Contacts of the helix formed by residues 1504 - 1515 (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 THR1504 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1503A ASP* 1.3 76.7 - - - +
1505A PRO* 1.3 75.3 - - + +
1506A THR 3.2 0.7 + - - -
1507A GLN* 2.9 31.0 + - - +
1508A GLN* 3.1 19.9 + - - +
1543A PRO 5.1 3.6 - - - +
1544A LEU 2.8 29.5 + - - +
1545A LEU 3.9 2.7 - - - -
1546A PRO* 3.7 28.0 - - + -
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Residues in contact with PRO1505 (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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1503A ASP 4.4 1.3 - - - +
1504A THR* 1.3 90.2 - - + +
1506A THR* 1.3 62.2 + - - +
1508A GLN* 3.3 11.4 + - + +
1509A LEU* 3.1 38.8 + - + +
1532A ILE* 4.7 16.2 - - + -
1544A LEU 5.3 0.2 - - - +
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Residues in contact with THR1506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1504A THR* 3.2 1.4 + - - -
1505A PRO* 1.3 78.3 - - - +
1507A GLN* 1.3 58.6 + - - +
1509A LEU* 3.1 2.9 + - - +
1510A ILE* 2.8 47.6 + - + +
1532A ILE* 3.8 14.5 + - - +
1533A LEU* 4.3 21.0 - - + +
1544A LEU* 3.8 42.0 + - + +
1545A LEU* 4.4 10.5 - - + -
1608A CYS* 4.6 9.6 - - + -
1648A TYR* 5.5 2.2 - - + -
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Residues in contact with GLN1507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1503A ASP* 3.3 21.8 + - + +
1504A THR* 2.9 37.0 + - - +
1506A THR* 1.3 75.5 - - - +
1508A GLN* 1.3 62.6 + - - +
1510A ILE* 3.5 10.1 + - + +
1511A GLN* 3.1 21.8 + - - +
1545A LEU* 3.7 18.0 - - + +
1546A PRO* 3.3 35.5 - - - +
1645A ILE* 6.2 0.9 - - + -
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Residues in contact with GLN1508 (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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1501A GLU* 3.3 40.2 + - - +
1503A ASP* 3.5 23.7 - - + +
1504A THR 3.1 12.7 + - - +
1505A PRO* 3.7 11.7 - - + +
1507A GLN* 1.3 75.4 - - - +
1509A LEU* 1.3 61.6 + - + +
1511A GLN* 3.3 9.1 - - - +
1512A ASP* 2.9 32.5 + - - +
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Residues in contact with LEU1509 (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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1505A PRO* 3.1 28.3 + - + +
1506A THR 3.8 2.2 - - - +
1508A GLN* 1.3 77.0 - - + +
1510A ILE* 1.3 56.6 + - - +
1511A GLN 3.1 0.9 - - - -
1512A ASP* 3.0 20.5 + - - +
1513A ILE* 2.7 40.1 + - - +
1526A ILE* 4.2 10.0 - - + +
1530A ASN* 3.6 48.9 - - + +
1532A ILE* 4.1 14.1 - - + -
1533A LEU* 3.9 17.5 - - + -
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Residues in contact with ILE1510 (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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1506A THR* 2.8 39.3 + - + +
1507A GLN* 3.7 9.9 - - - +
1509A LEU* 1.3 73.9 - - - +
1511A GLN* 1.3 58.9 + - - +
1513A ILE* 3.2 11.9 + - - +
1514A LYS* 2.8 30.1 + - + +
1533A LEU* 5.0 2.4 - - + +
1545A LEU* 5.2 0.9 - - + -
1608A CYS* 4.4 3.4 - - - -
1644A GLY 5.1 4.5 - - - +
1645A ILE* 4.3 20.9 - - + -
1648A TYR* 3.5 57.7 - - + -
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Residues in contact with GLN1511 (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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1507A GLN 3.1 13.9 + - - +
1508A GLN* 3.3 13.2 - - - +
1509A LEU 3.1 0.4 - - - -
1510A ILE* 1.3 79.1 - - - +
1512A ASP* 1.3 62.2 + - - +
1514A LYS* 3.3 33.1 + - - +
1515A GLU* 3.2 53.7 + - - +
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Residues in contact with ASP1512 (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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1508A GLN* 2.9 21.1 + - - +
1509A LEU* 3.0 32.0 + - + +
1511A GLN* 1.3 74.8 - - - +
1513A ILE* 1.3 61.9 + - - +
1515A GLU* 3.5 10.9 + - - +
1516A ASN* 2.8 34.4 + - - +
1526A ILE* 4.1 16.4 - - + +
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Residues in contact with ILE1513 (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 2.7 21.8 + - - +
1510A ILE* 3.3 8.7 - - - +
1512A ASP* 1.3 71.3 - - - +
1514A LYS* 1.3 68.8 + - - +
1516A ASN 2.9 3.7 + - - +
1517A CYS* 2.8 22.6 + - + -
1523A VAL* 4.5 11.4 - - + -
1526A ILE* 3.9 27.8 - - + -
1527A TYR* 3.5 40.4 - - + +
1533A LEU* 4.6 3.4 - - + -
1648A TYR* 3.9 17.3 - - + +
1651A PHE* 3.7 35.7 - - + -
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Residues in contact with LYS1514 (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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1510A ILE* 2.8 18.1 + - + +
1511A GLN* 3.4 38.0 + - - +
1513A ILE* 1.3 76.2 - - - +
1515A GLU* 1.3 61.8 + - + +
1517A CYS* 3.3 26.0 - - - -
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Residues in contact with GLU1515 (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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1511A GLN* 3.2 46.5 + - - +
1512A ASP* 3.5 10.7 + - - +
1513A ILE 3.2 0.8 - - - -
1514A LYS* 1.3 79.2 - - + +
1516A ASN* 1.3 67.5 + - - +
1517A CYS 3.7 0.2 - - - -
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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