Contacts of the helix formed by residues 1445 - 1453 (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 ILE1445 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1443B LEU 4.1 2.0 + - - -
1444B GLU* 1.3 76.7 - - - +
1446B GLN* 1.3 58.3 + - - +
1447B ALA* 3.1 14.6 - - + +
1448B THR* 2.7 50.3 + - - +
1449B TRP 3.4 3.6 + - - -
1463B TYR* 4.7 1.6 - - + -
1466B LYS* 4.0 41.7 - - + +
1475B GLU* 5.4 9.2 - - + +
1476B LEU* 3.9 22.4 - - + -
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Residues in contact with GLN1446 (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 MET* 5.7 6.7 - - + +
1444B GLU* 3.9 27.5 + - + +
1445B ILE* 1.3 72.9 - - - +
1447B ALA* 1.3 58.5 + - - +
1448B THR 3.4 0.2 - - - -
1449B TRP* 3.6 8.6 + - + +
1450B TYR* 3.0 54.1 + - + -
1462B ALA* 4.8 2.7 - - + -
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Residues in contact with ALA1447 (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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1445B ILE* 3.0 6.7 + - + +
1446B GLN* 1.3 76.6 - - - +
1448B THR* 1.3 58.7 + - - +
1450B TYR* 3.5 3.5 + - - -
1451B GLU* 2.8 28.8 + - - +
1459B ALA* 3.6 13.3 - - - +
1462B ALA* 3.7 21.2 + - + +
1463B TYR* 3.5 46.3 - - + +
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Residues in contact with THR1448 (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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1443B LEU* 4.8 11.9 - - + +
1445B ILE* 2.7 45.0 + - - +
1447B ALA* 1.3 69.9 - - - +
1449B TRP* 1.3 57.3 + - - -
1451B GLU* 3.5 7.7 + - + +
1452B LYS* 3.1 55.3 + - + +
1463B TYR* 3.6 17.0 + - - +
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Residues in contact with TRP1449 (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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1433B LEU* 3.8 31.4 - - + +
1436B ALA* 4.0 19.3 - - + -
1437B MET* 3.7 43.5 - - + +
1440B PHE 3.7 19.3 - - - -
1441B GLY* 4.4 4.2 - - - -
1443B LEU* 3.3 35.7 - - + -
1444B GLU* 3.5 47.8 + - + +
1445B ILE 3.4 3.9 + - - -
1446B GLN* 3.9 9.4 - - - +
1447B ALA 3.3 0.4 - - - -
1448B THR* 1.3 75.3 - - - +
1450B TYR* 1.3 59.7 + - - +
1452B LYS* 3.4 22.2 + - + +
1453B LEU* 3.1 34.8 + - - +
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Residues in contact with TYR1450 (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 MET* 4.9 14.5 - - + +
1446B GLN* 3.0 46.6 + - + +
1447B ALA 3.8 0.2 - - - +
1448B THR 3.5 0.2 - - - -
1449B TRP* 1.3 76.4 - - - +
1451B GLU* 1.3 59.0 + - - +
1453B LEU* 3.8 12.7 + - + -
1454B HIS 3.7 1.4 + - - -
1455B GLU* 2.9 63.5 + - + +
1458B ASP* 4.1 16.4 - - + -
1459B ALA* 3.7 17.0 - - + +
1462B ALA* 4.1 19.7 - - + -
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Residues in contact with GLU1451 (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 ALA 2.8 17.0 + - - +
1448B THR* 3.6 11.9 + - + +
1449B TRP 3.2 0.2 - - - -
1450B TYR* 1.3 75.2 - - - +
1452B LYS* 1.3 66.7 - - + +
1453B LEU 3.2 0.2 - - - -
1454B HIS* 3.2 12.6 + - - -
1456B TRP* 3.8 34.3 - - + -
1459B ALA* 3.8 8.7 - - + +
1463B TYR* 2.7 30.1 + - - +
1479B GLY 4.5 5.6 - - - -
1482B ARG* 3.1 48.7 + - - +
1483B CYS* 5.1 0.7 - - - -
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Residues in contact with LYS1452 (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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1433B LEU* 3.7 27.0 - - + +
1443B LEU* 3.2 39.4 + - - +
1448B THR* 3.1 38.5 + - + +
1449B TRP* 3.4 22.5 + - + +
1451B GLU* 1.3 77.4 - - + +
1453B LEU* 1.3 57.5 + - - +
1454B HIS* 3.3 15.7 + - - -
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Residues in contact with LEU1453 (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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1430B ALA* 4.7 10.5 - - + +
1433B LEU* 3.6 25.4 - - + -
1434B GLU* 3.3 31.0 - - + +
1437B MET* 3.8 21.8 - - - -
1449B TRP 3.1 21.9 + - - +
1450B TYR* 4.1 19.3 - - + +
1451B GLU 3.2 0.4 - - - -
1452B LYS* 1.3 75.5 - - - +
1454B HIS* 1.3 72.3 + - - +
1455B GLU* 3.4 20.1 + - + +
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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