Contacts of the helix formed by residues 1513 - 1528 (chain F) 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 ASP1513 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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712F VAL* 5.0 1.6 - - - +
713F GLY 2.8 29.5 + - - +
714F GLN* 3.1 8.8 - - - +
715F VAL* 3.1 31.2 + - - +
719F LYS* 4.1 4.1 + - - -
889F HIS* 3.6 32.0 + - + +
1511F SER 4.3 0.2 + - - -
1512F ILE* 1.3 74.5 - - - +
1514F MET* 1.3 54.0 + - - +
1515F ALA* 4.3 5.6 - - + +
1516F THR* 3.0 17.8 + - + +
1517F GLU* 2.6 36.0 + - - +
2501F ADP 5.0 0.5 + - - -
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Residues in contact with MET1514 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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889F HIS* 4.0 26.4 - - + +
890F LYS* 4.4 22.4 - - - +
891F LEU* 4.4 20.2 - - + +
894F LEU* 6.2 0.9 - - + -
1512F ILE 3.5 0.8 + - - -
1513F ASP* 1.3 70.5 - - - +
1515F ALA* 1.3 63.2 + - - +
1517F GLU* 3.9 4.0 - - - -
1518F ASN* 2.9 36.7 + - - +
1539F ARG* 3.3 39.7 - - - +
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Residues in contact with ALA1515 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714F GLN* 4.4 19.3 - - - +
1513F ASP* 3.2 2.8 - - + +
1514F MET* 1.3 80.4 - - - +
1516F THR* 1.3 61.9 + - + +
1518F ASN* 4.0 7.0 + - - +
1519F ILE* 3.7 18.0 + - - +
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Residues in contact with THR1516 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714F GLN* 3.6 36.1 - - + +
715F VAL* 4.8 6.6 - - + +
1512F ILE* 3.2 16.3 - - - +
1513F ASP* 3.0 20.1 + - + +
1515F ALA* 1.3 75.5 - - - +
1517F GLU* 1.3 59.9 + - - +
1519F ILE* 3.2 15.8 - - + +
1520F LEU* 2.9 31.4 + - - +
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Residues in contact with GLU1517 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1508F ALA* 3.6 4.4 - - - +
1509F THR* 3.5 38.2 + - + -
1512F ILE* 3.5 36.4 - - + +
1513F ASP 2.6 24.1 + - - +
1514F MET* 3.1 9.6 + - - +
1516F THR* 1.3 72.0 + - - +
1518F ASN* 1.3 62.0 + - - +
1520F LEU* 3.3 8.2 + - - +
1521F GLN* 2.9 58.5 + - + +
1539F ARG* 4.6 6.1 - - - +
1542F THR* 4.4 6.2 - - + +
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Residues in contact with ASN1518 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1514F MET* 2.9 28.0 + - - +
1515F ALA* 4.4 5.6 - - - +
1516F THR 3.4 0.2 - - - -
1517F GLU* 1.3 79.2 - - - +
1519F ILE* 1.3 61.0 + - + +
1521F GLN* 3.3 5.1 + - - +
1522F LYS* 3.0 35.8 + - - +
1539F ARG* 5.5 5.7 - - - +
1541F HIS* 3.5 37.0 + - + +
1542F THR* 5.2 8.3 - - - +
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Residues in contact with ILE1519 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1459F GLN* 3.6 29.8 - - + +
1515F ALA 3.7 15.0 + - - +
1516F THR* 3.2 21.5 - - + +
1518F ASN* 1.3 77.2 - - + +
1520F LEU* 1.3 63.1 + - - +
1522F LYS* 3.3 15.3 + - - +
1523F VAL* 2.9 38.2 + - + +
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Residues in contact with LEU1520 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1457F ILE 4.7 2.9 - - - +
1458F ALA* 4.1 17.0 - - - +
1459F GLN* 3.8 26.9 - - + -
1489F LEU* 4.3 8.3 - - + -
1492F LEU* 3.8 24.9 - - + -
1496F PHE* 5.2 5.2 - - + -
1508F ALA* 6.3 0.2 - - + -
1512F ILE* 3.7 33.9 - - + -
1516F THR* 2.9 19.4 + - - +
1517F GLU* 3.6 12.6 - - - +
1518F ASN 3.3 0.2 - - - -
