Contacts of the helix formed by residues 1512 - 1527 (chain A) in PDB entry 4C6J
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 ASP1512 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1509A PRO 4.7 0.2 - - - +
1510A ILE 3.7 0.4 - - - -
1511A ILE* 1.3 95.4 + - - +
1513A ALA* 1.3 64.9 + - - +
1514A PRO* 3.3 13.7 - - + +
1515A ALA* 2.9 38.5 + - - +
1516A LEU* 3.1 23.3 + - - +
1535A LEU* 4.4 6.0 - - - +
1544A THR* 6.1 0.2 - - - +
1545A LEU* 4.3 9.0 - - - -
1548A VAL* 5.4 0.2 - - - -
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Residues in contact with ALA1513 (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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1512A ASP* 1.3 72.7 - - - +
1514A PRO* 1.3 67.2 - - + +
1516A LEU* 3.3 7.4 + - - +
1517A ALA* 2.9 30.0 + - - +
1545A LEU* 5.2 1.4 - - - +
1548A VAL* 3.9 31.6 - - + +
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Residues in contact with PRO1514 (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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1512A ASP* 3.3 15.7 - - + +
1513A ALA* 1.3 95.4 - - + +
1515A ALA* 1.3 61.4 + - - +
1517A ALA* 3.3 7.6 + - + +
1518A LEU* 3.1 22.0 + - - +
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Residues in contact with ALA1515 (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 PRO* 4.7 14.6 - - + -
1509A PRO 3.4 25.1 - - - +
1510A ILE* 3.6 15.6 - - + +
1512A ASP* 2.9 23.2 + - - +
1514A PRO* 1.3 76.3 - - - +
1516A LEU* 1.3 58.4 + - - +
1518A LEU* 3.4 9.0 + - - +
1519A ALA* 2.9 29.5 + - - +
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Residues in contact with LEU1516 (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* 3.7 24.5 - - + +
1512A ASP 3.1 17.0 + - - +
1513A ALA* 3.6 4.3 - - - +
1515A ALA* 1.3 77.4 - - - +
1517A ALA* 1.3 56.8 + - - +
1519A ALA* 3.3 1.2 + - - -
1520A GLN* 2.8 48.2 + - + +
1533A LEU* 4.2 32.8 - - + +
1535A LEU* 4.3 15.3 - - + -
1548A VAL* 3.9 26.9 - - + +
1551A SER* 3.5 26.2 - - - +
1552A ALA* 5.0 4.0 - - + -
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Residues in contact with ALA1517 (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 ALA 2.9 17.1 + - - +
1514A PRO* 3.6 8.1 - - + +
1515A ALA 3.3 0.2 - - - -
1516A LEU* 1.3 77.3 - - - +
1518A LEU* 1.3 62.0 + - - +
1520A GLN* 3.5 15.0 + - - +
1521A LYS* 3.2 28.1 + - - +
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Residues in contact with LEU1518 (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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1477A PRO* 4.3 24.0 - - + -
1508A PRO* 4.4 17.7 - - + -
1514A PRO 3.1 12.9 + - - +
1515A ALA* 3.6 9.6 - - - +
1517A ALA* 1.3 77.8 - - - +
1519A ALA* 1.3 63.0 + - - +
1521A LYS* 3.2 7.6 + - + +
1522A LEU* 3.0 44.7 + - + +
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Residues in contact with ALA1519 (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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1476A GLU 5.3 0.2 - - - +
1477A PRO* 4.6 9.0 - - + -
1485A PHE* 4.0 7.3 - - + -
1510A ILE* 3.7 24.2 - - + -
1515A ALA 2.9 16.7 + - - +
1516A LEU* 3.8 4.5 - - - +
1518A LEU* 1.3 79.0 - - - +
1520A GLN* 1.3 58.1 + - - +
1522A LEU* 3.8 9.3 - - - +
1523A ALA* 2.8 31.9 + - - +
1533A LEU* 3.7 16.1 - - + +
