Contacts of the strand formed by residues 1366 - 1370 (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 ILE1366 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1208A GLY* 4.6 5.2 - - - +
1210A MET* 4.1 19.3 - - + -
1269A ILE* 4.0 39.5 - - + -
1285A ALA* 3.7 4.4 + - + +
1286A PHE* 3.5 35.4 - - + -
1287A GLY 3.1 22.2 + - - -
1364A ALA* 4.2 1.0 - - - +
1365A LYS* 1.3 85.3 - - + +
1367A LEU* 1.3 69.6 + - - +
1368A LEU* 5.0 0.2 - - + -
1396A THR* 3.6 25.6 - - + +
1398A ILE* 3.9 26.2 - - + -
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Residues in contact with LEU1367 (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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1287A GLY* 3.2 15.7 - - - +
1289A ILE* 6.0 2.9 - - + -
1356A LEU* 5.2 1.1 - - + -
1359A SER* 4.5 16.2 - - - +
1364A ALA* 4.3 11.0 - - + +
1365A LYS 4.2 7.6 - - - +
1366A ILE* 1.3 82.2 - - - +
1368A LEU* 1.3 65.2 + - - +
1369A LEU* 4.3 14.9 - - + +
1388A LEU* 5.7 0.2 - - + -
1392A PHE* 3.4 56.5 - - + -
1395A CYS* 4.7 2.0 - - + -
1396A THR 3.3 18.3 + - - +
1397A VAL* 3.9 5.1 - - + -
1398A ILE* 3.0 32.4 + - - +
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Residues in contact with LEU1368 (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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1254A LEU* 3.8 37.2 - - + +
1257A PHE* 4.1 35.0 - - + -
1258A LEU* 5.1 2.0 - - + -
1286A PHE* 4.5 18.4 - - + -
1287A GLY 3.0 10.0 + - - +
1288A VAL* 3.7 27.0 - - + +
1289A ILE* 3.2 27.7 + - - +
1366A ILE* 5.0 0.2 - - + -
1367A LEU* 1.3 72.5 - - - +
1369A LEU* 1.3 63.3 + - - +
1370A ASP* 4.1 1.0 + - - +
1398A ILE* 3.8 37.5 - - + -
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Residues in contact with LEU1369 (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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1254A LEU* 5.4 3.8 - - - +
1289A ILE* 3.7 19.3 - - + -
1367A LEU* 4.3 12.1 - - + -
1368A LEU* 1.3 82.5 - - - +
1370A ASP* 1.3 59.1 + - - +
1371A GLU 4.0 1.6 + - - -
1372A PRO* 4.9 12.6 - - + -
1388A LEU* 4.0 28.5 - - + -
1392A PHE* 6.6 0.2 - - + -
1397A VAL* 4.0 26.0 - - + -
1398A ILE 3.0 15.9 + - - +
1399A LEU* 3.8 27.1 - - + +
1400A CYS* 3.3 27.7 + - - +
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Residues in contact with ASP1370 (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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1250A LYS* 3.4 28.6 - - - +
1251A SER* 5.3 5.2 - - - -
1254A LEU* 3.3 32.8 - - + +
1288A VAL* 5.9 2.9 - - + -
1289A ILE* 4.0 14.0 + - - +
1290A PRO* 4.6 15.5 - - + +
1291A GLN* 3.1 41.2 + - - +
1368A LEU 4.1 1.7 + - - +
1369A LEU* 1.3 71.0 - - - +
1371A GLU* 1.3 68.8 + - - +
1372A PRO* 4.8 0.2 - - - +
1400A CYS* 4.9 1.1 - - - -
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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