Contacts of the strand formed by residues 1225 - 1234 (chain A) in PDB entry 5UAK
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 ALA1225 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1216A THR* 4.6 5.8 - - + -
1217A ALA 3.8 7.4 - - - -
1218A LYS* 4.5 9.9 - - - -
1223A GLY 3.5 4.2 + - - +
1224A ASN* 1.3 67.8 - - - +
1226A ILE* 1.3 64.0 + - - +
1227A LEU 3.6 7.0 - - - +
1228A GLU* 3.8 28.4 - - + +
1418A GLU* 5.2 5.4 - - - +
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Residues in contact with ILE1226 (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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1217A ALA* 3.5 6.5 + - + +
1218A LYS* 4.3 1.3 - - - -
1219A TYR* 3.9 28.7 - - + +
1224A ASN* 3.1 30.1 + - + +
1225A ALA* 1.3 74.8 - - - +
1227A LEU* 1.3 73.6 + - + +
1228A GLU* 4.2 1.6 + - - +
1245A ARG* 4.3 17.8 + - - +
1248A SER* 5.1 10.8 - - - +
1249A GLY 6.0 1.1 - - - +
1252A THR* 4.3 32.3 - - + +
1261A LEU* 5.3 0.9 - - + -
1418A GLU* 5.1 5.2 - - - +
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Residues in contact with LEU1227 (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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1215A LEU* 4.5 16.2 - - + +
1216A THR* 3.5 7.4 - - - +
1217A ALA* 3.2 43.0 + - + +
1225A ALA 4.0 1.2 - - - -
1226A ILE* 1.3 92.3 + - + +
1228A GLU* 1.3 61.2 + - - +
1230A ILE* 3.6 27.6 - - + -
1245A ARG* 6.1 2.0 - - - +
1252A THR* 5.1 4.5 - - + +
1253A LEU* 4.1 40.6 - - + +
1256A ALA* 4.3 20.6 - - + -
1416A ILE* 5.2 5.6 - - + -
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Residues in contact with GLU1228 (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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1215A LEU 3.9 0.6 + - - -
1216A THR* 3.2 25.2 + - - +
1225A ALA* 3.8 21.6 - - + +
1226A ILE 4.2 1.9 + - - +
1227A LEU* 1.3 73.6 - - - +
1229A ASN* 1.3 86.8 + - + +
1230A ILE* 3.3 10.5 + - - +
1419A ASN* 3.4 44.0 - - - +
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Residues in contact with ASN1229 (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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1214A ASP* 3.0 33.8 + - - +
1215A LEU 2.8 14.2 + - - -
1216A THR* 3.0 11.8 + - - +
1228A GLU* 1.3 87.3 - - + +
1230A ILE* 1.3 61.1 + - - +
1231A SER* 3.7 5.7 + - - -
1419A ASN 5.6 1.7 - - - +
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Residues in contact with ILE1230 (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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1212A VAL* 3.8 4.2 - - + +
1213A LYS* 3.4 2.1 - - - -
1214A ASP 2.8 25.6 + - - -
1215A LEU* 2.8 31.3 + - + +
1227A LEU* 3.6 43.7 - - + -
1228A GLU 4.0 14.1 - - - +
1229A ASN* 1.3 69.2 - - - +
1231A SER* 1.3 61.9 + - - +
1232A PHE* 3.4 26.2 - - + -
1253A LEU* 5.4 2.9 - - + -
1416A ILE* 5.3 4.0 - - + -
1417A GLU 5.8 1.8 - - - +
1419A ASN* 6.0 0.9 - - - -
1420A LYS* 5.4 5.6 - - - +
1421A VAL* 3.4 38.4 - - + +
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Residues in contact with SER1231 (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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1212A VAL 3.4 10.8 - - - -
1213A LYS* 3.5 5.9 - - - +
1214A ASP* 2.8 34.1 + - - -
1229A ASN 3.7 5.3 + - - -
1230A ILE* 1.3 73.1 + - - +
1232A PHE* 1.3 65.2 + - - +
1421A VAL* 3.9 13.6 + - - +
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Residues in contact with PHE1232 (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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1211A THR* 3.7 1.8 - - - +
1212A VAL* 2.8 63.2 + - + +
1215A LEU* 5.8 2.0 - - + -
1230A ILE* 3.4 31.9 - - + -
1231A SER* 1.3 73.3 - - - +
1233A SER* 1.3 64.1 + - - +
1234A ILE* 4.1 24.5 - - + -
1253A LEU* 5.7 7.2 - - + -
1257A PHE* 5.0 13.9 - + - -
1414A LEU* 4.1 31.0 - - + -
1421A VAL* 3.5 27.6 - - + +
1422A ARG* 5.3 0.4 - - - +
1423A GLN* 5.3 6.1 - - + +
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Residues in contact with SER1233 (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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1209A GLN* 5.0 6.4 + - - +
1210A MET 3.1 12.7 + - - -
1211A THR* 3.5 17.4 + - - -
1232A PHE* 1.3 79.1 - - - +
1234A ILE* 1.3 71.9 + - - +
1235A SER 4.3 0.4 - - - -
1412A GLN* 4.0 1.0 - - - +
1414A LEU* 4.5 0.5 - - - +
1423A GLN* 3.9 25.8 - - - +
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Residues in contact with ILE1234 (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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1208A GLY 5.5 0.4 - - - +
1209A GLN* 3.4 5.2 - - - +
1210A MET* 2.8 60.6 + - + +
1232A PHE* 4.1 24.5 - - + -
1233A SER* 1.3 81.7 + - - +
1235A SER* 1.3 68.4 + - - +
1240A VAL* 3.6 17.0 - - + -
1257A PHE* 5.7 3.6 - - + -
1396A THR* 4.5 11.2 - - + -
1398A ILE* 4.3 21.8 - - + -
1412A GLN* 3.3 22.4 - - - +
1414A LEU* 4.2 17.0 - - + -
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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