Contacts of the helix formed by residues 1061 - 1069 (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 GLY1061 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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496A TRP* 3.7 26.6 + - - -
1057A THR 3.4 6.9 + - - -
1058A SER* 3.9 6.2 + - - +
1059A LEU 3.5 0.2 - - - -
1060A LYS* 1.3 75.6 - - - +
1062A LEU* 1.3 57.8 + - - -
1063A TRP* 3.6 1.1 - - - -
1064A THR* 2.8 28.5 + - - -
1065A LEU* 3.0 19.8 + - - +
1074A PHE* 5.7 1.0 - - - -
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Residues in contact with LEU1062 (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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164A THR 4.5 5.8 - - - +
165A LEU* 3.9 28.7 - - + +
167A LEU* 5.9 1.1 - - + -
172A LEU* 3.7 28.9 - - + -
1058A SER 3.9 9.6 + - - +
1059A LEU* 3.7 24.4 + - + +
1060A LYS 3.2 5.5 + - - +
1061A GLY* 1.3 73.4 - - - +
1063A TRP* 1.3 64.9 + - + +
1065A LEU* 3.3 6.2 + - + +
1066A ARG* 2.8 84.5 + - + +
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Residues in contact with TRP1063 (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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169A SER* 4.8 8.4 + - - -
172A LEU* 4.5 29.4 - - + -
469A MET* 3.3 45.5 - - + -
472A MET* 4.4 11.4 - - + +
474A GLU* 3.9 23.1 - - + +
490A PHE* 4.5 18.2 - + + -
492A SER* 5.6 6.1 - - - -
494A PHE* 6.2 4.3 - + - -
1059A LEU 6.0 0.4 - - - -
1060A LYS 4.6 16.2 - - - -
1061A GLY* 6.1 0.2 - - - -
1062A LEU* 1.3 78.6 - - + +
1064A THR* 1.3 57.3 + - + +
1066A ARG* 3.8 17.6 - - - +
1067A ALA* 2.8 37.1 + - - +
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Residues in contact with THR1064 (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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490A PHE* 4.3 24.9 - - + +
492A SER* 4.5 16.6 - - - +
496A TRP* 3.2 35.3 + - + -
508A PHE* 5.2 5.0 - - - -
560A ARG* 4.5 12.3 - - - +
1061A GLY* 2.8 22.8 + - - -
1063A TRP* 1.3 76.4 - - + +
1065A LEU* 1.3 57.4 + - - +
1067A ALA* 4.5 3.6 - - - -
1068A PHE* 3.1 41.0 + - + +
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Residues in contact with LEU1065 (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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165A LEU* 3.6 32.5 - - + -
496A TRP* 6.2 0.2 - - - +
508A PHE* 5.3 3.1 - - + -
1058A SER 4.6 5.8 - - - +
1061A GLY 3.0 19.9 + - - +
1062A LEU* 3.5 7.9 - - + +
1064A THR* 1.3 76.3 + - - +
1066A ARG* 1.3 55.5 + - + +
1068A PHE* 5.2 0.9 - - - -
1069A GLY* 2.8 32.1 + - - -
1070A ARG* 3.3 47.5 + - + +
1071A GLN* 3.9 7.0 + - + +
1074A PHE* 3.5 43.5 - - + -
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Residues in contact with ARG1066 (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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165A LEU 3.6 22.2 + - - +
167A LEU* 2.7 39.6 + - - +
168A SER 4.8 1.6 + - - -
169A SER* 5.0 4.8 - - - +
172A LEU* 5.5 1.6 - - - +
380A TYR* 4.1 30.2 + - + +
382A THR* 5.4 3.3 + - - -
474A GLU* 3.2 38.5 + - - +
1062A LEU* 2.8 60.1 + - + +
1063A TRP* 3.8 16.8 - - - +
1065A LEU* 1.3 72.3 - - + +
1067A ALA* 1.3 65.0 + - - +
1069A GLY* 3.4 10.7 + - - -
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Residues in contact with ALA1067 (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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472A MET* 4.3 12.8 - - + -
488A ILE* 3.6 25.2 - - + +
489A SER 5.2 0.4 - - - -
490A PHE* 3.7 30.3 - - + +
564A LYS* 5.2 0.2 + - - -
1063A TRP 2.8 22.7 + - - +
1064A THR 4.1 2.9 - - - +
1066A ARG* 1.3 74.1 - - - +
1068A PHE* 1.3 64.6 + - + +
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Residues in contact with PHE1068 (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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488A ILE 5.0 1.3 - - - -
489A SER* 3.2 21.1 - - - -
490A PHE* 3.6 24.2 - - + -
508A PHE* 4.3 21.3 - + + -
560A ARG* 3.6 40.4 - - + -
561A ALA* 4.2 5.2 - - - -
564A LYS* 3.1 58.7 + - + +
1064A THR* 3.1 26.1 + - - +
1065A LEU 4.5 0.2 - - - +
1067A ALA* 1.3 84.0 - - + +
1069A GLY* 1.3 64.9 + - - +
1070A ARG* 3.8 18.4 - - + +
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Residues in contact with GLY1069 (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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1065A LEU 2.8 16.5 + - - -
1066A ARG* 3.8 8.7 - - - -
1067A ALA 3.4 2.4 - - - -
1068A PHE* 1.3 79.1 - - - +
1070A ARG* 1.3 62.1 + - - +
1071A GLN* 3.5 7.3 + - - +
1072A PRO* 4.4 6.1 - - - +
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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