Contacts of the helix formed by residues 1323 - 1329 (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 LYS1323 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1321B PHE 3.5 1.8 + - - -
1322B TRP* 1.3 72.7 - - + +
1324B SER* 1.3 58.4 + - - +
1326B GLY* 3.2 4.2 + - - -
1327B GLU* 2.5 62.7 + - + +
1339B THR* 3.7 4.9 - - + +
1347B TRP* 4.0 28.7 - - + +
1348B PHE 3.1 20.7 + - - +
1349B ASP* 3.9 32.4 + - + +
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Residues in contact with SER1324 (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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1295B LYS* 4.9 2.4 - - - +
1296B LEU 5.3 2.3 + - - -
1322B TRP* 2.9 29.7 + - - +
1323B LYS* 1.3 78.1 - - - +
1325B THR* 1.3 56.5 + - - +
1327B GLU* 3.7 15.0 - - - -
1328B ASN* 2.9 46.2 + - - -
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Residues in contact with THR1325 (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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1294B SER 2.6 25.1 + - - +
1295B LYS* 3.4 3.1 - - - -
1296B LEU* 3.3 26.9 + - + -
1301B LEU* 3.5 17.2 - - + +
1305B LEU* 4.7 2.5 - - + -
1309B HIS* 4.4 16.2 - - + +
1321B PHE* 6.0 0.2 - - + -
1322B TRP* 3.0 16.0 + - - +
1324B SER* 1.3 81.1 + - - +
1326B GLY* 1.3 62.7 + - - +
1328B ASN 3.3 0.7 + - - -
1329B LEU* 3.1 41.0 + - + +
1347B TRP* 5.5 2.2 - - + -
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Residues in contact with GLY1326 (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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1322B TRP 3.2 4.6 + - - -
1323B LYS 3.2 3.4 + - - -
1325B THR* 1.3 81.8 - - - +
1327B GLU* 1.3 59.1 + - - +
1329B LEU 3.5 5.0 - - - +
1338B LEU* 3.1 34.5 + - - +
1339B THR* 3.3 9.7 + - - -
1347B TRP* 3.3 31.8 - - - -
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Residues in contact with GLU1327 (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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1298B GLN* 4.9 2.1 + - - -
1323B LYS* 2.5 56.3 + - - +
1324B SER* 3.7 16.7 + - - +
1325B THR 3.2 0.2 - - - -
1326B GLY* 1.3 77.4 - - - +
1328B ASN* 1.3 68.7 + - - +
1329B LEU 3.5 0.2 - - - -
1330B LYS* 4.7 2.9 + - - -
1337B PRO* 3.8 19.1 - - - +
1339B THR* 3.3 24.0 - - + +
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Residues in contact with ASN1328 (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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1296B LEU 3.7 6.2 - - - +
1297B ASN* 4.8 0.3 - - - -
1298B GLN* 3.4 56.2 + - + +
1301B LEU* 3.5 29.3 - - + +
1302B GLN* 4.5 0.9 - - - +
1324B SER* 2.9 29.6 + - - +
1327B GLU* 1.3 89.0 + - - +
1329B LEU* 1.3 59.3 + - - +
1330B LYS* 3.3 19.0 + - - +
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Residues in contact with LEU1329 (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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1301B LEU* 3.3 28.3 - - + -
1302B GLN 3.2 37.2 - - - +
1303B ARG* 3.5 7.0 - - - +
1304B SER 3.6 20.9 - - - +
1305B LEU* 3.4 33.4 - - + -
1325B THR* 3.1 21.6 + - + +
1326B GLY 3.5 0.2 - - - +
1327B GLU 3.5 0.2 - - - -
1328B ASN* 1.3 78.6 - - - +
1330B LYS* 1.3 61.7 + - - +
1337B PRO* 3.1 8.7 - - - +
1338B LEU* 3.1 37.7 + - + -
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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