Contacts of the helix formed by residues 1612 - 1625 (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 ARG1612 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1605B TYR* 3.5 59.8 + - - +
1606B LYS* 5.6 1.6 - - - +
1607B LEU 5.7 1.0 - - - +
1608B VAL 4.8 0.6 + - - -
1609B PRO* 3.3 45.3 + - - +
1610B GLU 3.0 8.3 + - - +
1611B ARG* 1.3 72.5 - - - +
1613B GLU* 1.3 69.4 + - + +
1614B ILE 3.4 0.2 - - - -
1616B ARG* 3.2 37.4 + - - +
1643B VAL* 5.7 1.4 - - - +
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Residues in contact with GLU1613 (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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1610B GLU 4.8 1.0 + - - -
1612B ARG* 1.3 82.7 - - + +
1614B ILE* 1.3 62.6 + - + +
1615B ILE 3.5 0.2 - - - -
1616B ARG* 3.7 17.4 - - - +
1617B GLN* 3.1 34.8 + - + +
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Residues in contact with ILE1614 (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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1610B GLU* 4.7 10.8 - - + +
1611B ARG* 3.7 58.3 - - + +
1612B ARG 3.4 0.8 - - - +
1613B GLU* 1.3 77.0 - - + +
1615B ILE* 1.3 63.4 + - - +
1617B GLN* 3.5 8.1 + - - +
1618B ILE* 3.3 30.7 + - + +
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Residues in contact with ILE1615 (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* 3.7 30.7 - - + +
1604B GLN* 3.9 18.6 - - + +
1605B TYR* 3.8 25.6 - - + +
1611B ARG* 3.1 45.8 + - + +
1613B GLU 3.5 0.2 - - - -
1614B ILE* 1.3 77.1 - - + +
1616B ARG* 1.3 57.0 + - - +
1618B ILE* 3.5 8.5 + - + +
1619B TRP* 3.0 60.7 + - + +
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Residues in contact with ARG1616 (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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1605B TYR* 3.0 27.5 + - + +
1612B ARG* 3.2 24.1 + - - +
1613B GLU* 3.7 18.0 - - - +
1614B ILE 3.3 0.4 - - - -
1615B ILE* 1.3 77.1 - - - +
1617B GLN* 1.3 56.2 + - + +
1619B TRP* 3.5 14.9 - - + +
1620B TRP* 2.8 30.4 + - - +
1644B VAL* 4.2 25.2 - - + +
1648B GLU* 4.8 18.1 + - - +
1649B ASP* 5.6 11.1 - - - +
1651B ARG* 4.1 9.6 + - - +
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Residues in contact with GLN1617 (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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1613B GLU* 3.1 19.9 + - + +
1614B ILE* 3.9 8.0 - - - +
1615B ILE 3.4 0.2 - - - -
1616B ARG* 1.3 74.2 - - + +
1618B ILE* 1.3 57.0 + - + +
1620B TRP* 3.7 8.0 - - + +
1621B GLU* 2.7 58.4 + - - +
1651B ARG* 4.9 7.0 - - - +
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Residues in contact with ILE1618 (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* 4.7 7.4 - - - +
1611B ARG* 4.2 21.1 - - - +
1614B ILE* 3.3 24.4 + - + +
1615B ILE* 4.0 7.9 - - + +
1617B GLN* 1.3 74.4 - - + +
1619B TRP* 1.3 59.7 + - - +
1621B GLU* 4.0 12.7 - - + +
1622B ARG* 3.0 64.0 + - + +
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Residues in contact with TRP1619 (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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1598B GLU* 3.5 25.3 + - - -
1601B GLU* 3.3 24.6 + - - +
1602B VAL* 3.8 26.0 - - + -
1605B TYR* 4.7 3.6 - + - -
1615B ILE* 3.0 41.5 + - + +
1616B ARG* 3.5 15.0 - - + +
1618B ILE* 1.3 77.9 - - - +
1620B TRP* 1.3 58.6 + - - +
1622B ARG* 3.4 13.8 - - - +
1623B LEU* 3.6 3.3 - - - +
1640B ARG* 3.0 69.2 + - + +
1643B VAL* 3.8 24.0 - - + -
1644B VAL* 3.7 26.5 - - + -
1649B ASP* 5.8 3.6 - - - -
1652B THR* 6.1 0.7 - - - -
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Residues in contact with TRP1620 (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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1616B ARG 2.8 21.0 + - - +
1617B GLN* 3.7 8.7 - - + +
1619B TRP* 1.3 72.9 - - - +
1621B GLU* 1.3 68.6 + - + +
1623B LEU* 3.4 40.8 - - + +
1624B GLN* 3.2 53.4 + - + +
1651B ARG* 3.5 76.5 - - + +
1652B THR* 3.8 13.2 - - - +
1655B LYS* 4.2 9.6 - - + -
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Residues in contact with GLU1621 (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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1617B GLN* 2.7 49.9 + - - +
1618B ILE* 4.0 14.8 - - - +
1620B TRP* 1.3 79.5 - - + +
1622B ARG* 1.3 59.5 + - + +
1623B LEU 2.9 6.9 + - - -
1624B GLN* 3.7 6.6 + - - +
1625B GLY* 3.2 21.1 + - - -
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Residues in contact with ARG1622 (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* 3.5 22.5 + - - -
1598B GLU* 2.7 25.8 + - - +
1601B GLU* 3.3 35.2 + - - -
1618B ILE* 3.0 40.7 + - + +
1619B TRP* 3.4 7.9 - - - +
1621B GLU* 1.3 73.6 - - + +
1623B LEU* 1.3 61.7 + - - +
1626B CYS* 3.6 37.6 - - - +
1633B TRP* 4.9 1.0 - - - -
1640B ARG* 3.6 14.9 + - - +
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Residues in contact with LEU1623 (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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1619B TRP 3.6 5.4 - - - +
1620B TRP* 3.4 43.1 - - + +
1621B GLU 2.9 4.2 + - - -
1622B ARG* 1.3 72.8 - - - +
1624B GLN* 1.3 64.0 + - - +
1626B CYS 3.0 21.6 - - - +
1633B TRP* 3.2 53.7 - - + -
1636B ILE* 6.1 1.1 - - + -
1637B LEU* 4.8 6.1 - - + -
1640B ARG* 3.8 21.3 - - - +
1652B THR* 3.7 25.1 - - + +
1655B LYS* 4.1 19.1 - - + -
1656B TYR* 6.0 0.7 - - + -
1659B LEU* 5.0 1.2 - - - +
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Residues in contact with GLN1624 (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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1620B TRP* 3.2 66.5 + - + +
1621B GLU* 4.4 5.9 - - - +
1623B LEU* 1.3 80.6 - - - +
1625B GLY* 1.3 62.5 + - - +
1626B CYS 4.0 1.7 - - - +
1627B GLN* 4.9 7.8 + - - +
1655B LYS* 4.7 18.7 - - + +
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Residues in contact with GLY1625 (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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1621B GLU 3.2 12.6 + - - -
1624B GLN* 1.3 80.1 - - - +
1626B CYS* 1.3 62.8 + - - +
1627B GLN* 3.7 9.5 + - - +
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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