Contacts of the helix formed by residues 1299 - 1305 (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 THR1299 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1298A GLY* 1.3 75.1 - - - -
1300A PHE* 1.3 52.7 + - - +
1301A ARG* 3.9 5.8 + - - +
1302A LYS* 2.9 30.1 + - - +
1303A ASN* 2.7 40.7 + - - +
1335A LEU 3.5 9.4 - - - -
1336A ASP* 3.4 29.2 - - + +
1337A PHE 3.5 5.6 - - - +
1338A VAL* 4.9 6.5 - - + -
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Residues in contact with PHE1300 (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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1299A THR* 1.3 69.3 - - - +
1301A ARG* 1.3 63.4 + - - +
1303A ASN* 3.8 3.8 - - - -
1304A LEU* 3.4 31.8 + - + +
1328A ILE* 4.1 20.2 - - + -
1331A PHE* 4.4 16.8 - + + -
1334A LYS 5.1 1.8 - - - -
1335A LEU* 2.8 36.9 + - + +
1337A PHE* 3.8 37.9 - + + -
1339A LEU* 3.7 39.5 - - + -
1346A LEU* 4.1 22.4 - - + -
1354A MET* 3.7 27.1 - - + -
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Residues in contact with ARG1301 (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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1299A THR* 4.1 6.5 - - - +
1300A PHE* 1.3 78.4 - - - +
1302A LYS* 1.3 59.7 + - - +
1304A LEU* 4.4 2.1 - - - +
1305A ASP* 3.4 25.8 + - - +
1310A TRP 6.0 0.2 + - - -
1312A ASP* 2.9 40.9 + - - +
1315A ILE* 5.5 7.5 - - + +
1335A LEU* 3.0 40.0 + - + +
1336A ASP* 3.2 20.3 + - - +
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Residues in contact with LYS1302 (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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280A ALA 5.6 2.0 + - - -
284A MET* 3.6 47.3 - - + +
1296A PHE* 4.7 10.2 - - + -
1298A GLY* 5.5 4.5 - - - -
1299A THR* 2.9 26.0 + - - +
1301A ARG* 1.3 79.1 - - - +
1303A ASN* 1.3 65.8 + - - +
1305A ASP 4.0 4.7 - - - +
1306A PRO* 3.3 38.1 + - + +
1308A GLU* 4.7 18.9 + - + +
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Residues in contact with ASN1303 (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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277A TRP* 4.9 0.3 - - - -
1294A PHE 5.0 0.2 - - - +
1295A ILE* 4.7 2.3 - - - -
1296A PHE* 3.6 43.4 + - - +
1299A THR 2.7 41.9 + - - +
1300A PHE* 4.0 2.2 - - - +
1301A ARG 3.5 0.4 - - - -
1302A LYS* 1.3 75.7 - - - +
1304A LEU* 1.3 62.1 + - - +
1305A ASP 3.5 0.3 + - - -
1306A PRO* 3.9 9.5 - - - +
1339A LEU* 3.3 28.5 - - - +
1354A MET* 3.4 24.1 - - + +
1358A ARG* 3.5 30.2 + - - +
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Residues in contact with LEU1304 (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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1300A PHE 3.4 18.8 + - - +
1301A ARG* 4.6 2.7 - - - +
1303A ASN* 1.3 79.5 - - - +
1305A ASP* 1.3 60.3 + - + +
1306A PRO* 3.9 3.7 - - - +
1310A TRP* 5.0 1.0 - - - -
1315A ILE* 3.6 33.0 - - + +
1319A ALA* 5.8 3.8 - - + -
1324A LEU* 4.9 5.8 - - + -
1328A ILE* 5.9 2.0 - - + -
1335A LEU* 4.8 9.4 - - + -
1354A MET* 3.5 35.2 - - + +
1357A ALA* 4.2 24.9 - - + -
1358A ARG* 4.3 22.7 - - + +
1361A LEU* 4.2 22.1 - - + +
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Residues in contact with ASP1305 (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 3.4 19.1 + - - +
1302A LYS* 3.4 6.6 - - - +
1303A ASN 3.3 1.0 - - - -
1304A LEU* 1.3 83.0 - - + +
1306A PRO* 1.4 64.0 - - - +
1307A TYR* 3.5 8.8 + - - +
1308A GLU* 2.9 35.4 + - - +
1309A GLN 2.8 9.0 + - - -
1310A TRP* 2.8 55.4 + - + +
1315A ILE* 5.0 6.7 - - + +
1361A LEU* 5.2 0.7 - - + -
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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