Contacts of the helix formed by residues 1539 - 1546 (chain B) in PDB entry 5YWB
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 ARG1539 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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889B HIS* 4.4 6.9 + - - -
890B LYS* 3.5 32.1 - - - +
1509B THR* 3.3 38.0 + - + +
1510B ALA 5.8 0.2 + - - -
1512B ILE 3.5 15.6 + - - -
1514B MET* 3.3 45.7 - - - +
1517B GLU* 4.6 5.8 - - - +
1518B ASN* 5.5 5.6 - - - +
1537B ALA 3.1 1.6 - - - +
1538B HIS* 1.3 95.4 + - - +
1540B VAL* 1.3 65.1 + - - +
1541B HIS* 3.4 13.0 - - + +
1542B THR* 2.9 34.2 + - + +
1543B ILE* 3.2 15.6 - - - +
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Residues in contact with VAL1540 (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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862B VAL* 4.9 15.3 - - + -
1539B ARG* 1.3 75.8 - - - +
1541B HIS* 1.3 62.2 + - - +
1543B ILE* 3.2 10.0 + - + +
1544B LEU* 2.9 28.3 + - + +
1575B ALA 5.5 1.1 - - - +
1578B VAL* 3.9 25.6 - - + +
1579B ARG* 3.6 35.9 - - + +
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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
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1518B ASN* 3.5 30.2 + - + +
1522B LYS* 6.2 1.3 - - - -
1539B ARG* 3.4 6.8 - - + +
1540B VAL* 1.3 79.6 - - - +
1542B THR* 1.3 62.6 + - - +
1544B LEU* 2.9 38.3 + - + +
1545B SER* 3.0 20.3 + - - -
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Residues in contact with THR1542 (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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1509B THR* 4.9 3.4 - - - +
1517B GLU* 4.4 10.8 - - + +
1518B ASN* 5.2 7.6 - - - +
1521B GLN* 3.8 34.3 - - + +
1525B MET* 6.0 2.3 - - - +
1535B THR* 5.4 6.6 + - - -
1537B ALA* 3.5 16.2 - - + +
1539B ARG* 2.9 37.6 + - + +
1541B HIS* 1.3 75.8 - - - +
1543B ILE* 1.3 61.6 + - - +
1544B LEU 3.3 0.3 + - - -
1545B SER* 3.3 14.7 + - - -
1546B ALA* 3.8 9.2 + - - +
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Residues in contact with ILE1543 (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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1376B GLY* 5.0 1.3 - - - -
1377B ILE 3.3 32.5 - - - +
1378B CYS* 4.1 25.8 - - + -
1535B THR* 4.9 7.9 - - - +
1537B ALA* 3.6 22.2 - - + +
1539B ARG 3.2 17.7 - - - +
1540B VAL* 3.2 9.5 + - + +
1542B THR* 1.3 78.3 + - - +
1544B LEU* 1.3 62.2 + - - +
1546B ALA* 3.4 10.7 + - - +
1549B VAL* 3.5 31.1 - - + +
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Residues in contact with LEU1544 (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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1540B VAL* 2.9 17.9 + - + +
1541B HIS* 2.9 35.0 + - + +
1543B ILE* 1.3 78.7 - - - +
1545B SER* 1.3 63.7 + - - +
1546B ALA 3.1 8.0 + - - +
1563B PRO* 5.3 16.1 - - + +
1567B LEU* 5.2 15.5 - - + -
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Residues in contact with SER1545 (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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1525B MET* 5.7 7.5 - - - +
1541B HIS* 3.0 22.0 + - - -
1542B THR* 3.9 8.3 - - - -
1543B ILE 3.3 0.8 - - - -
1544B LEU* 1.3 78.8 - - - +
1546B ALA* 1.3 58.5 + - - +
1547B ASP* 4.1 6.1 + - - +
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Residues in contact with ALA1546 (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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1374B LYS* 4.5 14.8 - - + +
1375B ILE 4.7 1.3 - - - -
1376B GLY* 4.1 17.9 - - - +
1525B MET* 6.5 1.1 - - + -
1535B THR* 5.7 1.8 - - - +
1542B THR 3.8 7.2 + - - +
1543B ILE 3.4 14.1 + - - +
1544B LEU 3.1 10.5 - - - +
1545B SER* 1.3 80.8 - - - +
1547B ASP* 1.3 66.1 + - - +
1548B LEU 4.7 0.2 - - - +
1549B VAL* 3.7 18.3 - - + +
1561B ASP 5.0 0.2 - - - +
1563B PRO* 4.9 8.1 - - - +
1566B LEU* 5.7 1.7 - - - +
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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
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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