Contacts of the strand formed by residues 1314 - 1321 (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 GLY1314 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1279A PHE* 4.0 1.1 - - - -
1280A ASN* 3.4 9.6 - - - -
1312A ASP 3.6 2.8 + - - -
1313A GLU* 1.3 75.5 - - - +
1315A THR* 1.3 61.8 + - - -
1316A TYR* 3.9 8.7 - - - -
1333A LEU* 3.0 43.1 + - - +
1334A VAL* 3.9 13.2 - - - -
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Residues in contact with THR1315 (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* 3.8 1.0 - - - +
1279A PHE* 3.4 4.5 - - - -
1280A ASN* 2.9 44.6 + - - -
1281A GLU* 4.9 1.4 + - - -
1314A GLY* 1.3 72.8 - - - -
1316A TYR* 1.3 64.0 + - - +
1317A THR* 4.7 3.6 - - - +
1330A THR* 3.8 25.8 - - + -
1331A VAL 3.7 5.6 - - - +
1332A VAL* 4.3 19.7 - - + +
1334A VAL* 5.2 1.4 - - - +
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Residues in contact with TYR1316 (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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1250A LEU* 3.6 6.8 - - + +
1262A PHE* 3.6 37.7 - + + -
1278A ILE 3.3 6.1 - - - +
1279A PHE* 3.2 42.9 - + + -
1284A ILE* 5.1 2.7 - - + -
1290A TYR* 5.2 3.3 + + - -
1303A MET* 4.3 17.9 - - + -
1305A MET* 4.4 10.6 - - + +
1308A LEU* 4.8 1.4 - - - +
1312A ASP* 2.6 37.0 + - - +
1314A GLY 3.9 9.9 - - - -
1315A THR* 1.3 76.0 - - - +
1317A THR* 1.3 65.0 + - - +
1318A PHE* 5.7 2.9 - - + -
1330A THR* 3.4 1.1 - - - +
1331A VAL* 2.9 46.8 + - + +
1333A LEU* 3.8 20.2 - - + -
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Residues in contact with THR1317 (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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1250A LEU* 4.3 0.2 - - - -
1276A ASN 3.8 1.0 - - - +
1277A TYR* 3.7 2.4 - - - -
1278A ILE* 3.0 44.7 + - + +
1315A THR* 4.7 3.6 - - - +
1316A TYR* 1.3 75.4 + - - +
1318A PHE* 1.3 79.5 + - - +
1319A GLN* 3.8 25.8 - - + +
1328A HIS* 4.1 7.9 - - + -
1329A SER 3.4 12.3 - - - +
1330A THR* 2.9 26.6 + - - +
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Residues in contact with PHE1318 (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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1250A LEU* 3.7 31.1 - - + +
1262A PHE* 4.0 13.5 - + + -
1264A MET* 3.8 28.7 - - + -
1275A VAL* 4.3 1.6 - - + -
1276A ASN 3.8 2.5 - - - -
1277A TYR* 3.6 30.1 - + + -
1301A ILE* 3.8 46.0 - - + -
1302A GLU 4.4 0.7 - - - -
1303A MET* 3.9 28.5 - - + -
1316A TYR* 5.7 2.5 - + + -
1317A THR* 1.3 80.0 - - - +
1319A GLN* 1.3 61.9 + - - +
1320A LEU* 4.0 8.6 + - + +
1328A HIS* 3.3 6.6 - - - +
1329A SER 3.1 28.4 + - - +
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Residues in contact with GLN1319 (chain A).
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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1274A LYS 3.7 1.2 - - - +
1275A VAL* 3.3 6.8 - - - +
1276A ASN* 2.8 50.8 + - + +
1278A ILE* 4.2 20.3 - - + +
1317A THR* 3.8 20.9 - - + +
1318A PHE* 1.3 74.2 - - - +
1320A LEU* 1.3 63.3 + - - +
1321A GLN* 5.4 0.5 - - - +
1327A ASN 3.9 4.7 - - - +
1328A HIS* 4.1 13.3 - - - +
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Residues in contact with LEU1320 (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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1244A VAL* 4.1 26.9 - - + -
1246A VAL* 4.2 8.7 - - + -
1264A MET* 3.7 26.2 - - + -
1266A ALA* 5.0 5.4 - - + -
1274A LYS 3.7 3.1 - - - -
1275A VAL* 3.8 26.2 - - + -
1301A ILE* 3.8 18.6 - - + -
1318A PHE* 4.2 17.0 - - + +
1319A GLN* 1.3 78.0 - - - +
1321A GLN* 1.3 62.9 + - - +
1326A THR* 3.4 5.5 + - - +
1327A ASN* 3.0 42.3 + - + +
1328A HIS* 4.9 1.6 - - - +
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Residues in contact with GLN1321 (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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1244A VAL* 4.9 0.4 - - - -
1272A ASN 4.6 0.2 - - - +
1273A ALA* 3.4 2.5 - - - +
1274A LYS* 2.9 49.0 + - + +
1276A ASN* 5.2 8.7 + - - +
1319A GLN 5.4 0.4 - - - +
1320A LEU* 1.3 77.5 - - - +
1322A ASP* 1.3 62.9 + - - +
1323A GLY 4.2 13.2 + - - +
1324A LYS* 5.9 2.0 - - - +
1325A ALA 3.6 13.0 - - - +
1326A THR* 4.5 8.7 + - - +
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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