Contacts of the helix formed by residues 1352 - 1366 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1349B ASP* 2.9 24.4 + - - +
1351B ASN* 1.3 81.2 - - + +
1353B MET* 1.3 59.4 + - - +
1354B GLU* 3.8 8.0 + - - +
1355B SER* 2.6 59.6 + - - +
1356B THR* 3.5 5.4 + - - -
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Residues in contact with MET1353 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1213B GLN* 5.0 1.1 - - - +
1216B ASP* 3.1 28.5 - - - +
1217B PHE* 3.6 28.1 - - + -
1220B LYS* 4.8 9.0 - - + +
1221B PHE* 3.6 23.8 - - + -
1348B PHE* 4.0 24.2 - - + -
1349B ASP 3.0 14.8 + - - +
1350B GLU* 3.9 19.0 + - + +
1351B ASN 3.9 1.0 - - - -
1352B ASP* 1.3 73.2 - - - +
1354B GLU* 1.3 59.4 + - - +
1356B THR* 3.1 7.9 + - - -
1357B PHE* 2.9 28.8 + - - +
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Residues in contact with GLU1354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1221B PHE* 3.5 28.5 - - + -
1352B ASP* 3.2 8.1 + - - +
1353B MET* 1.3 79.0 - - - +
1355B SER* 1.3 57.9 + - - +
1357B PHE* 3.2 4.0 + - + +
1358B GLU* 2.8 47.2 + - + +
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Residues in contact with SER1355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1349B ASP* 4.8 3.3 - - - +
1352B ASP* 2.6 47.3 + - - +
1354B GLU* 1.3 77.4 - - - +
1356B THR* 1.3 57.3 + - - +
1358B GLU* 3.4 9.2 + - - +
1359B ARG* 3.0 29.6 + - - +
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Residues in contact with THR1356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1217B PHE* 4.2 10.1 - - + -
1320B VAL* 4.6 0.9 - - + -
1346B ILE* 4.0 17.0 - - + -
1347B TRP 3.9 3.6 + - - -
1348B PHE* 3.7 33.5 - - + -
1349B ASP* 3.1 26.7 + - - +
1352B ASP 3.5 6.5 + - - -
1353B MET* 3.1 12.4 + - - -
1355B SER* 1.3 80.4 + - - +
1357B PHE* 1.3 61.2 + - - +
1359B ARG* 3.2 8.1 + - - +
1360B ILE* 3.0 32.4 + - + +
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Residues in contact with PHE1357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1217B PHE* 3.9 10.9 - + + -
1221B PHE* 3.8 46.7 - + + -
1222B LEU* 4.2 20.6 - - + -
1225B ALA* 3.5 29.2 - - + -
1227B LYS* 5.0 6.7 - - + -
1353B MET 2.9 13.4 + - - +
1354B GLU* 3.5 8.5 - - + +
1356B THR* 1.3 75.6 - - - +
1358B GLU* 1.3 66.3 + - - +
1360B ILE* 3.2 8.8 + - + +
1361B LYS* 2.8 75.5 + - + +
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Residues in contact with GLU1358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1354B GLU* 2.8 39.0 + - + +
1355B SER* 3.7 8.1 - - - +
1356B THR 3.3 0.2 - - - -
1357B PHE* 1.3 78.5 - - - +
1359B ARG* 1.3 61.4 + - - +
1361B LYS* 3.0 38.7 + - - +
1362B GLU* 2.9 37.2 + - - +
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Residues in contact with ARG1359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1346B ILE* 4.3 28.7 - - + -
1355B SER 3.0 14.3 + - - +
1356B THR* 3.4 10.5 - - - +
1357B PHE 3.2 0.2 - - - -
1358B GLU* 1.3 77.4 - - - +
1360B ILE* 1.3 63.2 + - - +
1362B GLU* 3.3 23.6 + - - +
1363B LEU* 3.0 59.9 + - - +
1369B LEU* 4.4 7.9 - - - +
1372B ARG* 5.3 3.8 - - - +
1373B GLU* 3.8 24.0 + - - +
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Residues in contact with ILE1360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1199B ASN* 4.5 5.4 - - - +
1217B PHE* 3.8 21.8 - - + -
1222B LEU* 5.0 3.1 - - + -
1227B LYS* 6.5 0.9 - - - -
1289B PHE* 3.4 40.5 - - + -
1291B TYR* 3.2 29.4 - - + +
1320B VAL* 4.6 4.3 - - + -
1346B ILE* 4.0 17.5 - - + -
1356B THR* 3.0 22.9 + - + +
1357B PHE* 3.5 12.6 - - + +
1359B ARG* 1.3 76.8 - - - +
1361B LYS* 1.3 58.2 + - - +
1363B LEU 3.4 1.0 + - - -
1364B SER* 2.7 33.7 + - - +
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Residues in contact with LYS1361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1227B LYS* 6.0 4.9 - - - +
1357B PHE* 2.8 61.5 + - + +
1358B GLU* 3.0 36.6 + - - +
1360B ILE* 1.3 73.6 - - + +
1362B GLU* 1.3 68.4 + - - +
1364B SER* 2.9 15.3 + - - -
1365B SER* 2.8 22.1 + - - +
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Residues in contact with GLU1362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1358B GLU* 2.9 21.5 + - - +
1359B ARG* 3.3 34.8 + - - +
1361B LYS* 1.3 79.1 - - - +
1363B LEU* 1.3 65.2 + - + +
1365B SER* 3.3 13.2 + - - -
1366B ASP* 3.4 14.7 + - - +
1369B LEU* 4.5 13.1 - - + +
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Residues in contact with LEU1363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1196B MET* 4.7 0.9 - - - +
1289B PHE* 4.1 8.7 - - + -
1318B ILE* 4.0 27.1 - - + -
1344B GLY 5.3 0.4 - - - +
1346B ILE* 3.8 25.8 - - + -
1359B ARG* 3.0 39.0 + - - +
1360B ILE 3.9 6.5 - - - +
1361B LYS 3.2 0.2 - - - -
1362B GLU* 1.3 76.6 - - - +
1364B SER* 1.3 64.3 + - - +
1365B SER 3.1 1.2 + - - -
1366B ASP 3.4 18.9 - - - +
1367B ARG* 4.4 0.7 + - - +
1369B LEU* 3.3 34.8 - - + +
1370B TYR* 3.6 19.7 - - + +
1373B GLU* 3.7 13.7 - - + -
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Residues in contact with SER1364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1196B MET* 4.0 36.1 + - - +
1227B LYS* 4.8 14.5 + - - -
1289B PHE* 3.0 21.7 - - - -
1360B ILE* 2.7 23.8 + - - +
1361B LYS* 2.9 10.1 + - - -
1363B LEU* 1.3 77.6 - - - +
1365B SER* 1.3 60.0 + - - +
1366B ASP 5.1 0.4 - - - -
1367B ARG* 5.3 3.3 + - - +
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Residues in contact with SER1365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1361B LYS* 2.8 18.8 + - - +
1362B GLU* 3.6 8.1 - - - -
1363B LEU 3.1 0.2 - - - -
1364B SER* 1.3 80.6 - - - +
1366B ASP* 1.3 59.5 + - - +
1367B ARG* 4.0 2.4 + - - +
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Residues in contact with ASP1366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1362B GLU 3.4 9.9 + - - +
1363B LEU 3.4 8.2 + - - +
1365B SER* 1.3 79.3 - - - +
1367B ARG* 1.3 59.6 + - - +
1368B ALA* 2.8 25.3 + - - +
1369B LEU* 3.1 27.6 + - + +
1370B TYR 2.9 23.2 + - - -
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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