Contacts of the helix formed by residues 1537 - 1543 (chain A) in PDB entry 6AGF
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 GLY1537 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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409A GLU* 4.1 23.5 + - - +
1244A LYS* 3.7 12.5 - - - +
1512A GLY* 5.8 0.5 - - - -
1531A GLU* 4.5 3.6 - - - +
1532A ILE* 5.1 0.4 - - - -
1536A ALA* 1.3 73.9 - - - +
1538A TRP* 1.3 62.9 + - - +
1539A ASP* 3.2 14.2 + - - -
1540A GLY* 3.5 9.0 + - - -
1541A LEU* 3.6 18.2 + - - +
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Residues in contact with TRP1538 (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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1235A LEU* 4.8 8.3 - - + -
1238A LEU* 3.6 27.8 - - + -
1239A GLN* 3.6 31.4 - - + -
1242A THR* 3.7 24.7 + - - -
1244A LYS* 3.9 10.6 - - + +
1532A ILE* 3.7 26.0 - - + -
1535A SER* 3.1 35.4 + - - +
1536A ALA 3.4 1.8 + - - -
1537A GLY* 1.3 75.2 - - - +
1539A ASP* 1.3 62.0 + - - +
1540A GLY 3.2 1.1 - - - -
1541A LEU* 3.8 9.0 - - - +
1542A LEU* 3.1 48.1 + - + +
1578A PHE* 4.1 18.3 - - + -
1579A CYS* 5.3 2.0 - - - -
1582A ILE* 3.8 26.8 - - + +
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Residues in contact with ASP1539 (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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1239A GLN* 4.1 14.1 + - - +
1244A LYS* 3.8 11.4 - - - +
1245A GLY* 3.1 39.8 + - - -
1537A GLY* 3.4 15.8 - - - -
1538A TRP* 1.3 84.3 - - + +
1540A GLY* 1.3 64.3 + - - -
1542A LEU* 3.9 2.9 - - - +
1543A ASN* 3.3 24.9 + - - +
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Residues in contact with GLY1540 (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 SER* 3.3 13.9 + - - -
1512A GLY* 3.1 31.8 + - - -
1537A GLY 3.5 3.2 + - - -
1538A TRP 3.2 0.2 - - - -
1539A ASP* 1.3 86.3 + - - +
1541A LEU* 1.3 60.5 + - - +
1542A LEU 3.3 0.7 - - - -
1543A ASN* 3.9 2.2 - - - -
1544A PRO* 3.2 17.2 - - - +
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Residues in contact with LEU1541 (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 GLY* 3.6 22.7 - - - +
1513A ILE* 3.7 22.5 - - + +
1517A PHE* 6.2 0.2 - - + -
1519A PHE* 4.7 7.3 - - + -
1528A CYS* 4.0 29.4 - - + -
1531A GLU* 3.8 20.4 - - - +
1532A ILE* 3.6 29.2 - - + -
1537A GLY 3.6 13.9 + - - +
1538A TRP 4.1 3.1 - - - +
1540A GLY* 1.3 79.4 - - - +
1542A LEU* 1.3 58.7 + - - +
1543A ASN 3.4 0.4 + - - -
1544A PRO* 3.9 4.7 - - - +
1545A ILE* 3.4 21.3 - - - +
1578A PHE* 3.9 18.6 - - + -
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Residues in contact with LEU1542 (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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1235A LEU* 4.5 19.5 - - + -
1239A GLN* 4.4 10.8 - - - +
1538A TRP* 3.1 44.3 + - + +
1539A ASP 3.8 3.6 + - - +
1540A GLY 3.3 0.2 - - - -
1541A LEU* 1.3 78.8 - - - +
1543A ASN* 1.3 62.4 + - - +
1544A PRO 3.5 0.2 - - - -
1545A ILE* 3.2 13.6 + - + +
1546A LEU* 3.4 32.6 + - + +
1574A GLY* 3.7 32.8 - - - +
1575A ILE* 4.2 6.7 - - + +
1578A PHE* 3.7 18.6 - - + -
1579A CYS* 5.6 0.7 - - - -
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Residues in contact with ASN1543 (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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1224A LYS* 3.3 47.5 + - - +
1248A ASP* 5.3 7.7 + - - -
1510A GLU* 5.0 2.7 - - - -
1511A SER* 3.8 19.9 + - - +
1539A ASP 3.3 18.6 + - - +
1540A GLY* 4.2 0.8 - - - +
1541A LEU 3.4 0.2 - - - -
1542A LEU* 1.3 77.9 - - - +
1544A PRO* 1.3 67.9 - - + +
1545A ILE 3.6 0.2 + - - -
1546A LEU* 3.7 13.7 + - - +
1547A ASN 4.5 0.7 + - - -
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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