Contacts of the helix formed by residues 1447 - 1458 (chain E) in PDB entry 6BAA
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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1445E LYS 3.5 3.6 + - - -
1446E CYS* 1.3 75.8 - - - +
1448E ASP* 1.3 59.7 + - - +
1449E SER* 3.8 7.5 + - - -
1450E THR* 3.1 26.0 + - - -
1451E LEU* 2.9 27.9 + - - +
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Residues in contact with ASP1448 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1437E ARG* 6.2 4.5 - - + -
1446E CYS 3.9 1.0 + - - -
1447E SER* 1.3 72.8 - - - +
1449E SER* 1.3 57.6 + - - +
1451E LEU* 3.6 7.0 - - - +
1452E TRP* 2.9 30.5 + - - +
1471E LEU* 5.9 7.6 - - + -
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Residues in contact with SER1449 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1447E SER* 3.2 7.9 + - - -
1448E ASP* 1.3 78.2 - - - +
1450E THR* 1.3 56.7 + - - +
1452E TRP* 3.4 8.6 + - - +
1453E GLU* 2.9 31.1 + - - +
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Residues in contact with THR1450 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1446E CYS* 5.2 4.9 - - - -
1447E SER* 3.1 25.6 + - - -
1449E SER* 1.3 78.0 - - - +
1451E LEU* 1.3 58.7 + - - +
1453E GLU* 3.6 6.4 - - - +
1454E ALA* 2.9 30.8 + - - +
1497E VAL* 4.7 7.5 - - - +
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Residues in contact with LEU1451 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1437E ARG* 5.4 6.1 - - + +
1440E LEU* 3.8 34.4 - - + +
1446E CYS* 5.4 4.4 - - + +
1447E SER 2.9 16.7 + - - +
1448E ASP* 3.6 9.2 - - - +
1450E THR* 1.3 77.5 - - - +
1452E TRP* 1.3 57.6 + - - +
1454E ALA* 3.3 7.9 + - - +
1455E LEU* 2.9 27.4 + - - +
1493E ALA* 5.3 0.7 - - - +
1497E VAL* 5.3 3.6 - - - -
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Residues in contact with TRP1452 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1448E ASP 2.9 17.3 + - - +
1449E SER* 3.9 8.1 - - - +
1451E LEU* 1.3 75.8 - - - +
1453E GLU* 1.3 64.4 + - + +
1455E LEU* 3.3 6.3 + - - +
1456E GLU* 2.9 29.3 + - + +
1461E LYS* 3.4 39.3 + - + +
1464E VAL* 5.0 7.2 - - + -
1465E LYS* 4.4 12.1 - - + +
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Residues in contact with GLU1453 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1449E SER 2.9 18.7 + - - +
1450E THR* 3.6 8.3 - - - +
1452E TRP* 1.3 80.5 - - + +
1454E ALA* 1.3 60.0 + - - +
1456E GLU* 3.1 10.3 + - - +
1457E ILE* 2.9 26.5 + - - +
1496E PHE* 4.5 6.6 - - + -
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Residues in contact with ALA1454 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1450E THR 2.9 21.3 + - - +
1451E LEU* 3.5 5.6 - - - +
1453E GLU* 1.3 72.9 - - - +
1455E LEU* 1.3 57.4 + - - +
1457E ILE* 3.3 3.5 + - - +
1458E ALA* 2.9 23.9 + - - +
1493E ALA* 3.3 36.4 - - + +
1496E PHE* 3.6 19.8 - - + -
1497E VAL* 3.7 15.0 - - + -
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Residues in contact with LEU1455 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1451E LEU 2.9 13.5 + - - +
1452E TRP* 3.5 11.9 - - - +
1453E GLU 3.3 0.2 - - - -
1454E ALA* 1.3 73.4 - - - +
1456E GLU* 1.3 58.1 + - - +
1458E ALA 3.2 0.4 - - - +
1459E GLN 2.9 6.2 + - - -
1460E LEU* 2.5 41.1 + - + -
1461E LYS* 2.9 20.1 + - - +
1464E VAL* 4.5 8.5 - - + -
1493E ALA* 3.8 13.4 - - + +
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Residues in contact with GLU1456 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1452E TRP* 2.9 21.8 + - + +
1453E GLU* 3.1 13.0 + - - +
1455E LEU* 1.3 74.8 - - - +
1457E ILE* 1.3 65.4 + - - +
1459E GLN* 3.1 13.7 + - - +
1461E LYS* 3.4 13.9 - - + +
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Residues in contact with ILE1457 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1453E GLU 2.9 8.3 + - - +
1454E ALA 3.5 7.6 - - - +
1456E GLU* 1.3 76.2 - - - +
1458E ALA* 1.3 57.2 + - - +
1459E GLN* 3.4 4.7 + - - +
1496E PHE* 3.6 45.3 - - + -
1523E VAL* 5.6 4.9 - - - +
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Residues in contact with ALA1458 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1454E ALA 2.9 11.7 + - - +
1455E LEU 3.2 1.3 - - - -
1457E ILE* 1.3 74.3 - - - +
1459E GLN* 1.3 56.6 + - - +
1460E LEU* 2.9 22.4 + - - +
1489E LEU* 3.4 34.6 - - - +
1492E LEU* 3.7 13.9 - - + +
1493E ALA* 3.4 19.7 - - + +
1496E PHE* 5.7 0.9 - - + -
1523E VAL* 6.1 4.3 - - + -
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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