Contacts of the helix formed by residues 1278 - 1283 (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 THR1278 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1275A ASP 5.2 2.9 - - - +
1276A SER 3.6 6.2 + - - +
1277A ILE* 1.3 74.4 - - - +
1279A LEU* 1.3 59.9 + - - +
1280A GLN* 2.9 12.5 + - - +
1281A GLN* 2.9 26.2 + - - +
1282A TRP* 2.9 24.1 + - - -
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Residues in contact with LEU1279 (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* 3.9 51.4 - - + +
1259A ARG* 4.4 36.1 - - + +
1277A ILE 3.8 0.6 + - - -
1278A THR* 1.3 72.9 - - - +
1280A GLN* 1.3 69.7 + - + +
1282A TRP* 4.1 10.1 - - - +
1283A ARG* 2.8 60.0 + - - +
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Residues in contact with GLN1280 (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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276A CYS* 3.8 31.0 - - - +
278A GLU* 3.7 26.0 - - + +
958A GLN* 3.0 34.2 + - - +
1172A GLU 6.0 0.5 - - - -
1278A THR* 2.9 7.9 + - - +
1279A LEU* 1.3 89.7 - - + +
1281A GLN* 1.3 67.3 + - + +
1282A TRP 3.4 0.5 + - - -
1283A ARG* 3.4 24.1 + - - +
1284A LYS* 4.2 4.0 + - - -
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Residues in contact with GLN1281 (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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1277A ILE* 3.4 29.3 - - + +
1278A THR* 2.9 16.6 + - - +
1280A GLN* 1.3 81.0 - - + +
1282A TRP* 1.3 64.2 + - - +
1283A ARG 3.3 0.2 - - - -
1284A LYS* 3.4 33.0 + - + +
1285A ALA 4.6 0.2 + - - -
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Residues in contact with TRP1282 (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* 5.6 0.7 - - + -
1257A PHE 4.1 10.0 + - - -
1259A ARG* 4.8 11.4 - - + +
1267A ILE* 5.1 3.1 - - + -
1268A GLN 5.0 0.7 - - - -
1269A ILE* 3.3 48.5 - - + -
1272A VAL* 4.1 16.4 - - + -
1273A SER 3.7 21.5 - - - -
1274A TRP* 3.4 46.5 - + - -
1277A ILE* 3.3 24.5 - - + +
1278A THR 2.9 15.8 + - - +
1279A LEU* 4.1 10.5 - - - +
1281A GLN* 1.3 77.6 - - - +
1283A ARG* 1.3 70.1 + - + +
1284A LYS 3.2 1.2 + - - -
1285A ALA* 3.3 19.1 + - - +
1286A PHE* 3.8 20.6 + + - -
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Residues in contact with ARG1283 (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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273A LYS* 3.2 36.3 + - - +
274A ALA* 3.6 24.5 - - - +
276A CYS* 5.3 3.0 - - + +
1172A GLU* 5.8 1.2 + - - -
1258A LEU* 2.8 46.7 + - + +
1259A ARG* 3.4 17.2 + - - +
1260A LEU* 4.3 8.7 - - - +
1279A LEU* 2.8 56.8 + - - +
1280A GLN* 3.4 16.8 + - - +
1281A GLN 3.3 0.8 - - - -
1282A TRP* 1.3 79.1 - - + +
1284A LYS* 1.3 64.5 + - - +
1285A ALA 3.1 3.1 - - - -
1286A PHE* 3.0 27.4 + - - +
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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