Contacts of the helix formed by residues 61 - 71 (chain C) in PDB entry 5F28
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 ASP 61 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C ALA* 3.9 3.1 - - - -
60C THR* 1.3 84.5 - - + +
62C MET* 1.3 66.1 + - - +
63C ASP* 3.2 16.6 + - - +
64C LYS* 3.2 29.3 + - + +
65C VAL* 3.2 26.3 + - - +
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Residues in contact with MET 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C ALA* 3.8 17.7 - - - -
45C LEU 3.9 14.6 - - - +
46C ILE* 4.3 10.3 - - + -
56C GLN* 3.4 35.9 - - + +
57C TYR 3.4 30.5 - - - +
58C ALA* 3.7 11.5 - - + +
61C ASP* 1.3 71.3 + - - +
63C ASP* 1.3 68.6 + - - +
65C VAL* 3.0 12.9 + - - +
66C LEU* 3.1 30.1 + - + +
69D TYR* 3.1 26.5 - - + +
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Residues in contact with ASP 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C ASP* 3.2 8.0 + - - +
62C MET* 1.3 79.4 - - - +
64C LYS* 1.3 61.1 + - - +
66C LEU* 3.9 8.2 - - - +
67C LEU* 3.1 24.9 + - - +
69D TYR* 4.3 10.3 + - - -
959E LEU* 5.5 2.8 - - - +
962E ARG* 3.7 45.8 + - - +
963E THR* 4.5 17.6 + - + +
966E ALA* 4.5 8.7 - - - +
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Residues in contact with LYS 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C GLU* 5.5 12.4 - - - +
60C THR* 5.0 15.5 + - + +
61C ASP* 3.2 36.0 + - + +
62C MET 3.1 0.8 - - - -
63C ASP* 1.3 78.0 - - - +
65C VAL* 1.3 68.5 + - + +
67C LEU* 3.7 8.1 - - + +
68C LYS* 3.1 30.6 + - + +
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Residues in contact with VAL 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C GLU* 4.5 19.3 - - + +
43C ILE 4.4 14.6 - - - +
44C ALA* 3.7 29.2 - - + +
58C ALA* 5.2 0.9 - - + -
59C SER* 5.0 3.8 - - - +
60C THR* 6.2 0.7 - - - -
61C ASP 3.3 17.0 - - - +
62C MET* 3.0 8.0 + - - +
64C LYS* 1.3 81.8 - - + +
66C LEU* 1.3 58.0 + - - +
68C LYS* 3.2 9.8 + - - +
69C TYR* 2.9 24.8 + - - +
46D ILE* 3.9 20.2 - - + -
48D PHE* 3.9 12.3 - - + -
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Residues in contact with LEU 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C ALA* 4.6 3.6 - - + -
46C ILE* 4.6 6.5 - - + -
62C MET* 3.1 32.9 + - + +
63C ASP* 4.2 8.7 - - - +
65C VAL* 1.3 73.0 - - - +
67C LEU* 1.3 60.1 + - - +
69C TYR* 3.1 9.7 + - + +
70C THR* 3.0 31.3 + - - -
46D ILE* 4.5 20.0 - - + -
66D LEU* 4.0 24.2 - - + -
69D TYR* 3.6 35.7 - - + -
959E LEU* 4.2 24.7 - - + +
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Residues in contact with LEU 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C ASP 3.1 20.7 + - - +
64C LYS* 3.7 7.9 - - + +
65C VAL 3.3 0.2 - - - -
66C LEU* 1.3 73.5 - - - +
68C LYS* 1.3 65.0 + - - +
70C THR* 3.1 8.3 + - + -
71C GLU* 3.0 55.7 + - + +
963E THR* 6.0 2.7 - - - +
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Residues in contact with LYS 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C GLU* 2.8 24.2 + - + +
64C LYS* 3.1 18.9 + - + +
65C VAL* 3.2 11.9 + - - +
67C LEU* 1.3 80.5 - - - +
69C TYR* 1.3 61.2 + - - +
71C GLU* 3.4 23.6 - - - +
72C TYR* 3.7 5.5 - - + +
48D PHE* 3.7 37.3 - - + -
52D ASN* 2.6 37.6 + - - -
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Residues in contact with TYR 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C VAL 2.9 12.6 + - - +
66C LEU* 3.3 15.7 - - + +
67C LEU 3.0 0.2 - - - -
68C LYS* 1.3 75.9 - - - +
70C THR* 1.3 73.6 + - - +
72C TYR* 3.3 18.7 + - - +
76C HIS* 4.9 3.0 + + - -
46D ILE* 3.5 30.5 - - + -
48D PHE* 3.9 8.1 - - + -
54D LEU* 3.8 22.9 - - + -
56D GLN* 2.7 32.4 + - - -
62D MET* 3.3 19.2 - - + +
63D ASP* 4.8 3.6 + - - -
66D LEU* 3.6 28.5 - - + -
955E LYS* 4.4 11.7 - - - -
959E LEU* 6.2 0.7 - - + -
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Residues in contact with THR 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C LEU 3.0 14.5 + - - -
67C LEU* 3.1 11.5 + - + -
69C TYR* 1.3 82.0 - - - +
71C GLU* 1.3 61.9 + - + +
72C TYR 3.0 10.4 + - - +
955E LYS* 5.2 5.3 - - - +
956E GLU* 4.0 31.6 - - + +
959E LEU* 3.5 23.0 - - + +
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Residues in contact with GLU 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C LEU* 3.0 47.0 + - + +
68C LYS* 3.4 12.4 - - - +
70C THR* 1.3 76.4 - - + +
72C TYR* 1.3 60.5 + - - +
73C ASN* 4.4 2.9 - - - -
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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