Contacts of the helix formed by residues 1519 - 1530 (chain A) in PDB entry 3PZD
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1516A ASN* 3.0 20.0 + - + +
1517A CYS 4.8 0.4 - - - -
1518A LEU* 1.3 77.0 - - - +
1520A SER* 1.3 65.9 + - - +
1521A ASP* 3.4 22.3 + - - +
1522A VAL* 3.2 30.2 + - + +
1523A VAL* 3.2 20.3 + - - +
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Residues in contact with SER1520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1517A CYS 5.2 1.5 + - - -
1518A LEU 3.7 5.5 + - - -
1519A ASN* 1.3 73.1 + - - +
1521A ASP* 1.3 69.8 + - - +
1523A VAL* 3.4 1.8 + - - -
1524A GLU* 3.1 25.2 + - - +
1655A ARG* 3.6 26.2 + - - +
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Residues in contact with ASP1521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1519A ASN* 3.3 10.5 - - - +
1520A SER* 1.3 81.7 + - - +
1522A VAL* 1.3 58.1 + - + +
1524A GLU* 3.3 8.8 + - - +
1525A GLN* 2.9 30.6 + - - +
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Residues in contact with VAL1522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1516A ASN* 3.7 32.5 - - + +
1519A ASN* 3.2 36.5 + - + +
1521A ASP* 1.3 75.1 - - + +
1523A VAL* 1.3 61.7 + - - +
1525A GLN* 3.1 8.1 + - + +
1526A ILE* 2.9 40.1 + - + +
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Residues in contact with VAL1523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1513A ILE* 4.4 13.7 - - + +
1516A ASN* 3.2 28.0 - - + +
1517A CYS* 3.9 16.2 - - - +
1519A ASN 3.2 6.1 + - - +
1520A SER* 3.8 7.2 - - - +
1522A VAL* 1.3 76.2 - - - +
1524A GLU* 1.3 56.9 + - - +
1526A ILE* 3.4 9.5 + - - +
1527A TYR* 3.0 52.0 + - + -
1651A PHE* 4.0 15.3 - - + -
1655A ARG* 3.8 21.3 - - - +
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Residues in contact with GLU1524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1520A SER* 3.1 12.2 + - - +
1521A ASP* 3.4 12.1 - - - +
1523A VAL* 1.3 77.5 - - - +
1525A GLN* 1.3 57.9 + - - +
1527A TYR* 3.4 5.0 + - - +
1528A LYS* 2.9 29.6 + - - +
1616A LYS* 2.3 35.7 + - - +
1655A ARG* 2.6 35.0 + - - -
1659A GLN* 4.1 10.0 + - - +
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Residues in contact with GLN1525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1521A ASP 2.9 15.5 + - - +
1522A VAL* 3.1 10.7 + - + +
1524A GLU* 1.3 75.4 - - - +
1526A ILE* 1.3 58.3 + - + +
1528A LYS* 3.7 25.7 + - - +
1529A ARG* 2.9 95.1 + - - +
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Residues in contact with ILE1526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1509A LEU* 4.2 13.5 - - + +
1512A ASP* 4.1 32.5 - - + +
1513A ILE* 3.9 19.5 - - + +
1516A ASN* 4.4 3.4 - - + +
1522A VAL* 2.9 37.3 + - + +
1523A VAL* 3.6 11.4 - - - +
1525A GLN* 1.3 75.0 - - + +
1527A TYR* 1.3 63.0 + - - +
1529A ARG* 5.1 0.4 - - - -
1530A ASN* 2.8 41.5 + - - +
1533A LEU* 3.8 18.6 - - + -
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Residues in contact with TYR1527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1513A ILE* 3.5 17.9 - - + +
1523A VAL* 3.0 37.3 + - + +
1524A GLU* 3.7 4.9 - - - +
1526A ILE* 1.3 77.8 - - - +
1528A LYS* 1.3 61.2 + - - +
1530A ASN 3.5 8.8 + - - +
1533A LEU* 3.7 22.2 - - + -
1534A ARG* 2.8 25.2 + - + +
1615A ASN* 3.3 31.3 + - - +
1616A LYS* 3.8 32.3 - - + -
1648A TYR* 2.8 37.9 + - - -
1651A PHE* 3.9 8.7 - - - -
1652A HIS* 4.8 8.2 + - - +
1655A ARG* 4.3 15.6 - - - -
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Residues in contact with LYS1528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1524A GLU 2.9 18.3 + - - +
1525A GLN* 3.3 27.8 + - - +
1527A TYR* 1.3 78.5 - - - +
1529A ARG* 1.3 60.0 + - + +
1531A PRO* 4.3 1.0 - - - +
1534A ARG* 2.9 31.7 + - - +
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Residues in contact with ARG1529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1525A GLN* 2.9 55.0 + - - +
1526A ILE* 5.1 0.4 - - - +
1528A LYS* 1.3 77.8 - - + +
1530A ASN* 1.3 71.2 + - - +
1531A PRO* 3.4 10.5 - - - +
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Residues in contact with ASN1530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1509A LEU* 3.6 39.3 - - + +
1526A ILE* 2.8 32.1 + - - +
1527A TYR 3.5 6.8 + - - +
1528A LYS 3.3 0.8 - - - -
1529A ARG* 1.3 91.7 - - - +
1531A PRO* 1.3 55.1 - - - +
1532A ILE* 3.1 6.6 - - + +
1533A LEU* 2.8 45.5 + - + +
1534A ARG 4.3 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