1519F ILE* 1.3 82.2 - - - +
1521F GLN* 1.3 58.4 + - + +
1523F VAL* 3.4 2.7 + - + +
1524F VAL* 2.9 30.4 + - + +
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Residues in contact with GLN1521 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1505F MET* 3.0 36.6 - - - +
1508F ALA* 4.8 3.0 - - - +
1509F THR* 5.5 1.4 + - - -
1517F GLU* 2.9 39.9 + - - +
1518F ASN* 3.8 4.9 - - - +
1520F LEU* 1.3 74.3 - - + +
1522F LYS* 1.3 61.2 + - - +
1524F VAL* 3.2 12.4 - - - +
1525F MET* 2.9 65.5 + - + +
1535F THR* 5.3 1.5 - - - +
1542F THR* 3.8 25.3 - - + +
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Residues in contact with LYS1522 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1518F ASN* 3.0 24.0 + - - +
1519F ILE* 3.6 15.7 - - - +
1521F GLN* 1.3 77.0 - - - +
1523F VAL* 1.3 59.1 + - + +
1525F MET* 3.3 7.0 + - - +
1526F THR* 3.0 42.3 + - + +
1541F HIS* 6.2 1.6 - - - -
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Residues in contact with VAL1523 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1457F ILE* 3.7 34.3 - - + +
1459F GLN* 4.4 17.0 - - - +
1519F ILE* 2.9 25.0 + - + +
1520F LEU* 3.9 5.6 - - + +
1522F LYS* 1.3 79.1 - - + +
1524F VAL* 1.3 57.5 + - - +
1526F THR* 2.8 21.8 + - - +
1527F ALA* 2.9 17.3 + - + +
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Residues in contact with VAL1524 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1492F LEU* 5.6 4.7 - - + -
1496F PHE* 3.5 37.7 - - + -
1505F MET* 4.7 14.1 - - + -
1520F LEU* 2.9 15.6 + - + +
1521F GLN* 3.2 46.9 - - - +
1523F VAL* 1.3 77.4 - - - +
1525F MET* 1.3 62.6 + - + +
1527F ALA* 3.9 4.3 - - - -
1528F PHE* 3.2 36.2 + - + +
1533F VAL* 6.0 0.3 - - - +
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Residues in contact with MET1525 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1374F LYS* 4.3 37.4 + - + -
1505F MET* 5.8 0.7 - - + -
1521F GLN* 2.9 42.8 + - + +
1522F LYS* 3.7 5.8 - - - +
1524F VAL* 1.3 81.5 - - + +
1526F THR* 1.3 65.9 + - + +
1527F ALA 3.2 0.4 + - - -
1528F PHE 3.5 19.2 - - - +
1529F ALA* 3.6 6.9 + - - +
1533F VAL* 5.3 10.3 - - + -
1535F THR* 4.7 17.3 - - + -
1542F THR 6.0 2.0 - - - +
1545F SER* 5.7 7.9 - - - +
1546F ALA* 6.5 0.9 - - + -
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Residues in contact with THR1526 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1522F LYS* 3.0 28.3 + - + +
1523F VAL* 2.8 26.9 + - - +
1525F MET* 1.3 76.2 - - + +
1527F ALA* 1.3 59.7 + - - +
1529F ALA* 4.2 11.4 - - - +
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Residues in contact with ALA1527 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1457F ILE* 4.2 25.4 - - + -
1523F VAL* 2.9 18.2 + - + +
1524F VAL* 4.2 4.5 - - - +
1526F THR* 1.3 80.2 + - - +
1528F PHE* 1.3 74.9 + - + +
1529F ALA* 3.3 5.2 + - - +
1531F ARG* 5.3 3.8 + - - -
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Residues in contact with PHE1528 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1374F LYS* 2.5 28.8 + - - +
1496F PHE* 3.3 66.2 - + + -
1503F PHE* 3.4 29.2 - + - -
1524F VAL* 3.2 31.4 + - + +
1525F MET* 3.5 8.0 - - - +
1527F ALA* 1.3 83.8 - - + +
1529F ALA* 1.3 52.1 + - - +
1530F ASP 3.7 1.3 - - - -
1531F ARG* 3.3 49.1 - - + +
1533F VAL* 4.5 10.9 - - + +
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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