Contacts of the helix formed by residues 1525 - 1536 (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 GLN1525 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1494B HIS* 3.2 32.8 + - - -
1520B ALA* 2.9 19.2 + - + +
1523B LEU* 3.7 26.3 - - + +
1524B GLY* 1.3 76.1 - - - +
1526B TRP* 1.3 59.2 + - - +
1527B ASP 3.5 2.2 - - - -
1528B SER* 3.7 20.7 + - - +
1529B MET* 3.1 22.2 + - - +
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Residues in contact with TRP1526 (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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1520B ALA 5.9 0.2 - - - -
1521B TRP* 4.1 18.6 - + - -
1524B GLY* 3.2 38.7 + - - -
1525B GLN* 1.3 71.8 - - - +
1527B ASP* 1.3 68.6 + - - +
1529B MET* 3.3 37.5 - - + -
1530B GLU* 3.3 24.1 + - - +
1549B VAL* 4.5 4.3 - - + -
1550B LEU* 3.7 11.2 - - + +
1553B HIS* 3.5 64.1 + + + +
1642B LEU* 3.8 27.4 - - + -
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Residues in contact with ASP1527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1525B GLN 3.5 0.2 - - - -
1526B TRP* 1.3 80.8 - - - +
1528B SER* 1.3 63.2 + - - +
1530B GLU* 3.4 9.2 + - - +
1531B GLU* 3.2 35.6 + - - +
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Residues in contact with SER1528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1494B HIS* 3.6 29.7 + - - -
1520B ALA* 3.9 3.4 - - - -
1525B GLN* 3.5 29.7 + - - +
1526B TRP 3.4 0.2 - - - -
1527B ASP* 1.3 76.8 - - - +
1529B MET* 1.3 62.2 + - - +
1531B GLU* 3.7 11.5 + - - +
1532B TYR* 3.4 31.1 + - - -
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Residues in contact with MET1529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1517B ALA* 3.8 22.4 - - + +
1520B ALA* 3.6 13.0 - - + +
1521B TRP* 3.8 19.1 - - + -
1525B GLN 3.1 15.6 + - - +
1526B TRP* 3.3 44.4 - - + +
1527B ASP 3.3 0.4 - - - -
1528B SER* 1.3 75.0 - - - +
1530B GLU* 1.3 54.0 + - - +
1532B TYR* 3.2 4.8 + - - +
1533B THR* 2.6 53.3 + - - +
1546B TYR* 4.7 11.4 - - - +
1549B VAL* 4.1 15.3 - - + -
1550B LEU* 3.7 20.4 - - + -
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Residues in contact with GLU1530 (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 3.3 16.6 + - - +
1527B ASP* 3.4 9.5 + - - +
1529B MET* 1.3 78.8 - - - +
1531B GLU* 1.3 62.0 + - - +
1533B THR* 4.1 0.2 - - - -
1534B CYS* 3.2 37.2 + - - -
1550B LEU* 3.8 25.8 - - + +
1554B GLN* 3.9 24.7 + - - +
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Residues in contact with GLU1531 (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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1527B ASP* 3.2 24.4 + - - +
1528B SER* 3.8 13.8 + - - +
1529B MET 3.2 0.6 - - - -
1530B GLU* 1.3 78.9 - - - +
1532B TYR* 1.3 68.5 + - + +
1534B CYS* 3.5 12.4 + - - +
1535B MET* 3.5 16.3 + - - +
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Residues in contact with TYR1532 (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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1494B HIS* 4.3 16.8 - + - -
1497B CYS* 3.5 18.3 - - - -
1498B CYS* 3.4 26.2 + - - -
1501B TRP* 3.7 37.7 - + - -
1513B ALA* 3.6 23.7 - - - +
1516B ALA* 3.7 26.7 - - + -
1517B ALA* 4.2 8.7 - - - +
1528B SER* 3.4 23.0 + - - +
1529B MET 3.2 3.8 + - - +
1531B GLU* 1.3 84.0 - - + +
1533B THR* 1.3 62.2 - - - +
1535B MET* 3.5 13.5 + - + +
1536B ILE* 3.4 26.2 + - - +
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Residues in contact with THR1533 (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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1517B ALA* 4.4 3.5 - - - +
1529B MET* 2.6 37.2 + - - +
1530B GLU 4.1 2.5 - - - -
1532B TYR* 1.3 71.2 - - - +
1534B CYS* 1.3 64.8 + - - +
1535B MET 3.2 0.2 - - - -
1536B ILE* 3.2 20.0 + - + +
1543B GLY 4.7 0.2 - - - +
1546B TYR* 3.9 22.7 - - + +
1547B ARG* 3.0 46.7 + - + +
1550B LEU* 3.2 30.2 - - + +
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Residues in contact with CYS1534 (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* 3.2 28.1 + - - -
1531B GLU* 3.6 10.3 - - - +
1532B TYR 3.4 0.2 - - - -
1533B THR* 1.3 79.6 - - - +
1535B MET* 1.3 60.0 + - + +
1536B ILE 3.6 4.9 + - - +
1538B ARG* 6.1 2.9 - - - -
1547B ARG* 3.8 11.1 + - - +
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Residues in contact with MET1535 (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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1501B TRP* 4.2 13.0 - - - -
1509B GLN* 3.4 32.8 - - + +
1510B ALA* 5.7 3.5 - - - +
1513B ALA* 3.5 23.5 - - + +
1531B GLU 3.5 15.2 + - - +
1532B TYR* 3.5 14.1 + - + +
1533B THR 3.2 0.8 - - - -
1534B CYS* 1.3 78.0 - - + +
1536B ILE* 1.3 63.1 + - - +
1537B PRO* 3.7 7.3 - - - +
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Residues in contact with ILE1536 (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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1510B ALA 5.3 1.8 - - - +
1513B ALA* 3.6 19.7 - - + +
1514B ARG* 3.7 44.0 - - + +
1517B ALA* 3.8 5.6 - - + -
1532B TYR 3.4 13.5 - - - +
1533B THR* 3.2 10.6 + - + +
1534B CYS 3.8 1.8 - - - +
1535B MET* 1.3 75.6 - - - +
1537B PRO* 1.4 72.5 - - + +
1540B THR* 4.9 0.2 - - - +
1542B ASP 4.5 0.2 - - - -
1543B GLY* 3.4 30.1 - - - +
1546B TYR* 3.8 26.9 - - + -
1547B ARG* 2.9 29.5 + - - -
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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