Contacts of the helix formed by residues 1513 - 1529 (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 ASP1513 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1511G SER* 5.0 2.5 - - - -
1512G ILE* 1.3 81.4 + - - +
1514G MET* 1.3 62.1 + - - +
1515G ALA* 4.2 2.9 - - + +
1516G THR* 3.6 23.6 - - - +
1517G GLU* 3.2 23.8 - - - +
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Residues in contact with MET1514 (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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1513G ASP* 1.3 74.7 - - - +
1515G ALA* 1.3 60.4 + - - +
1516G THR 3.2 0.2 - - - -
1517G GLU* 4.4 1.1 - - - +
1518G ASN* 3.0 33.3 + - - +
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Residues in contact with ALA1515 (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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1513G ASP* 4.2 2.4 - - + +
1514G MET* 1.3 79.3 - - - +
1516G THR* 1.3 57.4 + - - +
1518G ASN* 3.9 4.3 - - - +
1519G ILE* 2.9 29.3 + - - +
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Residues in contact with THR1516 (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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1485G GLY* 5.6 8.5 - - - -
1512G ILE* 4.2 13.9 - - - -
1513G ASP* 3.6 21.2 - - - +
1514G MET 3.2 0.6 - - - -
1515G ALA* 1.3 79.6 - - - +
1517G GLU* 1.3 61.1 + - - +
1519G ILE* 3.7 5.3 - - - +
1520G LEU* 2.8 30.3 + - - +
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Residues in contact with GLU1517 (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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1511G SER* 6.5 0.4 - - - -
1512G ILE* 4.5 9.3 - - + +
1513G ASP 3.2 25.1 + - - +
1514G MET* 4.4 0.9 - - - +
1516G THR* 1.3 77.3 - - - +
1518G ASN* 1.3 58.3 + - - +
1520G LEU* 3.6 6.9 - - - +
1521G GLN* 2.9 31.2 + - - +
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Residues in contact with ASN1518 (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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1514G MET 3.0 22.4 + - - +
1515G ALA* 3.9 5.4 - - - +
1517G GLU* 1.3 74.0 - - - +
1519G ILE* 1.3 58.5 + - - +
1521G GLN* 3.5 6.9 + - - +
1522G LYS* 2.9 28.5 + - - +
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Residues in contact with ILE1519 (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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1459G GLN* 6.5 1.3 - - + -
1515G ALA 2.9 20.5 + - - +
1516G THR* 3.7 6.5 - - - +
1518G ASN* 1.3 73.6 - - - +
1520G LEU* 1.3 57.7 + - - +
1522G LYS* 3.2 7.0 + - - +
1523G VAL* 2.8 35.9 + - - +
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Residues in contact with LEU1520 (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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1516G THR 2.8 21.9 + - - +
1517G GLU* 3.6 8.1 - - - +
1519G ILE* 1.3 71.7 - - - +
1521G GLN* 1.3 53.2 + - - +
1523G VAL* 3.4 7.4 + - - +
1524G VAL* 2.8 34.4 + - - +
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Residues in contact with GLN1521 (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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1517G GLU 2.9 18.3 + - - +
1518G ASN* 3.7 7.4 - - - +
1520G LEU* 1.3 73.9 - - - +
1522G LYS* 1.3 59.8 + - - +
1524G VAL* 3.5 7.6 - - - +
1525G MET* 2.8 29.3 + - - +
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Residues in contact with LYS1522 (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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1518G ASN 2.9 18.6 + - - +
1519G ILE* 3.2 8.7 + - - +
1521G GLN* 1.3 74.7 - - - +
1523G VAL* 1.3 58.4 + - - +
1525G MET* 3.3 7.0 + - - +
1526G THR* 2.9 29.9 + - - -
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Residues in contact with VAL1523 (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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1458G ALA* 6.1 5.2 - - - -
1492G LEU* 5.7 9.4 - - + -
1519G ILE 2.8 20.0 + - - +
1520G LEU* 3.6 7.9 - - - +
1522G LYS* 1.3 69.3 - - - +
1524G VAL* 1.3 57.3 + - - +
1526G THR* 3.8 5.9 - - - +
1527G ALA* 2.8 36.7 + - - +
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Residues in contact with VAL1524 (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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1520G LEU 2.8 21.1 + - - +
1521G GLN* 3.5 9.2 - - - +
1523G VAL* 1.3 74.3 - - - +
1525G MET* 1.3 57.6 + - - +
1527G ALA* 3.8 5.5 - - - +
1528G PHE* 2.8 34.5 + - - +
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Residues in contact with MET1525 (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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1521G GLN 2.8 20.5 + - - +
1522G LYS* 3.3 8.5 + - - +
1524G VAL* 1.3 74.4 - - - +
1526G THR* 1.3 61.5 + - - +
1528G PHE* 3.9 3.3 - - - +
1529G ALA* 3.1 22.3 + - - +
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Residues in contact with THR1526 (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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1522G LYS 2.9 16.9 + - - -
1523G VAL* 3.9 5.2 - - - -
1525G MET* 1.3 72.8 - - - +
1527G ALA* 1.3 66.2 + - - +
1529G ALA* 3.4 21.7 + - - +
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Residues in contact with ALA1527 (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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1523G VAL 2.8 23.8 + - - +
1524G VAL* 3.8 5.8 - - - +
1526G THR* 1.3 73.6 - - - +
1528G PHE* 1.3 60.7 + - - +
1529G ALA 3.3 3.8 + - - +
1531G ARG* 3.2 38.9 - - - +
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Residues in contact with PHE1528 (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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1372G GLY 2.9 17.9 - - - +
1374G LYS* 3.8 29.6 - - + +
1524G VAL 2.8 23.2 + - - +
1525G MET* 4.2 4.0 - - - +
1527G ALA* 1.3 70.2 - - - +
1529G ALA* 1.3 63.1 + - - +
1530G ASP 3.1 0.2 + - - -
1531G ARG* 2.8 24.7 - - - +
1533G VAL* 3.8 18.8 - - + -
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Residues in contact with ALA1529 (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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1372G GLY 4.6 1.8 - - - -
1525G MET 3.1 13.9 + - - +
1526G THR* 3.4 17.6 - - - +
1527G ALA 3.2 8.2 - - - +
1528G PHE* 1.3 75.0 - - - +
1530G ASP* 1.3 64.0 + - - +
1531G ARG* 3.2 7.5 + - - +
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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