Contacts of the helix formed by residues 1586 - 1606 (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 ALA1586 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1424B GLN* 5.2 9.2 - - - +
1575B LEU* 4.4 11.2 - - + +
1581B GLU 4.3 2.6 + - - -
1582B SER 3.3 23.6 - - - +
1583B TYR* 3.2 15.4 + - + +
1585B ARG* 1.3 74.3 - - - +
1587B TYR* 1.3 62.8 + - - +
1589B ALA* 3.5 13.8 + - - +
1590B MET* 3.5 14.9 + - - +
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Residues in contact with TYR1587 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1583B TYR* 2.8 48.1 + + + +
1584B SER* 4.8 4.0 - - - +
1586B ALA* 1.3 72.3 - - - +
1588B GLY* 1.3 59.4 + - - +
1590B MET* 3.2 15.2 + - + +
1591B VAL* 3.1 26.2 + - + +
1627B GLN 4.2 3.6 + - - -
1628B ARG* 3.7 40.2 - - + +
1629B ILE* 4.1 19.8 + - + +
1632B ASP* 3.7 19.7 - - - -
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Residues in contact with GLY1588 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1584B SER 3.3 21.1 + - - -
1585B ARG* 3.3 10.7 - - - -
1586B ALA 3.3 0.6 - - - -
1587B TYR* 1.3 77.5 - - - +
1589B ALA* 1.3 58.3 + - - +
1591B VAL* 3.5 15.9 - - - +
1592B SER* 3.1 26.0 + - - -
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Residues in contact with ALA1589 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1571B LEU* 4.4 15.2 - - + +
1575B LEU* 3.7 28.7 - - + -
1585B ARG* 2.6 20.6 + - - +
1586B ALA 3.6 7.9 - - - +
1587B TYR 3.2 0.4 - - - -
1588B GLY* 1.3 70.9 - - - +
1590B MET* 1.3 56.8 + - + +
1591B VAL 3.2 0.2 - - - -
1592B SER* 3.6 6.0 - - - +
1593B CYS* 2.7 38.9 + - - +
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Residues in contact with MET1590 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1586B ALA 3.5 8.6 + - - +
1587B TYR* 3.2 19.2 + - + +
1589B ALA* 1.3 78.0 - - + +
1591B VAL* 1.3 56.8 + - - +
1593B CYS* 3.6 22.2 - - - -
1594B HIS* 3.1 27.3 + - + +
1628B ARG* 3.1 28.8 + - - +
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Residues in contact with VAL1591 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1587B TYR* 3.1 21.3 + - + +
1588B GLY* 3.5 15.7 - - - +
1590B MET* 1.3 77.7 - - - +
1592B SER* 1.3 60.0 + - - +
1594B HIS* 3.5 4.2 - - - +
1595B MET* 3.0 44.9 + - + +
1628B ARG* 4.1 13.5 - - - +
1632B ASP* 3.4 50.9 - - + +
1635B LYS* 5.4 5.4 - - + -
1636B ILE* 5.2 3.9 - - + +
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Residues in contact with SER1592 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1541B HIS* 3.8 18.7 + - - -
1545B PHE* 5.5 0.2 - - - -
1571B LEU* 3.8 20.6 - - - +
1588B GLY 3.1 17.9 + - - -
1589B ALA 3.1 4.0 + - - -
1591B VAL* 1.3 78.2 - - - +
1593B CYS* 1.3 51.8 + - - +
1595B MET* 3.3 12.8 + - - +
1596B LEU* 2.8 39.8 + - - +
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Residues in contact with CYS1593 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1568B ARG* 6.4 1.1 - - + -
1571B LEU* 5.0 3.6 - - + +
1589B ALA 2.7 22.5 + - - +
1590B MET* 3.6 32.1 - - - -
1592B SER* 1.3 70.5 - - - +
1594B HIS* 1.3 57.7 + - - +
1596B LEU* 4.0 11.5 - - + +
1597B SER* 2.7 36.0 + - - -
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Residues in contact with HIS1594 (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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1590B MET* 3.1 19.9 + - + +
