Contacts of the helix formed by residues 1311 - 1322 (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 SER1311 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1310A TRP* 1.3 73.0 - - - +
1312A ASP* 1.3 59.9 + - - +
1313A GLN* 4.3 10.6 + - - +
1314A GLU* 2.8 37.1 + - - +
1315A ILE* 3.1 29.2 + - - +
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Residues in contact with ASP1312 (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 ARG* 2.9 44.7 + - - +
1310A TRP 5.0 1.1 - - - +
1311A SER* 1.3 71.4 - - - +
1313A GLN* 1.3 57.5 + - + +
1315A ILE* 3.6 15.5 - - - +
1316A TRP* 2.8 50.8 + - + -
1335A LEU* 4.9 5.4 - - - +
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Residues in contact with GLN1313 (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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1311A SER* 3.3 9.6 + - - +
1312A ASP* 1.3 79.4 - - + +
1314A GLU* 1.3 51.6 + - - +
1316A TRP* 3.4 5.4 + - - +
1317A LYS* 2.8 34.7 + - - +
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Residues in contact with GLU1314 (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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1310A TRP* 3.5 35.4 - - + -
1311A SER* 2.8 38.3 + - - +
1313A GLN* 1.3 76.4 - - - +
1315A ILE* 1.3 62.8 + - - +
1317A LYS* 3.8 18.3 - - - +
1318A VAL* 2.8 39.4 + - + +
1361A LEU* 4.5 9.9 - - + +
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Residues in contact with ILE1315 (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 ARG* 5.5 7.9 - - + +
1304A LEU* 3.6 31.7 - - + +
1305A ASP* 5.0 10.1 - - + +
1310A TRP* 3.4 32.1 - - + +
1311A SER 3.1 22.4 + - - +
1312A ASP* 3.6 15.0 - - - +
1314A GLU* 1.3 76.0 - - + +
1316A TRP* 1.3 54.5 + - - +
1318A VAL* 3.8 4.4 - - - +
1319A ALA* 2.8 36.4 + - + +
1335A LEU* 3.9 22.7 - - + -
1361A LEU* 4.4 14.6 - - + -
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Residues in contact with TRP1316 (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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1312A ASP* 2.8 37.7 + - + +
1313A GLN* 3.7 5.4 - - - +
1315A ILE* 1.3 72.5 - - - +
1317A LYS* 1.3 58.5 + - - +
1319A ALA* 3.4 11.0 + - + +
1320A ASP* 2.9 28.9 + - - +
1325A ARG* 4.2 23.2 + - - -
1328A ILE* 3.7 20.6 - - + -
1329A GLU* 3.6 41.7 - - + -
1334A LYS* 3.9 50.0 - - + +
1335A LEU* 3.8 22.0 - - + +
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Residues in contact with LYS1317 (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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1313A GLN 2.8 21.9 + - - +
1314A GLU* 3.8 16.2 - - - +
1315A ILE 3.4 0.4 - - - -
1316A TRP* 1.3 72.5 - - - +
1318A VAL* 1.3 64.9 - - - +
1320A ASP* 3.6 8.4 + - + +
1321A GLU* 3.3 38.2 + - + +
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Residues in contact with VAL1318 (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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1314A GLU* 2.8 28.2 + - + +
1315A ILE* 3.9 4.9 - - - +
1317A LYS* 1.3 75.6 - - + +
1319A ALA* 1.3 57.7 + - - +
1321A GLU* 3.0 14.8 + - - +
1322A VAL* 2.8 51.8 + - + +
1357A ALA* 4.4 15.9 - - + +
1360A VAL* 4.1 18.2 - - + -
1361A LEU* 4.5 22.7 - - + +
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Residues in contact with ALA1319 (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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1304A LEU* 5.8 3.8 - - + -
1315A ILE* 2.8 26.2 + - + +
1316A TRP* 3.6 17.9 - - + +
1318A VAL* 1.3 73.6 - - - +
1320A ASP* 1.3 59.3 + - - +
1322A VAL* 3.8 10.1 - - - -
1323A GLY 3.2 1.4 + - - -
1324A LEU* 2.8 45.6 + - + -
1325A ARG* 3.0 10.2 + - - +
1328A ILE* 5.3 5.8 - - + -
1335A LEU* 6.2 2.2 - - + -
1357A ALA* 5.7 0.2 - - - -
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Residues in contact with ASP1320 (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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1316A TRP 2.9 17.6 + - - +
1317A LYS* 3.6 10.9 - - - +
1318A VAL 3.1 0.2 - - - -
1319A ALA* 1.3 75.6 - - - +
1321A GLU* 1.3 67.7 + - - +
1323A GLY* 3.7 7.6 + - - -
1325A ARG* 3.2 35.3 - - - +
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Residues in contact with GLU1321 (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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1317A LYS* 3.3 26.4 + - + +
1318A VAL* 3.0 17.8 + - + +
1320A ASP* 1.3 83.1 - - + +
1322A VAL* 1.3 64.6 + - + +
1323A GLY* 3.4 0.7 + - - -
1360A VAL* 5.5 6.0 - - + +
1387A THR* 3.5 14.2 + - - -
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Residues in contact with VAL1322 (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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1318A VAL* 2.8 39.0 + - + +
1319A ALA* 3.8 12.3 - - - +
1321A GLU* 1.3 73.9 - - + +
1323A GLY* 1.3 59.8 + - - +
1324A LEU* 3.9 11.9 - - + -
1353A LEU* 3.5 21.8 - - + +
1356A LEU* 4.6 12.8 - - + +
1357A ALA* 3.8 28.9 - - + +
1360A VAL* 4.0 27.1 - - + -
1387A THR* 3.7 17.8 - - - +
1391A ALA* 5.7 4.5 - - + -
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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