Contacts of the helix formed by residues 1249 - 1259 (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 GLY1249 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1226A ILE* 6.0 1.2 - - - +
1245A ARG 4.2 1.4 + - - -
1247A GLY* 3.3 6.0 - - - +
1248A SER* 1.3 84.9 + - - +
1250A LYS* 1.3 63.5 + - - +
1251A SER* 3.4 3.4 - - - -
1252A THR* 3.9 19.1 + - - -
1253A LEU* 3.9 11.6 + - - +
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Residues in contact with LYS1250 (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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1242A LEU* 5.1 5.5 - - + +
1249A GLY* 1.3 71.2 - - - +
1251A SER* 1.3 62.0 + - - +
1252A THR 3.4 0.2 - - - -
1253A LEU* 3.5 7.7 + - - +
1254A LEU* 3.0 32.5 + - + +
1370A ASP* 3.4 20.2 - - - +
1371A GLU* 3.0 44.8 + - - +
1400A CYS* 3.4 38.1 - - + -
1401A GLU* 6.1 0.7 - - - +
1402A HIS* 3.3 27.2 + - + +
1416A ILE* 6.5 0.9 - - - -
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Residues in contact with SER1251 (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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1249A GLY* 3.4 1.3 - - - -
1250A LYS* 1.3 81.8 - - - +
1252A THR* 1.3 54.9 + - - +
1254A LEU* 3.3 14.2 + - - +
1255A SER* 2.8 41.2 + - - -
1370A ASP* 5.5 4.8 + - - -
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Residues in contact with THR1252 (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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1219A TYR* 5.5 7.9 - - + -
1226A ILE* 4.3 33.9 - - + +
1227A LEU* 5.1 5.3 - - + +
1248A SER 5.0 2.0 + - - -
1249A GLY* 3.9 17.3 + - - -
1250A LYS 3.4 0.6 - - - -
1251A SER* 1.3 77.1 - - - +
1253A LEU* 1.3 61.9 + - - +
1255A SER* 3.6 8.6 + - - -
1256A ALA* 3.4 17.8 + - - +
1261A LEU* 4.1 22.7 - - + +
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Residues in contact with LEU1253 (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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1227A LEU* 4.1 34.2 - - + +
1230A ILE* 5.4 3.4 - - + -
1232A PHE* 5.7 6.5 - - + -
1242A LEU* 5.2 13.5 - - + -
1249A GLY 3.9 9.8 + - - +
1250A LYS* 3.5 9.1 + - - +
1251A SER 3.3 0.4 - - - -
1252A THR* 1.3 77.2 - - - +
1254A LEU* 1.3 60.1 + - + +
1256A ALA* 3.0 26.6 + - + +
1257A PHE* 3.4 43.4 + - + -
1416A ILE* 3.6 39.0 - - + -
1421A VAL* 6.1 0.7 - - + -
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Residues in contact with LEU1254 (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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1242A LEU* 5.2 11.9 - - + -
1250A LYS* 3.0 27.3 + - + +
1251A SER* 3.3 11.0 + - - +
1253A LEU* 1.3 76.7 - - - +
1255A SER* 1.3 59.3 + - - +
1256A ALA 3.6 0.2 + - - -
1257A PHE* 3.7 21.4 + - + +
1258A LEU* 3.9 13.0 + - - +
1288A VAL* 5.8 4.9 - - + -
1368A LEU* 3.8 47.3 - - + +
1369A LEU 5.4 3.4 - - - +
1370A ASP* 3.3 40.6 - - + +
1398A ILE* 6.0 0.9 - - + -
1400A CYS* 5.8 3.4 - - + -
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Residues in contact with SER1255 (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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270A GLN* 4.5 12.5 + - - -
1251A SER* 2.8 31.3 + - - -
1252A THR* 3.6 10.1 - - - -
1253A LEU 3.2 0.2 - - - -
1254A LEU* 1.3 72.9 - - - +
1256A ALA* 1.3 53.8 + - - +
1258A LEU* 3.6 2.0 + - - +
1259A ARG 2.8 29.5 + - - -
1260A LEU* 3.0 31.3 + - - +
1261A LEU* 3.4 15.3 - - - -
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Residues in contact with ALA1256 (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* 5.1 10.7 - - + +
1217A ALA* 4.6 9.9 - - + -
1227A LEU* 4.3 19.7 - - + -
1252A THR 3.4 10.3 + - - +
1253A LEU* 3.0 13.6 + - + +
1255A SER* 1.3 75.7 - - - +
1257A PHE* 1.3 64.6 + - - +
1259A ARG* 3.6 13.9 + - - +
1261A LEU* 3.4 13.4 - - + +
1263A THR* 4.5 8.7 - - + +
1267A ILE* 5.0 7.1 - - - +
1274A TRP* 5.0 4.3 - - - -
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Residues in contact with PHE1257 (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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1210A MET* 3.7 36.1 - - + -
1212A VAL* 5.3 8.1 - - + -
1215A LEU* 6.3 1.6 - - + -
1232A PHE* 5.0 12.1 - + - -
1234A ILE* 5.7 2.0 - - + -
1242A LEU* 5.8 6.3 - - + -
1253A LEU* 3.4 45.6 + - + -
1254A LEU* 3.9 17.0 - - + +
1255A SER 3.3 0.4 - - - -
1256A ALA* 1.3 80.6 - - + +
1258A LEU* 1.3 62.7 + - + +
1259A ARG* 3.7 7.8 - - - +
1267A ILE* 5.7 6.7 - - + -
1274A TRP* 4.4 5.1 - - - -
1282A TRP* 4.1 16.3 + - - -
1286A PHE* 4.1 19.6 - + + -
1368A LEU* 4.1 34.5 - - + -
1398A ILE* 5.0 11.7 - - + -
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Residues in contact with LEU1258 (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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274A ALA* 3.5 32.3 - - + +
1254A LEU 3.9 10.0 + - - +
1255A SER 3.6 5.2 + - - +
1257A PHE* 1.3 79.5 - - + +
1259A ARG* 1.3 63.9 - - - +
1260A LEU* 4.3 18.8 - - + -
1282A TRP* 5.8 0.4 - - - -
1283A ARG* 2.8 58.9 + - + +
1286A PHE* 4.0 32.3 - - + -
1288A VAL* 3.7 24.9 - - + -
1368A LEU* 5.1 1.1 - - + -
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Residues in contact with ARG1259 (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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1172A GLU* 5.1 5.9 - - - +
1255A SER 2.8 10.4 + - - -
1256A ALA* 3.6 12.3 + - - +
1257A PHE 3.2 11.5 - - - +
1258A LEU* 1.3 82.8 - - - +
1260A LEU* 1.3 58.3 + - - +
1261A LEU 3.5 7.6 + - - +
1263A THR* 4.0 28.5 + - + +
1274A TRP* 3.3 60.3 + - + +
1275A ASP* 6.1 0.2 - - - +
1277A ILE 5.5 1.6 + - - -
1279A LEU* 4.4 36.0 - - + +
1282A TRP* 4.8 11.6 - - + +
1283A ARG* 3.4 14.9 + - - +
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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