1629 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1587B TYR* 4.1 23.8 + - + +
1628B ARG* 1.3 76.2 - - - +
1630B VAL* 1.3 78.2 + - + +
1631B GLU* 2.9 34.3 + - - +
1632B ASP* 2.9 21.2 + - - +
1633B TRP* 3.2 8.9 + - - -
1663B SER* 6.2 0.2 - - - -
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Residues in contact with VAL1630 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1628B ARG 3.8 1.4 + - - -
1629B ILE* 1.3 77.6 - - + +
1631B GLU* 1.3 72.6 + - - +
1633B TRP* 3.2 10.1 + - - +
1634B GLN* 3.1 22.3 + - - +
1656B TYR* 4.3 3.6 - - + -
1659B LEU* 4.9 3.8 - - + +
1660B CYS* 3.7 21.1 - - + +
1663B SER* 3.2 33.4 - - - +
1665B ARG* 4.1 13.0 - - + +
1668B LEU* 3.6 30.7 - - + -
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Residues in contact with GLU1631 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1456B TRP* 4.9 9.8 + - - +
1486B ALA* 3.2 31.6 - - + +
1629B ILE* 2.9 35.2 + - - +
1630B VAL* 1.3 82.2 - - - +
1632B ASP* 1.3 66.5 + - - +
1634B GLN* 3.5 27.3 + - - +
1635B LYS* 3.9 10.0 + - - +
1665B ARG* 2.9 33.2 + - - +
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Residues in contact with ASP1632 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1587B TYR* 3.7 19.4 + - - -
1591B VAL* 3.4 43.8 - - + +
1628B ARG* 4.3 10.5 - - + -
1629B ILE* 2.9 20.6 + - - +
1631B GLU* 1.3 80.8 - - - +
1633B TRP* 1.3 59.1 + - - +
1635B LYS* 3.2 12.4 + - - +
1636B ILE* 3.1 30.4 + - + +
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Residues in contact with TRP1633 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1622B ARG 4.9 0.9 - - - -
1623B LEU* 3.2 65.5 - - + -
1626B CYS* 3.7 17.4 - - + +
1627B GLN* 4.9 1.1 - - - +
1628B ARG* 3.5 46.3 + - + +
1629B ILE 3.2 5.8 + - - +
1630B VAL* 3.2 13.0 + - - +
1632B ASP* 1.3 74.3 - - - +
1634B GLN* 1.3 62.3 + - - +
1636B ILE* 3.6 24.6 - - + +
1637B LEU* 3.2 32.2 + - + +
1655B LYS* 5.1 0.4 - - + -
1656B TYR* 4.2 33.2 - + + -
1659B LEU* 3.3 33.2 - - + -
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Residues in contact with GLN1634 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1485B GLU 5.2 0.6 + - - -
1486B ALA 3.7 8.5 + - - -
1487B LEU 2.9 33.5 + - - +
1488B GLY* 3.4 16.8 - - - +
1490B TRP* 3.9 17.9 + - + -
1630B VAL 3.1 13.2 + - - +
1631B GLU* 3.5 12.6 + - - +
1632B ASP 3.2 0.4 - - - -
1633B TRP* 1.3 76.5 - - - +
1635B LYS* 1.3 57.7 + - + +
1637B LEU* 3.5 3.3 + - - +
1638B MET* 3.0 41.4 + - - +
1656B TYR* 3.5 23.3 + - - +
1665B ARG* 3.9 7.7 - - - +
1668B LEU* 4.1 16.1 - - + +
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Residues in contact with LYS1635 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1485B GLU* 5.0 13.9 + - - -
1490B TRP* 5.1 14.4 - - + -
1518B ALA* 5.4 8.6 - - - +
1521B TRP* 4.2 4.6 - - + -
1546B TYR* 5.2 7.0 + - - -
1591B VAL* 5.4 5.6 - - + -
1595B MET* 3.7 31.1 - - + +
1631B GLU 4.2 10.8 - - - +
1632B ASP* 3.2 11.5 + - - +
1634B GLN* 1.3 80.1 - - + +
1636B ILE* 1.3 63.0 + - - +
1638B MET* 3.4 21.3 + - + +
1639B VAL* 3.3 25.8 + - - +
