Contacts of the helix formed by residues 1540 - 1554 (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 THR1540 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1514B ARG* 3.6 31.8 + - - +
1537B PRO* 3.6 22.1 + - - +
1538B ARG 3.2 10.0 - - - +
1539B ASP* 1.3 77.6 - - - +
1541B HIS* 1.3 66.7 + - - +
1542B ASP* 4.0 18.4 - - - +
1543B GLY 3.5 3.3 + - - -
1544B ALA* 3.2 17.5 + - - +
1570B LEU* 4.1 1.3 - - - -
1574B GLU* 4.8 11.0 - - - +
1585B ARG* 5.6 0.2 - - - +
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Residues in contact with HIS1541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1539B ASP 3.9 1.4 + - - -
1540B THR* 1.3 72.1 - - - +
1542B ASP* 1.3 85.7 + - - +
1544B ALA* 3.1 7.1 + - - +
1545B PHE* 2.9 40.9 + + + +
1567B ALA* 3.1 20.2 + - + +
1570B LEU* 3.9 14.8 + - - +
1571B LEU* 3.8 55.6 - - + +
1574B GLU* 5.4 2.8 + - - +
1585B ARG* 3.9 9.2 - - - +
1592B SER* 3.8 19.7 + - - -
1596B LEU* 4.3 14.1 - - + -
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Residues in contact with ASP1542 (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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1514B ARG* 3.6 42.2 - - + +
1536B ILE* 4.5 0.4 - - + -
1540B THR* 3.4 8.7 - - + +
1541B HIS* 1.3 93.7 - - - +
1543B GLY* 1.3 61.7 + - - +
1545B PHE* 3.4 6.4 + - - +
1546B TYR* 3.1 39.5 + - + -
1585B ARG* 3.5 17.2 + - - -
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Residues in contact with GLY1543 (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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1533B THR* 4.7 0.4 - - - +
1536B ILE* 3.4 30.3 - - - +
1537B PRO 3.5 10.1 - - - -
1540B THR* 3.5 4.6 + - - -
1541B HIS 3.3 0.4 - - - -
1542B ASP* 1.3 79.5 - - - +
1544B ALA* 1.3 59.5 + - - +
1545B PHE 3.4 0.3 + - - -
1546B TYR* 3.6 4.1 + - - +
1547B ARG* 3.1 39.8 + - - -
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Residues in contact with ALA1544 (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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1537B PRO 4.5 0.2 + - - -
1538B ARG* 4.2 7.5 + - + +
1540B THR 3.2 13.5 + - - +
1541B HIS 3.1 9.0 + - - +
1543B GLY* 1.3 76.0 - - - +
1545B PHE* 1.3 61.6 + - - +
1547B ARG* 4.0 5.9 + - - +
1548B ALA 3.9 2.1 + - - -
1563B CYS* 3.3 31.3 - - - +
1566B LYS* 4.6 3.1 - - + -
1567B ALA* 3.7 24.7 - - + +
1570B LEU* 3.9 14.4 - - + -
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Residues in contact with PHE1545 (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* 4.1 20.2 - + - -
1541B HIS* 2.9 28.8 + + + +
1542B ASP* 3.6 7.2 - - - +
1543B GLY 3.2 0.4 - - - -
1544B ALA* 1.3 76.3 - - - +
1546B TYR* 1.3 78.3 + + - +
1548B ALA* 3.0 25.8 + - + +
1549B VAL* 3.3 26.1 + - + +
1567B ALA* 4.0 4.9 - - + +
1592B SER 5.5 0.2 - - - -
1595B MET* 3.8 31.4 - - + -
1596B LEU* 3.6 31.2 - - + -
1599B LEU* 3.8 23.3 - - + -
1639B VAL* 4.7 4.9 - - + -
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Residues in contact with TYR1546 (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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1514B ARG* 3.7 22.7 + - + +
1517B ALA* 3.9 9.6 - - + -
1518B ALA* 3.5 31.4 - - - +
1521B TRP* 4.2 22.3 - + - -
1529B MET* 4.7 11.4 - - - -
1533B THR* 3.9 21.3 - - + +
1536B ILE* 3.8 19.5 - - + -
1542B ASP* 3.1 34.9 + - + +
1543B GLY 3.6 2.2 + - - +
1545B PHE* 1.3 90.0 - + - +
1547B ARG* 1.3 60.4 + - - +
1548B ALA 3.3 0.2 - - - -
1549B VAL* 3.4 9.6 + - + +
1550B LEU* 3.1 32.4 + - - +
1635B LYS* 5.2 6.8 + - - -
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Residues in contact with ARG1547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1533B THR* 3.0 36.6 + - + +
