Contacts of the helix formed by residues 1447 - 1458 (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 SER1447 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1446B CYS* 1.3 77.7 - - - +
1448B ASP* 1.3 70.0 + - - +
1449B SER* 3.3 13.6 + - - -
1450B THR* 3.1 27.4 + - - -
1451B LEU* 3.3 11.9 + - - +
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Residues in contact with ASP1448 (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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1437B ARG* 2.7 42.8 + - - +
1446B CYS 4.5 3.6 - - - +
1447B SER* 1.3 79.2 + - - +
1449B SER* 1.3 57.9 + - - +
1451B LEU* 3.4 3.4 + - - +
1452B TRP* 2.9 42.3 + - + +
1471B LEU* 4.4 10.9 - - + +
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Residues in contact with SER1449 (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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1447B SER* 3.8 13.2 + - - -
1448B ASP* 1.3 78.0 - - - +
1450B THR* 1.3 61.0 + - - +
1452B TRP* 3.7 8.4 - - - +
1453B GLU* 2.9 31.4 + - - +
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Residues in contact with THR1450 (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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1446B CYS* 4.8 9.0 - - + -
1447B SER* 3.1 27.4 + - - -
1449B SER* 1.3 82.1 + - - +
1451B LEU* 1.3 65.6 + - + +
1453B GLU* 3.3 9.7 + - - +
1454B ALA* 2.9 27.1 + - + +
1497B VAL* 5.3 7.9 - - + -
1499B LYS* 5.0 17.5 - - - +
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Residues in contact with LEU1451 (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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1437B ARG* 4.6 20.4 - - + +
1440B LEU* 4.0 37.2 - - + -
1441B ASP* 5.0 6.5 - - + -
1446B CYS* 3.6 37.2 - - + +
1447B SER 3.3 8.2 + - - +
1448B ASP 4.0 5.6 - - - +
1449B SER 3.4 0.2 - - - -
1450B THR* 1.3 79.1 - - + +
1452B TRP* 1.3 60.5 + - - +
1454B ALA* 3.3 4.4 + - - +
1455B LEU* 2.9 35.6 + - - +
1471B LEU* 4.2 22.0 - - + -
1497B VAL* 4.1 17.3 - - + -
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Residues in contact with TRP1452 (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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1448B ASP* 2.9 35.2 + - + +
1449B SER* 3.7 7.9 - - - +
1451B LEU* 1.3 77.5 - - - +
1453B GLU* 1.3 56.9 + - - +
1455B LEU* 3.3 8.4 + - + +
1456B GLU* 2.9 29.7 + - - +
1461B LYS* 3.9 34.3 - - + +
1464B VAL* 3.8 27.8 - - + -
1465B LYS* 3.7 41.7 - - + -
1470B GLY* 4.9 9.2 - - - -
1471B LEU* 3.6 30.4 - - + +
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Residues in contact with GLU1453 (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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1449B SER 2.9 18.6 + - - +
1450B THR* 3.7 8.7 - - - +
1452B TRP* 1.3 75.8 - - - +
1454B ALA* 1.3 56.9 + - - +
1456B GLU* 3.3 5.8 + - + +
1457B ILE* 2.9 57.7 + - + +
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Residues in contact with ALA1454 (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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1440B LEU* 6.2 1.3 - - + -
1450B THR* 2.9 17.6 + - + +
1451B LEU* 3.3 7.2 + - + +
1453B GLU* 1.3 76.3 - - - +
1455B LEU* 1.3 60.2 + - + +
1457B ILE* 3.7 6.5 + - - -
1458B ALA* 3.1 27.7 + - - +
1493B ALA* 4.8 5.8 - - + +
1496B PHE* 3.7 18.8 - - + -
1497B VAL* 3.6 28.5 - - + -
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Residues in contact with LEU1455 (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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1436B ILE* 5.1 3.6 - - + -
1440B LEU* 3.9 28.0 - - + -
1451B LEU 2.9 20.4 + - - +
1452B TRP* 3.8 9.2 - - + +
1454B ALA* 1.3 76.6 - - + +
1456B GLU* 1.3 63.5 + - - +
1457B ILE 3.1 0.2 - - - -
1458B ALA* 3.1 8.8 + - + -
1460B LEU* 3.1 52.2 + - + -
1461B LYS* 4.1 14.1 - - + +
1464B VAL* 3.7 33.7 - - + -
1471B LEU* 4.4 13.7 - - + -
1490B PHE* 4.9 1.1 - - + -
1493B ALA* 4.3 13.5 - - + -
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Residues in contact with GLU1456 (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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1452B TRP 2.9 17.2 + - - +
1453B GLU* 3.8 7.2 - - - +
1455B LEU* 1.3 76.9 - - - +
1457B ILE* 1.3 61.2 + - + +
1459B GLN* 3.7 16.1 + - - -
1461B LYS* 3.7 36.5 - - + +
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Residues in contact with ILE1457 (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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1453B GLU* 2.9 48.5 + - + +
1454B ALA* 4.0 6.1 - - - +
1456B GLU* 1.3 75.3 - - + +
1458B ALA* 1.3 56.4 + - - +
1459B GLN* 3.1 22.0 + - - +
1496B PHE* 3.5 22.6 - - + -
1520B LEU* 4.7 2.3 - - - +
1523B VAL* 3.7 25.7 - - + +
1527B ALA* 4.2 20.4 - - + -
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Residues in contact with ALA1458 (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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1454B ALA 3.1 18.9 + - - +
1455B LEU* 3.1 7.2 + - - +
1457B ILE* 1.3 73.8 - - - +
1459B GLN* 1.3 71.8 + - - +
1460B LEU* 3.3 5.8 + - + -
1489B LEU* 3.5 33.4 - - - +
1492B LEU* 5.0 3.1 - - + +
1493B ALA* 4.6 8.7 - - + +
1496B PHE* 3.5 22.6 - - + -
1520B LEU* 4.1 8.3 - - + +
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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