Contacts of the helix formed by residues 1513 - 1528 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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712B VAL* 5.0 1.4 - - - +
713B GLY 2.8 30.4 + - - +
714B GLN* 3.1 9.9 - - - +
715B VAL* 3.1 30.8 + - - +
719B LYS* 4.1 4.6 + - - -
889B HIS* 3.6 31.7 + - + +
1512B ILE* 1.3 73.5 - - - +
1514B MET* 1.3 55.0 + - - +
1515B ALA* 3.2 5.2 - - + +
1516B THR* 3.0 19.3 + - + +
1517B GLU* 2.6 35.3 + - - +
2501B ADP 5.0 0.3 + - - -
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Residues in contact with MET1514 (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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889B HIS* 4.0 26.9 - - + +
890B LYS* 4.4 22.7 - - - +
891B LEU* 4.4 20.2 - - + -
894B LEU* 6.2 1.3 - - + -
1512B ILE 3.5 0.6 + - - -
1513B ASP* 1.3 72.8 - - - +
1515B ALA* 1.3 63.2 + - - +
1517B GLU* 3.9 3.8 - - - -
1518B ASN* 2.9 38.2 + - - +
1539B ARG* 3.3 41.1 - - - +
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Residues in contact with ALA1515 (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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714B GLN* 4.4 19.7 - - - +
1513B ASP* 3.2 2.1 - - + +
1514B MET* 1.3 79.9 - - - +
1516B THR* 1.3 62.1 + - + +
1518B ASN* 4.0 7.0 + - - +
1519B ILE* 3.7 17.7 + - - +
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Residues in contact with THR1516 (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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714B GLN* 3.6 35.4 - - + +
715B VAL* 4.8 5.8 - - + +
1512B ILE* 3.2 16.2 - - - +
1513B ASP* 3.0 20.3 + - + +
1515B ALA* 1.3 75.9 - - + +
1517B GLU* 1.3 59.7 + - - +
1519B ILE* 3.2 14.1 - - + +
1520B LEU* 2.9 31.0 + - - +
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Residues in contact with GLU1517 (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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1508B ALA* 3.6 4.4 - - - +
1509B THR* 3.5 38.4 + - + -
1512B ILE* 3.5 36.1 - - + +
1513B ASP 2.6 22.8 + - - +
1514B MET* 3.7 9.6 - - - +
1516B THR* 1.3 71.4 + - - +
1518B ASN* 1.3 62.6 + - - +
1520B LEU* 3.3 8.7 + - - +
1521B GLN* 2.9 58.5 + - + +
1539B ARG* 4.6 5.8 - - - +
1542B THR* 4.4 6.0 - - + +
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Residues in contact with ASN1518 (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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1514B MET* 2.9 28.5 + - - +
1515B ALA* 4.4 5.4 - - - +
1517B GLU* 1.3 80.2 - - - +
1519B ILE* 1.3 60.8 + - + +
1521B GLN* 3.3 4.7 + - - +
1522B LYS* 3.0 34.9 + - - +
1539B ARG* 5.5 5.5 - - - +
1541B HIS* 3.5 36.4 + - + +
1542B THR* 5.2 8.3 - - - +
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Residues in contact with ILE1519 (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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1459B GLN* 3.6 29.8 - - + +
1515B ALA 3.7 14.8 + - - +
1516B THR* 3.2 21.1 - - - +
1518B ASN* 1.3 76.0 - - + +
1520B LEU* 1.3 62.2 + - - +
1522B LYS* 3.3 16.7 + - - +
1523B VAL* 2.9 38.1 + - + +
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Residues in contact with LEU1520 (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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1457B ILE 4.7 2.9 - - - +
1458B ALA* 4.1 17.0 - - - +
1459B GLN* 3.8 27.4 - - + -
1489B LEU* 4.3 8.7 - - + -
1492B LEU* 3.8 24.9 - - + -
1496B PHE* 5.2 5.2 - - + -
1508B ALA* 6.3 0.2 - - + -
1512B ILE* 3.7 33.9 - - + -
1516B THR* 2.9 19.6 + - - +
1517B GLU* 3.6 12.3 - - - +
1518B ASN 3.3 0.2 - - - -
1519B ILE* 1.3 81.4 - - - +
1521B GLN* 1.3 60.0 + - + +
1523B VAL* 3.4 2.8 + - + +
1524B VAL* 2.9 30.0 + - + +