1591B VAL* 3.5 5.2 - - - +
1593B CYS* 1.3 83.8 - - - +
1595B MET* 1.3 52.8 + - - +
1597B SER* 2.8 8.1 + - - -
1598B GLU* 2.8 52.5 + - + +
1622B ARG* 3.5 39.6 + - + -
1626B CYS* 4.5 9.0 - - + -
1628B ARG* 3.2 32.5 + - - +
1636B ILE* 4.0 30.4 - - + +
1640B ARG* 4.5 2.6 + - - -
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Residues in contact with MET1595 (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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1521B TRP* 4.2 6.7 - - + -
1545B PHE* 3.8 33.0 - - + -
1591B VAL* 3.0 32.9 + - - +
1592B SER* 3.3 13.7 + - - +
1594B HIS* 1.3 77.5 - - - +
1596B LEU* 1.3 52.5 + - - +
1598B GLU* 3.5 7.7 - - - +
1599B LEU* 2.7 36.3 + - - +
1635B LYS* 3.7 46.4 - - + +
1636B ILE* 4.1 24.0 - - + -
1639B VAL* 4.2 12.1 - - + +
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Residues in contact with LEU1596 (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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1541B HIS* 4.3 18.8 - - + -
1545B PHE* 3.6 29.6 - - + -
1548B ALA* 5.9 0.2 - - + -
1564B ILE* 4.1 38.3 - - + +
1567B ALA* 4.3 14.4 - - + +
1568B ARG* 4.3 26.2 - - + +
1571B LEU* 4.9 3.8 - - + -
1592B SER* 2.8 29.4 + - - +
1593B CYS* 4.0 9.9 - - + +
1594B HIS 3.4 0.2 - - - -
1595B MET* 1.3 73.3 - - - +
1597B SER* 1.3 57.0 + - - +
1599B LEU* 3.4 6.2 + - + +
1600B GLU* 3.1 32.0 + - - +
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Residues in contact with SER1597 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1568B ARG* 4.8 10.2 - - - +
1593B CYS 2.7 24.0 + - - -
1594B HIS* 2.8 17.3 + - - -
1596B LEU* 1.3 72.2 - - - +
1598B GLU* 1.3 62.7 + - - +
1600B GLU* 3.4 14.3 + - - +
1601B GLU* 3.2 31.0 + - - +
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Residues in contact with GLU1598 (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* 2.8 44.3 + - + +
1595B MET* 3.5 8.3 - - - +
1597B SER* 1.3 74.0 + - - +
1599B LEU* 1.3 58.1 + - - +
1601B GLU* 3.1 10.9 + - - +
1602B VAL* 3.0 28.4 + - - +
1619B TRP* 3.5 20.4 + - - -
1622B ARG* 2.7 35.5 + - - +
1636B ILE* 4.0 6.7 - - + +
1639B VAL* 4.0 10.1 - - + -
1640B ARG* 2.8 43.0 + - - +
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Residues in contact with LEU1599 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1545B PHE* 3.8 23.6 - - + -
1548B ALA* 3.9 28.9 - - + -
1549B VAL* 4.5 8.1 - - + -
1552B LEU* 3.5 27.3 - - + +
1564B ILE* 4.2 13.6 - - + +
1595B MET 2.7 20.6 + - - +
1596B LEU* 3.7 7.6 - - + +
1598B GLU* 1.3 72.7 - - - +
1600B GLU* 1.3 57.8 + - - +
1602B VAL* 3.7 4.5 - - + +
1603B ILE* 3.2 25.5 + - - +
1639B VAL* 3.6 25.7 - - + +
1642B LEU* 3.8 16.6 - - + -
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Residues in contact with GLU1600 (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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1561B GLN* 3.4 23.8 + - - +
1564B ILE* 3.3 35.2 - - + +
1568B ARG* 2.9 36.1 + - - -
1596B LEU 3.1 15.0 + - - +
1597B SER* 3.6 12.9 - - - +
1598B GLU 3.3 0.2 - - - -
1599B LEU* 1.3 77.0 - - - +
1601B GLU* 1.3 57.9 + - - +
1603B ILE* 3.3 14.7 - - + +
1604B GLN* 3.2 21.3 + - - +