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Residues in contact with GLN1520 (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 LEU* 2.8 31.0 + - + +
1517A ALA* 3.6 17.8 - - - +
1519A ALA* 1.3 77.1 - - - +
1521A LYS* 1.3 60.1 + - + +
1523A ALA* 3.7 2.3 - - - +
1524A GLU* 2.8 41.6 + - - +
1531A PHE* 5.2 1.8 - - - -
1533A LEU* 3.6 17.7 - - + +
1551A SER* 3.8 26.1 + - - -
1808A ASP* 4.0 20.4 + - - +
1811A LYS* 4.1 21.1 + - - +
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Residues in contact with LYS1521 (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 ALA 3.2 12.5 + - - +
1518A LEU* 3.2 11.8 + - + +
1520A GLN* 1.3 77.2 - - + +
1522A LEU* 1.3 67.1 + - + +
1524A GLU* 3.4 24.8 + - + +
1525A ALA* 3.1 26.2 + - - +
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Residues in contact with LEU1522 (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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1476A GLU* 3.8 30.1 - - + +
1477A PRO* 3.8 33.9 - - + -
1485A PHE* 3.7 12.9 - - + -
1518A LEU* 3.0 41.8 + - + +
1519A ALA 3.8 2.9 - - - +
1521A LYS* 1.3 76.2 - - + +
1523A ALA* 1.3 58.4 + - - +
1525A ALA* 3.4 6.0 + - + +
1526A GLY* 3.0 26.2 + - - -
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Residues in contact with ALA1523 (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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1485A PHE* 3.6 33.8 - - + -
1519A ALA 2.8 17.5 + - - +
1520A GLN 3.7 0.9 - - - +
1522A LEU* 1.3 74.9 - - - +
1524A GLU* 1.3 60.7 + - - +
1527A ALA* 2.8 34.8 + - - +
1531A PHE* 3.4 33.2 - - + -
1533A LEU* 4.4 2.5 - - + -
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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 GLN* 2.8 27.4 + - - +
1521A LYS* 3.4 32.8 + - + +
1523A ALA* 1.3 73.6 - - - +
1525A ALA* 1.3 55.7 + - - +
1531A PHE* 3.9 18.2 - - + -
1804A GLY* 3.2 25.6 - - - +
1806A GLY 4.0 6.7 - - - +
1807A GLN* 5.5 1.3 - - - -
1808A ASP* 4.1 10.8 + - + +
1811A LYS* 3.8 29.6 - - - +
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Residues in contact with ALA1525 (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 LYS 3.1 17.0 + - - +
1522A LEU* 3.8 5.8 - - + +
1524A GLU* 1.3 79.8 - - - +
1526A GLY* 1.3 58.3 + - - +
1803A PRO* 3.3 10.4 - - - +
1804A GLY* 3.2 15.3 + - - -
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Residues in contact with GLY1526 (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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1476A GLU* 5.5 1.6 - - - -
1485A PHE* 3.8 12.3 - - - -
1486A ALA* 3.2 25.8 - - - -
1522A LEU 3.0 13.8 + - - -
1525A ALA* 1.3 78.8 - - - +
1527A ALA* 1.3 66.0 + - - +
1528A ARG 3.5 0.2 + - - -
1803A PRO* 3.4 14.9 - - - +
1804A GLY 3.6 2.0 - - - -
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Residues in contact with ALA1527 (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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1485A PHE* 3.9 7.4 - - + +
1489A THR* 3.7 16.6 - - + -
1523A ALA* 2.8 27.4 + - + +
1526A GLY* 1.3 71.2 - - - +
1528A ARG* 1.3 59.6 + - - +
1529A CYS 3.5 17.7 - - - +
1531A PHE* 3.6 18.6 - - + -
1804A GLY* 2.8 21.9 + - - -
1806A GLY* 2.9 16.0 + - - -
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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