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Residues in contact with GLN1521 (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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1505B MET* 3.0 37.4 - - - +
1508B ALA* 4.8 2.6 - - - +
1509B THR* 5.5 1.2 + - - -
1517B GLU* 2.9 40.8 + - - +
1518B ASN* 3.8 4.7 - - - +
1520B LEU* 1.3 74.1 - - + +
1522B LYS* 1.3 60.7 + - - +
1524B VAL* 3.2 12.5 - - - +
1525B MET* 2.9 65.7 + - + +
1535B THR* 5.3 1.5 - - - +
1542B THR* 3.8 25.3 - - + +
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Residues in contact with LYS1522 (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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1518B ASN* 3.0 24.7 + - - +
1519B ILE* 3.3 15.0 + - - +
1521B GLN* 1.3 77.7 - - - +
1523B VAL* 1.3 60.3 + - + +
1525B MET* 3.3 6.8 + - - +
1526B THR* 3.0 43.4 + - + +
1541B HIS* 6.2 1.8 - - - -
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Residues in contact with VAL1523 (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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1457B ILE* 3.7 34.8 - - + +
1459B GLN* 4.4 17.9 - - + +
1519B ILE* 2.9 26.5 + - + +
1520B LEU* 3.9 5.2 - - + +
1522B LYS* 1.3 80.2 - - + +
1524B VAL* 1.3 58.4 + - - +
1526B THR* 2.8 21.9 + - - +
1527B ALA* 2.9 17.5 + - + +
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Residues in contact with VAL1524 (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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1492B LEU* 5.6 4.9 - - + -
1496B PHE* 3.5 37.9 - - + -
1505B MET* 4.7 14.6 - - + -
1520B LEU* 2.9 16.0 + - + +
1521B GLN* 3.2 46.4 - - - +
1523B VAL* 1.3 77.4 - - - +
1525B MET* 1.3 63.5 + - + +
1527B ALA* 3.9 4.3 - - - -
1528B PHE* 3.2 37.5 + - + +
1533B VAL* 6.0 0.3 - - - +
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Residues in contact with MET1525 (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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1374B LYS* 4.3 39.2 + - + -
1505B MET* 5.8 0.7 - - + -
1521B GLN* 2.9 42.3 + - + +
1522B LYS* 3.7 6.5 - - - +
1524B VAL* 1.3 81.1 - - + +
1526B THR* 1.3 64.6 + - + +
1527B ALA 3.2 0.6 + - - -
1528B PHE 3.5 18.8 - - - +
1529B ALA* 3.6 7.3 + - - +
1533B VAL* 5.3 9.9 - - + -
1535B THR* 4.7 17.5 - - + -
1542B THR 6.0 1.8 - - - +
1545B SER* 5.7 8.3 - - - +
1546B ALA* 6.5 0.9 - - + -
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Residues in contact with THR1526 (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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1522B LYS* 3.0 28.8 + - + +
1523B VAL* 2.8 27.7 + - - +
1525B MET* 1.3 76.8 - - + +
1527B ALA* 1.3 61.0 + - - +
1529B ALA* 4.2 10.9 - - - +
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Residues in contact with ALA1527 (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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1457B ILE* 4.2 25.4 - - + -
1523B VAL* 2.9 17.8 + - + +
1524B VAL* 4.2 3.8 - - - +
1526B THR* 1.3 81.5 + - - +
1528B PHE* 1.3 74.7 + - + +
1529B ALA* 3.3 5.5 + - - +
1531B ARG* 5.3 4.2 + - - -
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Residues in contact with PHE1528 (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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1374B LYS* 2.5 29.1 + - - +
1496B PHE* 3.3 66.6 - + + -
1503B PHE* 3.4 27.8 - + - -
1524B VAL* 3.2 33.3 + - + +
1525B MET* 3.5 8.1 - - - +
1527B ALA* 1.3 83.2 - - + +
1529B ALA* 1.3 53.1 + - - +
1530B ASP 3.7 0.7 - - - -
1531B ARG* 3.3 50.2 - - + +
1533B VAL* 4.5 12.7 - - + +
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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