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Residues in contact with GLU1601 (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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1597B SER* 3.2 20.5 + - - +
1598B GLU* 3.1 12.6 + - - +
1600B GLU* 1.3 77.5 - - - +
1602B VAL* 1.3 63.3 + - - +
1603B ILE 3.4 0.2 - - - -
1604B GLN* 3.4 11.8 - - + +
1605B TYR* 3.2 18.0 + - - +
1615B ILE* 3.7 22.0 - - + +
1618B ILE* 4.7 8.0 - - - +
1619B TRP* 3.3 27.5 + - - +
1622B ARG* 3.3 30.7 + - - -
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Residues in contact with VAL1602 (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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1552B LEU* 4.9 4.5 - - + -
1598B GLU 3.0 18.3 + - - +
1599B LEU* 3.5 9.8 + - + +
1601B GLU* 1.3 74.5 - - - +
1603B ILE* 1.3 63.6 + - - +
1605B TYR* 3.2 15.6 + - - +
1606B LYS* 3.2 29.2 + - + +
1619B TRP* 3.8 22.0 - - + -
1639B VAL* 3.3 30.5 - - + +
1640B ARG* 4.5 0.2 - - - -
1642B LEU* 4.0 28.7 - - + -
1643B VAL* 4.3 8.9 - - + +
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Residues in contact with ILE1603 (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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1552B LEU* 3.7 24.8 - - + +
1557B PHE* 3.3 51.8 - - + +
1560B ALA* 4.3 4.5 - - + -
1561B GLN* 4.5 20.2 - - + +
1564B ILE* 5.4 2.9 - - + -
1599B LEU 3.2 8.0 + - - +
1600B GLU* 3.3 24.5 - - + +
1602B VAL* 1.3 74.8 - - - +
1604B GLN* 1.3 70.0 + - + +
1605B TYR 3.6 0.2 + - - -
1606B LYS* 3.7 14.9 + - - +
1607B LEU* 4.0 14.8 - - + +
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Residues in contact with GLN1604 (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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1600B GLU 3.2 19.0 + - - +
1601B GLU* 3.4 14.6 - - + +
1603B ILE* 1.3 81.7 - - + +
1605B TYR* 1.3 62.7 + - - +
1606B LYS 3.5 0.3 + - - -
1607B LEU* 5.7 0.2 - - - -
1608B VAL* 3.3 40.7 + - + +
1611B ARG* 4.9 14.6 + - - +
1615B ILE* 3.9 13.8 - - + +
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Residues in contact with TYR1605 (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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1601B GLU 3.2 8.3 + - - +
1602B VAL* 3.2 11.3 + - - +
1604B GLN* 1.3 79.3 - - - +
1606B LYS* 1.3 55.4 + - - +
1607B LEU 3.2 5.8 + - - -
1608B VAL 3.4 13.7 - - - +
1611B ARG 3.9 7.6 - - - -
1612B ARG* 3.5 71.4 + - - +
1615B ILE* 3.8 28.0 - - + -
1616B ARG* 3.0 42.0 + - + -
1619B TRP* 4.7 2.7 - + + -
1643B VAL* 3.4 37.5 - - + -
1644B VAL* 4.0 17.2 - - + +
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Residues in contact with LYS1606 (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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1552B LEU* 2.5 48.6 + - + +
1555B ASP* 3.0 26.3 + - - +
1557B PHE* 3.5 26.7 - - + -
1602B VAL* 3.4 31.0 - - + +
1603B ILE* 4.0 8.7 - - - +
1604B GLN 3.4 0.8 - - - -
1605B TYR* 1.3 74.8 - - - +
1607B LEU* 1.3 62.0 + - - +
1612B ARG* 5.6 2.2 - - - +
1642B LEU* 5.5 7.6 - - - -
1643B VAL* 3.7 22.7 - - + -
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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
------------------------------------------------------------
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