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Residues in contact with ILE1636 (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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1591B VAL* 5.2 3.8 - - + -
1594B HIS* 4.0 22.4 - - + +
1595B MET* 4.1 18.2 - - + -
1598B GLU* 4.0 7.9 - - + +
1623B LEU* 6.1 1.3 - - + -
1628B ARG* 3.8 21.8 - - - -
1632B ASP* 3.1 22.9 + - + +
1633B TRP* 3.6 32.3 - - + +
1634B GLN 3.3 0.2 - - - -
1635B LYS* 1.3 76.8 - - - +
1637B LEU* 1.3 63.5 + - + +
1639B VAL* 3.4 13.9 + - - +
1640B ARG* 3.4 43.1 + - - +
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Residues in contact with LEU1637 (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* 4.8 7.2 - - + -
1633B TRP* 3.2 24.4 + - + +
1634B GLN* 4.0 2.9 - - - +
1636B ILE* 1.3 75.0 - - + +
1638B MET* 1.3 52.9 + - - +
1640B ARG* 3.0 27.2 + - + +
1641B SER* 2.7 40.3 + - - -
1652B THR* 3.8 27.8 - - + -
1653B TRP* 4.3 28.6 - - + +
1656B TYR* 3.4 48.5 - - + -
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Residues in contact with MET1638 (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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1490B TRP* 3.9 32.1 - - + -
1518B ALA* 4.2 8.1 - - + +
1521B TRP* 3.5 57.0 + - + +
1522B GLY* 4.0 24.5 - - - +
1634B GLN* 3.0 33.1 + - - +
1635B LYS* 3.6 13.9 - - + +
1636B ILE 3.3 0.2 - - - -
1637B LEU* 1.3 76.6 - - - +
1639B VAL* 1.3 59.9 + - - +
1641B SER* 3.6 19.9 - - - +
1642B LEU* 3.9 5.7 + - - +
1653B TRP* 6.1 1.8 - - + -
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Residues in contact with VAL1639 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1521B TRP* 3.9 19.5 - - + -
1545B PHE* 4.7 2.5 - - + -
1595B MET* 4.2 23.8 - - + +
1598B GLU* 4.0 9.9 - - + +
1599B LEU* 3.6 37.7 - - + +
1602B VAL* 3.3 29.6 - - + +
1635B LYS 3.3 16.1 + - - +
1636B ILE* 3.5 8.5 - - - +
1637B LEU 3.2 0.4 - - - -
1638B MET* 1.3 74.2 - - - +
1640B ARG* 1.3 63.4 + - - +
1642B LEU* 3.4 20.2 - - - +
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Residues in contact with ARG1640 (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 HIS* 4.5 2.2 + - - -
1598B GLU* 2.8 36.8 + - - +
1602B VAL* 4.5 0.4 - - - -
1619B TRP* 3.0 70.0 + - + +
1622B ARG* 3.6 22.0 + - - +
1623B LEU* 3.8 18.3 - - - +
1636B ILE* 3.4 30.6 + - - +
1637B LEU* 3.0 25.6 + - + +
1639B VAL* 1.3 74.8 - - + +
1641B SER* 1.3 63.6 + - - +
1642B LEU 3.2 0.4 + - - -
1643B VAL* 3.5 4.7 + - - +
1644B VAL* 3.1 27.4 + - + +
1652B THR* 4.5 8.3 - - - +
1653B TRP* 5.9 1.1 - - + +
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Residues in contact with SER1641 (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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1637B LEU 2.7 25.9 + - - -
1638B MET* 3.6 15.3 - - - +
1639B VAL 3.3 0.4 - - - -
1640B ARG* 1.3 71.7 - - - +
1642B LEU* 1.3 64.8 + - - +
1643B VAL 3.3 0.7 + - - -
1644B VAL 3.6 18.2 + - - +
1645B SER* 4.7 2.9 + - - +
1646B PRO* 6.0 2.5 - - - -
1653B TRP* 3.3 27.1 - - - -
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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