Contacts of the strand formed by residues 1274 - 1279 (chain A) in PDB entry 2Y23
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 LYS1274 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1272A ASN 3.7 17.5 - - - +
1273A ALA* 1.3 73.7 - - - +
1275A VAL* 1.3 71.7 + - - +
1276A ASN* 5.4 6.1 + - - +
1294A ILE* 5.4 2.0 - - - -
1296A ARG* 5.3 2.0 - - - +
1319A GLN 3.7 1.7 - - - +
1320A LEU* 3.7 0.2 - - - -
1321A GLN* 2.9 54.0 + - + +
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Residues in contact with VAL1275 (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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1269A LEU* 5.9 2.0 - - + -
1273A ALA* 5.8 0.9 - - + -
1274A LYS* 1.3 84.8 - - - +
1276A ASN* 1.3 83.4 + - - +
1277A TYR* 3.7 40.2 - - + +
1294A ILE* 4.0 22.7 - - + +
1301A ILE* 4.1 16.4 - - + -
1318A PHE* 4.3 5.4 - - + -
1319A GLN 3.3 10.5 - - - +
1320A LEU* 3.8 25.6 - - + -
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Residues in contact with ASN1276 (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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1274A LYS* 5.4 5.9 + - - +
1275A VAL* 1.3 83.2 - - - +
1277A TYR* 1.3 63.7 + - - +
1278A ILE* 4.7 5.2 - - + -
1283A GLU* 2.9 29.4 - - - +
1317A THR 3.8 0.7 - - - +
1318A PHE* 3.8 0.5 - - - -
1319A GLN* 2.8 51.2 + - + +
1321A GLN* 5.2 8.9 + - - +
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Residues in contact with TYR1277 (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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1275A VAL* 3.7 27.1 - - + +
1276A ASN* 1.3 75.1 - - - +
1278A ILE* 1.3 62.9 + - - +
1283A GLU* 3.2 26.6 + - - +
1284A ILE* 3.2 34.4 + - + +
1292A MET* 4.0 36.1 - - + +
1294A ILE* 3.8 19.5 - - + +
1301A ILE* 3.8 16.3 - - + +
1302A GLU 4.3 8.7 + - - -
1303A MET* 4.3 10.3 - - + -
1317A THR 3.7 3.8 - - - +
1318A PHE* 3.6 45.1 - + + -
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Residues in contact with ILE1278 (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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1276A ASN* 4.9 4.0 - - + -
1277A TYR* 1.3 85.8 - - - +
1279A PHE* 1.3 63.1 + - - +
1280A ASN 4.9 0.2 - - - +
1281A GLU* 3.7 30.7 - - + +
1282A LYS 3.5 6.7 - - - +
1283A GLU* 3.9 26.2 - - + +
1284A ILE* 4.5 3.5 - - - +
1315A THR 3.8 1.1 - - - +
1316A TYR* 3.3 8.5 - - - +
1317A THR* 3.0 48.5 + - - +
1319A GLN* 4.2 28.3 - - + +
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Residues in contact with PHE1279 (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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1278A ILE* 1.3 73.7 - - - +
1280A ASN* 1.3 101.3 + - + +
1281A GLU 3.3 0.4 - - - -
1282A LYS* 2.9 26.3 + - - +
1284A ILE* 4.2 20.6 - - + +
1290A TYR* 4.2 15.3 - - - -
1311A GLU 3.5 25.4 - - - -
1312A ASP* 3.5 20.6 - - - -
1313A GLU 3.6 6.3 - - - -
1314A GLY* 4.0 0.9 - - - -
1315A THR 3.4 5.4 - - - -
1316A TYR* 3.2 47.1 - + + -
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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