Contacts of the helix formed by residues 1323 - 1329 (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 LYS1323 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1321A PHE 3.5 2.0 + - - -
1322A TRP* 1.3 71.4 - - + +
1324A SER* 1.3 63.7 + - - +
1326A GLY* 2.9 4.9 + - - -
1327A GLU* 2.8 51.9 + - + +
1339A THR* 3.9 4.1 - - + +
1347A TRP* 4.0 26.2 - - + +
1348A PHE 3.2 21.6 + - - +
1349A ASP* 3.2 34.5 + - + +
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Residues in contact with SER1324 (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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1295A LYS* 5.0 1.4 - - - +
1296A LEU 5.4 3.3 + - - -
1301A LEU* 4.5 1.0 - - - +
1322A TRP* 2.8 34.0 + - - +
1323A LYS* 1.3 77.8 - - - +
1325A THR* 1.3 56.3 + - - +
1327A GLU* 3.7 17.5 - - - -
1328A ASN* 2.9 41.0 + - - +
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Residues in contact with THR1325 (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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1294A SER* 2.7 30.4 + - - +
1295A LYS* 3.7 4.9 - - - -
1296A LEU 4.5 2.6 + - - -
1301A LEU* 4.1 19.2 - - + +
1305A LEU* 4.8 1.6 - - + -
1309A HIS* 4.4 20.0 - - + +
1322A TRP* 2.9 20.6 + - - +
1324A SER* 1.3 79.6 + - - +
1326A GLY* 1.3 63.8 + - - +
1328A ASN* 3.3 1.2 + - - +
1329A LEU* 3.0 50.5 + - + +
1347A TRP* 5.5 2.0 - - + -
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Residues in contact with GLY1326 (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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1322A TRP 3.2 4.0 + - - -
1323A LYS 2.9 5.5 + - - -
1325A THR* 1.3 80.1 - - - +
1327A GLU* 1.3 59.6 + - - +
1329A LEU 3.4 3.6 - - - +
1338A LEU* 3.0 36.5 + - - +
1339A THR* 3.3 8.0 + - - -
1347A TRP* 3.2 33.7 - - - -
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Residues in contact with GLU1327 (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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1323A LYS* 2.8 55.1 + - - +
1324A SER* 3.7 14.8 - - - +
1326A GLY* 1.3 79.0 - - - +
1328A ASN* 1.3 69.8 + - - +
1329A LEU 4.3 0.6 - - - +
1337A PRO* 3.8 18.1 - - - +
1339A THR* 3.4 25.1 - - + +
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Residues in contact with ASN1328 (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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1298A GLN* 2.7 49.4 + - + +
1301A LEU* 3.8 33.6 - - + +
1302A GLN* 4.2 1.9 - - - +
1324A SER* 2.9 27.3 + - - +
1325A THR 3.3 0.4 + - - -
1327A GLU* 1.3 87.6 + - - +
1329A LEU* 1.3 60.8 + - - +
1330A LYS* 4.1 8.7 + - - +
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Residues in contact with LEU1329 (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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1301A LEU* 3.7 16.6 - - + -
1302A GLN 3.5 33.2 - - - +
1303A ARG* 3.8 2.9 - - - +
1304A SER* 3.7 28.5 - - - +
1305A LEU* 3.4 34.5 - - + -
1325A THR* 3.0 31.0 + - + +
1326A GLY 3.4 0.5 - - - +
1327A GLU 3.5 0.2 - - - -
1328A ASN* 1.3 79.8 - - - +
1330A LYS* 1.3 60.7 + - - +
1337A PRO* 3.3 7.8 - - - +
1338A LEU* 3.1 40.6 + - + -
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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