Contacts of the helix formed by residues 1519 - 1530 (chain B) in PDB entry 3AU5
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 ASN1519 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1516B ASN* 2.8 24.3 + - + +
1517B CYS 3.8 2.7 - - - +
1518B LEU* 1.3 79.9 - - - +
1520B SER* 1.3 59.1 + - - +
1521B ASP* 2.9 12.6 + - - +
1522B VAL* 2.8 51.9 + - + +
1523B VAL* 3.3 7.4 - - - +
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Residues in contact with SER1520 (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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1517B CYS 5.4 0.4 - - - -
1518B LEU 3.8 4.6 + - - -
1519B ASN* 1.3 72.7 + - - +
1521B ASP* 1.3 68.1 + - - +
1523B VAL* 3.2 5.9 + - - +
1524B GLU* 2.8 38.8 + - - +
1655B ARG* 6.2 2.2 - - - +
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Residues in contact with ASP1521 (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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1519B ASN* 2.9 8.1 + - - +
1520B SER* 1.3 82.7 - - - +
1522B VAL* 1.3 58.4 + - - +
1524B GLU* 3.2 8.9 + - - +
1525B GLN* 2.8 31.2 + - - +
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Residues in contact with VAL1522 (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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1516B ASN* 3.2 47.1 - - + +
1519B ASN* 2.8 48.8 + - + +
1521B ASP* 1.3 72.0 - - - +
1523B VAL* 1.3 66.8 + - - +
1525B GLN* 2.8 9.7 + - - +
1526B ILE* 2.8 41.3 + - + +
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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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1513B ILE* 3.5 38.4 - - + +
1516B ASN* 3.3 29.8 - - + +
1517B CYS* 4.3 5.2 - - - +
1519B ASN 3.3 6.5 - - - +
1520B SER* 3.2 7.1 + - - +
1522B VAL* 1.3 82.4 - - + +
1524B GLU* 1.3 61.0 + - - +
1526B ILE* 3.0 10.5 + - - +
1527B TYR* 3.0 46.0 + - + -
1651B PHE* 3.9 15.3 - - + -
1655B ARG* 5.2 2.5 - - - +
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Residues in contact with GLU1524 (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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1520B SER* 2.8 31.5 + - - +
1521B ASP* 3.5 9.0 - - - +
1523B VAL* 1.3 73.5 - - - +
1525B GLN* 1.3 58.3 + - - +
1527B TYR* 4.0 7.1 - - - +
1528B LYS* 3.5 22.3 + - - +
1616B LYS* 3.5 21.4 + - - -
1655B ARG* 2.6 41.3 + - - +
1659B GLN* 5.2 2.2 - - - -
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Residues in contact with GLN1525 (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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1521B ASP 2.8 12.3 + - - +
1522B VAL* 2.8 13.9 + - - +
1524B GLU* 1.3 76.3 - - - +
1526B ILE* 1.3 57.2 + - + +
1527B TYR 3.2 0.4 - - - -
1528B LYS* 4.0 5.7 - - - +
1529B ARG* 2.7 39.2 + - + +
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Residues in contact with ILE1526 (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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1509B LEU* 3.9 26.9 - - + +
1512B ASP* 3.9 24.2 - - + +
1513B ILE* 3.7 29.8 - - + -
1516B ASN* 4.9 0.4 - - - +
1522B VAL* 2.8 39.8 + - + +
1523B VAL* 3.0 15.5 + - + +
1525B GLN* 1.3 78.7 - - + +
1527B TYR* 1.3 59.4 + - - +
1529B ARG* 4.1 1.3 - - - -
1530B ASN* 3.2 26.7 + - - +
1533B LEU* 3.6 7.7 - - + +
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Residues in contact with TYR1527 (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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1513B ILE* 3.2 22.2 - - + -
1523B VAL* 3.0 27.0 + - + +
1524B GLU* 4.2 8.7 - - - +
1526B ILE* 1.3 76.3 - - - +
1528B LYS* 1.3 59.0 + - - +
1530B ASN 3.0 15.0 - - - +
1533B LEU* 3.9 17.7 - - + -
1534B ARG* 2.7 31.4 + - - -
1615B ASN* 3.7 32.5 - - - +
1616B LYS* 4.3 12.1 - - + -
1648B TYR* 2.6 43.4 + - - -
1651B PHE* 3.5 9.9 - - - -
1652B HIS* 4.8 6.9 + - - -
1655B ARG* 3.8 32.2 + - - -
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Residues in contact with LYS1528 (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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1524B GLU 3.5 17.5 + - - +
1525B GLN* 3.5 5.8 + - - +
1527B TYR* 1.3 79.0 - - - +
1529B ARG* 1.3 65.8 + - - +
1531B PRO* 4.5 1.0 - - - +
1534B ARG* 3.2 29.9 + - - +
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Residues in contact with ARG1529 (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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1525B GLN* 2.7 26.0 + - + +
1526B ILE* 4.4 0.9 - - - -
1528B LYS* 1.3 77.8 - - - +
1530B ASN* 1.3 73.6 + - - +
1531B PRO* 3.3 10.9 - - - +
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Residues in contact with ASN1530 (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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1509B LEU* 3.2 48.4 - - + +
1526B ILE* 3.2 22.5 + - - +
1527B TYR 3.0 14.7 - - - +
1528B LYS 3.3 0.4 - - - -
1529B ARG* 1.3 92.2 - - - +
1531B PRO* 1.3 68.1 - - - +
1532B ILE* 3.3 4.9 - - + -
1533B LEU* 3.2 15.6 + - + +
1534B ARG* 4.2 0.5 + - - -
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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