Contacts of the helix formed by residues 1352 - 1365 (chain A) in PDB entry 1Y8Z
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 ASP1352 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1349A ASP* 3.1 24.8 + - - +
1350A GLU 3.2 0.2 - - - -
1351A ASN* 1.3 81.2 - - - +
1353A MET* 1.3 61.6 + - - +
1354A GLU* 3.5 8.5 + - - +
1355A SER* 2.8 49.1 + - - +
1356A THR* 3.6 4.3 + - - -
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Residues in contact with MET1353 (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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1213A GLN* 5.0 1.6 - - - +
1216A ASP* 3.6 22.7 - - - +
1217A PHE* 3.7 39.1 - - + -
1220A LYS* 4.1 20.2 - - + +
1221A PHE* 3.5 21.1 - - + -
1348A PHE* 4.0 18.2 - - + -
1349A ASP 3.5 14.4 - - - +
1350A GLU* 3.9 19.9 + - + +
1351A ASN 4.1 0.2 - - - -
1352A ASP* 1.3 72.8 - - - +
1354A GLU* 1.3 58.8 + - - +
1356A THR* 3.1 8.1 + - - -
1357A PHE* 2.8 30.3 + - - +
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Residues in contact with GLU1354 (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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1221A PHE* 3.5 26.8 - - + -
1352A ASP* 3.1 8.0 - - - +
1353A MET* 1.3 78.5 - - - +
1355A SER* 1.3 57.6 + - - +
1357A PHE* 3.2 4.0 + - + +
1358A GLU* 2.9 53.8 + - + +
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Residues in contact with SER1355 (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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1349A ASP* 4.7 3.6 - - - +
1352A ASP* 2.8 45.8 + - - +
1354A GLU* 1.3 77.3 - - - +
1356A THR* 1.3 64.1 + - - +
1358A GLU* 3.2 10.8 + - - +
1359A ARG* 3.0 23.9 + - - +
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Residues in contact with THR1356 (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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1217A PHE* 3.9 12.3 - - + -
1320A VAL* 4.7 1.6 - - + -
1346A ILE* 4.2 12.5 - - + +
1347A TRP 4.1 3.6 + - - -
1348A PHE* 3.6 31.8 - - + -
1349A ASP* 3.1 27.5 + - - +
1352A ASP 3.6 5.6 + - - -
1353A MET* 3.1 13.0 + - - -
1355A SER* 1.3 83.9 + - - +
1357A PHE* 1.3 62.4 + - - +
1359A ARG* 3.3 8.4 + - - +
1360A ILE* 3.1 29.1 + - + +
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Residues in contact with PHE1357 (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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1217A PHE* 4.0 10.7 - + + -
1221A PHE* 4.0 32.5 - + + -
1222A LEU* 3.9 30.3 - - + -
1225A ALA* 3.2 34.8 - - + -
1227A LYS* 4.6 11.4 - - + -
1353A MET 2.8 15.6 + - - +
1354A GLU* 3.7 3.6 - - + +
1356A THR* 1.3 73.8 - - - +
1358A GLU* 1.3 66.9 + - - +
1360A ILE* 3.3 14.1 + - + +
1361A LYS* 2.9 67.4 + - + +
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Residues in contact with GLU1358 (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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1354A GLU* 2.9 48.0 + - + +
1355A SER* 3.4 11.2 - - - +
1356A THR 3.2 0.2 - - - -
1357A PHE* 1.3 80.1 - - - +
1359A ARG* 1.3 64.3 + - - +
1361A LYS* 3.2 23.7 + - - +
1362A GLU* 3.0 32.9 + - - +
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Residues in contact with ARG1359 (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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1346A ILE* 4.4 24.7 - - + -
1355A SER 3.0 12.2 + - - +
1356A THR* 3.5 10.3 - - - +
1358A GLU* 1.3 76.2 - - - +
1360A ILE* 1.3 63.2 + - - +
1362A GLU* 3.3 24.4 + - - +
1363A LEU* 3.0 63.0 + - - +
1369A LEU* 4.0 15.9 - - - +
1373A GLU* 3.7 25.0 + - - +
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Residues in contact with ILE1360 (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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1199A ASN* 4.6 4.9 - - - +
1217A PHE* 3.9 21.8 - - + -
1222A LEU* 5.4 0.4 - - + -
1227A LYS* 6.2 3.6 - - + -
1289A PHE* 3.4 38.1 - - + -
1291A TYR* 3.2 28.3 - - + +
1320A VAL* 4.8 3.8 - - + -
1346A ILE* 3.9 18.2 - - + -
1356A THR* 3.1 21.9 + - + +
1357A PHE* 3.5 20.0 - - + +
1358A GLU 3.2 0.2 - - - -
1359A ARG* 1.3 77.6 - - - +
1361A LYS* 1.3 54.2 + - + +
1363A LEU 3.4 0.7 + - - -
1364A SER* 2.6 39.5 + - - +
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Residues in contact with LYS1361 (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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1227A LYS* 6.3 1.6 - - - -
1357A PHE* 2.9 62.5 + - + +
1358A GLU* 3.2 24.6 + - - +
1360A ILE* 1.3 74.5 - - - +
1362A GLU* 1.3 64.9 + - - +
1364A SER* 3.2 15.3 + - - -
1365A SER* 3.2 19.4 + - - -
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Residues in contact with GLU1362 (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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1358A GLU* 3.0 22.4 + - + +
1359A ARG* 3.5 32.9 + - - +
1361A LYS* 1.3 79.2 - - + +
1363A LEU* 1.3 62.1 + - - +
1365A SER* 3.2 11.4 + - - -
1366A ASP* 3.4 16.3 + - - +
1369A LEU* 4.5 14.6 - - + +
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Residues in contact with LEU1363 (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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1196A MET* 4.7 1.0 - - - +
1289A PHE* 4.0 9.0 - - + -
1318A ILE* 3.8 24.5 - - + -
1344A GLY 5.2 1.1 - - - +
1346A ILE* 3.6 32.3 - - + -
1359A ARG* 3.0 39.7 + - - +
1360A ILE 3.8 3.8 - - - +
1362A GLU* 1.3 79.0 - - - +
1364A SER* 1.3 62.0 + - - +
1365A SER 3.3 1.0 + - - -
1366A ASP 3.4 18.0 + - - +
1367A ARG* 4.9 0.2 - - - -
1369A LEU* 3.5 21.5 - - + -
1370A TYR* 3.7 29.0 - - + +
1373A GLU* 3.7 13.7 - - + -
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Residues in contact with SER1364 (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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1196A MET* 3.7 36.9 + - - +
1227A LYS* 4.9 13.0 + - - -
1289A PHE* 3.0 21.9 - - - -
1360A ILE* 2.6 25.7 + - - +
1361A LYS* 3.2 8.4 + - - -
1363A LEU* 1.3 76.2 - - - +
1365A SER* 1.3 59.5 + - - +
1366A ASP 3.5 0.8 + - - -
1367A ARG* 5.1 5.6 + - - +
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Residues in contact with SER1365 (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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1361A LYS 3.2 15.3 + - - -
1362A GLU* 3.2 3.6 + - - -
1363A LEU 3.2 0.6 - - - -
1364A SER* 1.3 79.8 + - - +
1366A ASP* 1.3 61.2 + - - +
1367A ARG* 4.1 2.2 - - - -
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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