1534B CYS* 3.8 15.2 + - - +
1536B ILE 2.9 24.0 + - - -
1537B PRO 3.6 2.6 + - - -
1538B ARG* 3.4 49.8 - - + +
1543B GLY* 3.1 36.5 + - - +
1544B ALA* 4.1 4.5 - - - +
1545B PHE 3.3 0.6 - - - -
1546B TYR* 1.3 77.3 - - - +
1548B ALA* 1.3 57.7 + - - +
1550B LEU* 4.2 6.0 - - + +
1551B ALA* 3.2 29.8 + - - +
1559B LEU* 5.0 4.4 - - + +
1563B CYS* 3.7 24.8 - - - -
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Residues in contact with ALA1548 (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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1544B ALA 3.9 2.9 + - - +
1545B PHE* 3.0 17.2 + - + +
1547B ARG* 1.3 77.4 - - - +
1549B VAL* 1.3 61.7 + - - +
1552B LEU* 3.3 31.2 + - - +
1560B ALA* 3.8 26.6 - - - +
1563B CYS* 3.9 14.9 - - + +
1564B ILE* 4.0 7.6 - - + +
1599B LEU* 3.9 17.9 - - + -
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Residues in contact with VAL1549 (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* 3.6 44.9 - - + +
1526B TRP* 4.5 3.4 - - + -
1529B MET* 4.1 12.6 - - + -
1545B PHE* 3.3 43.9 + - + +
1546B TYR* 3.4 13.4 + - + +
1548B ALA* 1.3 74.8 - - - +
1550B LEU* 1.3 64.8 + - - +
1552B LEU* 3.2 9.5 + - - +
1553B HIS* 3.2 20.6 + - - +
1599B LEU* 4.5 8.1 - - + -
1642B LEU* 4.5 8.9 - - + +
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Residues in contact with LEU1550 (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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1526B TRP* 3.7 25.4 - - + +
1529B MET* 3.7 30.7 - - + -
1530B GLU* 3.8 26.5 - - + +
1533B THR* 3.2 43.5 - - + +
1546B TYR 3.1 12.8 + - - +
1547B ARG* 4.2 5.6 - - + +
1549B VAL* 1.3 75.9 - - - +
1551B ALA* 1.3 61.8 + - - +
1553B HIS* 3.5 7.8 + - + +
1554B GLN* 3.3 34.4 + - + +
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Residues in contact with ALA1551 (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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1547B ARG 3.2 21.3 + - - +
1548B ALA 3.9 0.4 - - - +
1549B VAL 3.3 0.2 - - - -
1550B LEU* 1.3 77.3 - - - +
1552B LEU* 1.3 55.7 + - - +
1554B GLN* 3.3 3.1 + - - -
1555B ASP 3.0 8.3 + - - -
1556B LEU* 2.8 62.0 + - + +
1559B LEU* 4.4 9.6 - - + -
1560B ALA* 3.9 18.4 - - + +
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Residues in contact with LEU1552 (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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1548B ALA 3.3 18.1 + - - +
1549B VAL 3.2 7.4 + - - +
1551B ALA* 1.3 73.4 - - - +
1553B HIS* 1.3 64.6 + - - +
1555B ASP* 3.6 0.3 + - - +
1556B LEU 4.6 2.7 - - - +
1557B PHE* 4.8 2.2 - - + -
1560B ALA* 3.7 11.7 - - + -
1564B ILE* 5.3 1.8 - - + -
1599B LEU* 3.5 44.9 - - + +
1602B VAL* 4.9 3.1 - - + -
1603B ILE* 3.7 39.3 - - + -
1606B LYS* 2.5 51.5 + - + +
1642B LEU* 4.6 13.6 - - + +
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Residues in contact with HIS1553 (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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1526B TRP* 3.5 78.9 + + + +
1549B VAL 3.2 7.7 + - - +
1550B LEU* 3.7 9.5 + - - +
1551B ALA 3.3 0.2 - - - -
1552B LEU* 1.3 78.2 - - - +
1554B GLN* 1.3 68.1 + - + +
1555B ASP* 3.2 11.3 + - - +
1642B LEU* 4.6 6.4 - - + +
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Residues in contact with GLN1554 (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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1530B GLU* 3.9 26.7 + - - +
1550B LEU* 3.3 24.8 + - + +
1551B ALA* 3.3 3.9 + - - +
1553B HIS* 1.3 87.5 - - + +
1555B ASP* 1.3 69.4 + - - +
1556B LEU* 3.4 26.1 + - + +
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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