Contacts of the helix formed by residues 1447 - 1458 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1445G LYS 3.5 4.1 + - - -
1446G CYS* 1.3 74.8 - - - +
1448G ASP* 1.3 59.0 + - - +
1449G SER* 3.8 7.6 + - - -
1450G THR* 3.1 26.4 + - - -
1451G LEU* 2.9 28.7 + - - +
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Residues in contact with ASP1448 (chain G).
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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1437G ARG* 6.2 5.2 - - + -
1446G CYS 3.9 1.0 + - - -
1447G SER* 1.3 72.8 - - - +
1449G SER* 1.3 56.8 + - - +
1451G LEU* 3.6 8.4 - - - +
1452G TRP* 2.9 30.7 + - - +
1471G LEU* 5.9 7.0 - - + -
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Residues in contact with SER1449 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1447G SER* 3.2 7.5 + - - -
1448G ASP* 1.3 79.2 - - - +
1450G THR* 1.3 57.5 + - - +
1452G TRP* 3.4 9.8 + - - +
1453G GLU* 2.9 31.1 + - - +
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Residues in contact with THR1450 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1446G CYS* 5.2 4.7 - - - -
1447G SER* 3.1 24.9 + - - -
1449G SER* 1.3 76.5 - - - +
1451G LEU* 1.3 57.7 + - - +
1453G GLU* 3.5 6.8 + - - +
1454G ALA* 2.9 30.9 + - - +
1497G VAL* 4.7 6.9 - - - +
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Residues in contact with LEU1451 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1437G ARG* 5.4 6.1 - - + +
1440G LEU* 3.8 35.7 - - + +
1446G CYS* 5.4 3.5 - - + +
1447G SER 2.9 16.9 + - - +
1448G ASP* 3.6 8.5 - - - +
1449G SER 3.3 0.2 - - - -
1450G THR* 1.3 77.7 - - - +
1452G TRP* 1.3 57.2 + - - +
1454G ALA* 3.3 7.5 + - - +
1455G LEU* 2.9 27.8 + - - +
1493G ALA* 5.3 1.0 - - - +
1497G VAL* 5.3 4.0 - - - -
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Residues in contact with TRP1452 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1448G ASP 2.9 17.8 + - - +
1449G SER* 3.9 7.9 - - - +
1451G LEU* 1.3 76.1 - - - +
1453G GLU* 1.3 65.7 + - + +
1455G LEU* 3.3 6.7 + - - +
1456G GLU* 2.9 29.8 + - + +
1461G LYS* 3.4 39.6 + - + +
1464G VAL* 5.0 7.2 - - + -
1465G LYS* 4.4 11.4 - - + +
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Residues in contact with GLU1453 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1449G SER 2.9 19.0 + - - +
1450G THR* 3.6 7.9 - - - +
1452G TRP* 1.3 81.6 - - + +
1454G ALA* 1.3 59.3 + - - +
1456G GLU* 3.1 9.8 + - - +
1457G ILE* 2.9 27.2 + - - +
1496G PHE* 4.5 6.6 - - + -
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Residues in contact with ALA1454 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1450G THR 2.9 22.1 + - - +
1451G LEU* 3.5 5.8 - - - +
1453G GLU* 1.3 72.5 - - - +
1455G LEU* 1.3 57.7 + - - +
1457G ILE* 3.3 3.1 + - - +
1458G ALA* 2.9 24.4 + - - +
1493G ALA* 3.3 36.5 - - + +
1496G PHE* 3.6 20.5 - - + -
1497G VAL* 3.7 14.6 - - + -
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Residues in contact with LEU1455 (chain G).
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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1451G LEU 2.9 13.4 + - - +
1452G TRP* 3.5 12.1 - - - +
1454G ALA* 1.3 74.3 - - - +
1456G GLU* 1.3 59.7 + - - +
1458G ALA 3.2 0.2 - - - -
1459G GLN 2.9 6.4 + - - -
1460G LEU* 2.5 40.9 + - + -
1461G LYS* 3.4 20.0 - - - +
1464G VAL* 4.5 8.5 - - + -
1493G ALA* 3.8 13.2 - - + +
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Residues in contact with GLU1456 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1452G TRP* 2.9 22.5 + - + +
1453G GLU* 3.1 13.4 + - - +
1455G LEU* 1.3 73.6 - - - +
1457G ILE* 1.3 65.4 + - - +
1459G GLN* 3.1 14.2 + - - +
1461G LYS* 3.4 14.3 - - + +
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Residues in contact with ILE1457 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1453G GLU 2.9 7.3 + - - +
1454G ALA 3.5 7.6 - - - +
1456G GLU* 1.3 76.2 - - - +
1458G ALA* 1.3 57.7 + - - +
1459G GLN* 3.4 4.2 + - - +
1496G PHE* 3.6 45.8 - - + -
1523G VAL* 5.6 5.0 - - - +
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Residues in contact with ALA1458 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1454G ALA 2.9 12.7 + - - +
1455G LEU 3.2 1.8 - - - -
1457G ILE* 1.3 74.7 - - + +
1459G GLN* 1.3 56.7 + - - +
1460G LEU* 2.9 22.4 + - - +
1489G LEU* 3.4 34.8 - - - +
1492G LEU* 3.7 13.7 - - + +
1493G ALA* 3.4 19.7 - - + +
1496G PHE* 5.7 0.9 - - + -
1523G VAL* 6.1 3.6 - - - -
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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