Contacts of the helix formed by residues 69 - 77 (chain C) in PDB entry 5T46
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 VAL 69 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37C HIS* 2.9 28.7 + - + +
39C LEU* 3.7 21.3 - - + +
68C THR* 1.3 70.8 - - - +
70C GLU* 1.3 69.2 + - - +
72C PHE* 3.3 8.0 + - + +
73C TRP* 3.1 37.5 + - + +
138C ILE* 5.6 0.2 - - - -
612D TYR* 4.0 11.7 - - + -
616D PHE* 4.4 5.2 - - + -
617D LEU* 3.9 23.8 - - + +
620D PHE* 3.7 36.8 - - + -
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Residues in contact with GLU 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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34C TYR* 2.6 31.1 + - + -
36C LYS* 3.4 27.5 - - + +
37C HIS* 2.7 43.3 + - - -
68C THR 3.3 0.2 - - - -
69C VAL* 1.3 78.7 + - - +
71C ASP* 1.3 59.3 + - - +
73C TRP 3.3 0.9 + - - -
74C ALA* 2.8 29.7 + - - +
620D PHE* 3.7 9.5 - - + -
623D ILE* 3.8 22.0 - - + -
625D ALA* 4.1 7.9 - - + -
626D SER* 3.5 18.7 + - - +
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Residues in contact with ASP 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C LYS* 2.7 32.8 + - - +
66C PHE* 3.8 23.6 - - + +
67C ASP* 4.8 3.5 + - - +
68C THR* 2.7 33.5 + - - +
70C GLU* 1.3 74.7 - - - +
72C PHE* 1.3 64.3 + - - +
74C ALA* 3.9 8.9 - - - +
75C LEU* 3.1 23.9 + - - +
630D PRO* 5.2 1.2 - - - +
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Residues in contact with PHE 72 (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 PHE* 3.6 44.9 - + + -
68C THR 3.0 11.9 + - - +
69C VAL* 3.3 7.6 + - - +
71C ASP* 1.3 74.9 - - - +
73C TRP* 1.3 103.5 + + - +
75C LEU* 3.2 5.5 + - + +
76C TYR* 2.9 36.6 + + + +
93C LEU* 5.7 0.7 - - + -
131C LEU* 4.1 8.7 - - + -
134C LEU* 4.0 44.0 - - + -
135C LEU* 4.2 2.9 - - + -
138C ILE* 3.5 32.8 - - + -
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Residues in contact with TRP 73 (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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69C VAL* 3.1 31.8 + - + +
70C GLU 3.8 0.2 - - - +
72C PHE* 1.3 100.6 - + - +
74C ALA* 1.3 57.2 + - - +
76C TYR* 3.7 20.6 - + - -
77C ASN* 2.7 39.4 + - - +
131C LEU* 3.8 22.9 - - + -
135C LEU* 4.0 13.0 - - + -
617D LEU* 2.9 29.5 + - - +
618D LEU* 3.8 26.7 - - + -
620D PHE* 3.8 9.0 - - + -
621D GLN* 3.4 49.8 - - + +
626D SER* 3.5 22.2 - - - +
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Residues in contact with ALA 74 (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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70C GLU 2.8 21.4 + - - +
71C ASP* 3.9 11.4 - - - +
73C TRP* 1.3 73.2 - - - +
75C LEU* 1.3 62.2 + - - +
78C HIS* 2.7 26.7 + - - -
625D ALA 4.0 8.5 - - - +
626D SER 3.2 16.0 + - - +
628D GLN 3.4 21.8 - - - +
630D PRO* 3.4 15.5 - - + +
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Residues in contact with LEU 75 (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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45C LEU* 3.9 30.3 - - + -
63C ILE* 4.0 23.6 - - + -
64C SER* 4.1 13.5 - - - -
66C PHE* 3.8 30.7 - - + -
71C ASP 3.1 13.2 + - - +
72C PHE* 3.5 7.6 - - + +
74C ALA* 1.3 76.0 - - - +
76C TYR* 1.3 67.1 + - - +
78C HIS* 3.0 12.3 + - - +
79C ILE* 3.4 27.4 + - + +
630D PRO* 4.0 9.1 - - + +
633D LEU* 4.0 21.3 - - + -
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Residues in contact with TYR 76 (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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72C PHE* 2.9 34.0 + + + +
73C TRP* 3.7 25.1 - + + +
75C LEU* 1.3 74.1 - - - +
77C ASN* 1.3 69.0 + - - +
78C HIS 3.2 1.2 + - - -
79C ILE* 3.5 30.7 + - + +
81C LEU* 3.9 15.6 - - + +
127C ASP* 4.6 2.6 + - - +
130C TRP* 5.0 8.1 - + - -
131C LEU* 3.8 27.7 - - + +
134C LEU* 3.9 24.5 - - + -
302C GOL 2.7 38.5 + - - -
621D GLN* 4.0 9.6 - - - -
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Residues in contact with ASN 77 (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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73C TRP* 2.7 22.6 + - - +
75C LEU 3.2 0.2 - - - -
76C TYR* 1.3 77.9 - - - +
78C HIS* 1.3 75.0 + - + +
79C ILE 3.6 2.0 + - - -
621D GLN* 2.9 56.3 + - - +
622D PHE* 4.6 3.3 - - - -
626D SER 3.1 17.9 + - - +
627D MET* 3.6 17.3 - - + +
641D LEU* 4.3 8.8 - - - +
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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