Contacts of the helix formed by residues 65 - 77 (chain C) in PDB entry 4A8X
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 THR 65 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63C ASP 3.4 8.5 + - - +
64C ALA* 1.3 77.6 - - - +
66C LEU* 1.3 64.7 + - - +
67C LYS* 3.5 4.2 + - - +
68C GLU* 3.0 27.9 + - - +
69C LEU* 3.0 28.5 + - - +
118C ASP 3.4 12.0 + - - -
119C SER* 3.7 24.7 - - - +
120C MET 3.1 6.7 - - - -
121C THR* 4.0 5.6 - - + -
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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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65C THR* 1.3 73.0 - - - +
67C LYS* 1.3 58.0 + - - +
69C LEU* 3.8 11.8 - - + -
70C THR* 2.7 34.6 + - - -
89C PHE* 3.8 35.8 - - + -
106C ILE* 4.0 17.3 - - + -
107C GLY* 3.9 34.3 - - - +
108C SER 4.1 0.7 - - - +
109C THR* 3.8 11.2 - - + -
117C ASP* 3.5 27.8 - - + +
118C ASP 3.5 0.8 + - - -
120C MET* 3.0 27.3 + - + +
121C THR 6.0 1.6 - - - -
122C LEU* 5.6 3.4 - - + -
133C LEU* 5.9 0.7 - - + -
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Residues in contact with LYS 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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65C THR* 3.9 3.4 - - - +
66C LEU* 1.3 77.9 - - - +
68C GLU* 1.3 60.9 + - - +
70C THR* 3.3 8.4 + - - -
71C SER* 3.1 21.7 + - - -
109C THR* 4.6 4.5 - - - -
118C ASP* 2.9 45.4 + - + +
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Residues in contact with GLU 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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22C ARG* 2.7 45.2 + - - -
60C THR* 4.6 4.7 + - - -
61C TRP* 5.4 0.5 - - - -
63C ASP 4.5 0.7 - - - +
64C ALA* 3.4 18.9 - - + -
65C THR* 3.0 21.7 + - - +
67C LYS* 1.3 78.6 - - - +
69C LEU* 1.3 60.2 + - - +
71C SER* 2.7 23.3 + - - +
72C LEU* 3.3 23.4 + - + +
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Residues in contact with LEU 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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30C LEU* 4.2 19.1 - - + -
58C ILE* 4.7 7.5 - - + +
60C THR* 4.4 9.4 - - + +
64C ALA* 4.2 20.2 - - + -
65C THR 3.0 24.4 + - - +
66C LEU* 3.9 13.2 - - + +
68C GLU* 1.3 73.0 - - + +
70C THR* 1.3 66.6 + - - +
72C LEU* 3.2 19.0 + - + +
73C VAL* 3.0 28.3 + - + +
89C PHE* 4.1 11.4 - - + -
122C LEU* 4.2 19.7 - - + -
133C LEU* 3.9 23.6 - - + -
135C ILE* 5.7 0.4 - - + -
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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
----------------------------------------------------------
66C LEU 2.7 24.7 + - - -
67C LYS* 3.4 8.3 - - - -
69C LEU* 1.3 76.3 - - - +
71C SER* 1.3 57.7 + - - +
73C VAL* 3.2 8.1 + - - +
74C LYS* 2.9 52.6 + - - +
87C PHE* 3.7 22.6 - - + -
89C PHE* 3.3 14.2 - - - -
109C THR* 2.8 25.1 + - - +
110C MET 6.0 0.4 - - - -
111C SER 5.8 0.9 - - - +
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Residues in contact with SER 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 LYS* 3.1 12.8 + - - +
68C GLU* 2.7 24.6 + - - +
70C THR* 1.3 73.6 - - - +
72C LEU* 1.3 61.7 + - - +
74C LYS* 3.3 14.0 + - - +
75C GLU* 3.0 27.4 + - - +
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Residues in contact with LEU 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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58C ILE* 4.0 39.5 - - + -
59C TYR 5.6 1.8 - - - +
60C THR* 5.3 3.6 - - - +
68C GLU* 3.3 27.3 + - + +
69C LEU* 3.2 16.7 + - + +
71C SER* 1.3 78.0 - - - +
73C VAL* 1.3 63.3 + - - +
75C GLU* 3.1 37.3 + - - +
76C VAL* 3.2 14.5 + - - +
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Residues in contact with VAL 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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32C VAL* 5.0 1.8 - - + -
34C THR* 4.9 5.4 - - + -
56C LEU* 4.5 20.0 - - + -
58C ILE* 4.9 7.2 - - + -
69C LEU* 3.0 17.9 + - + +
70C THR* 3.5 10.1 - - - +
72C LEU* 1.3 77.7 - - - +
74C LYS* 1.3 57.7 + - - +
76C VAL* 3.1 4.7 + - - +
77C TYR* 2.9 41.6 + - + +
80C ALA* 5.1 2.0 - - + -
87C PHE* 4.1 22.2 - - + -
89C PHE* 5.7 0.4 - - + -
135C ILE* 3.9 26.5 - - + -
137C ILE* 4.3 11.4 - - + -
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Residues in contact with LYS 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 THR* 2.9 39.8 + - - +
71C SER* 3.7 12.1 - - - +
72C LEU 3.3 0.2 - - - -
73C VAL* 1.3 73.4 - - - +
75C GLU* 1.3 64.7 + - - +
77C TYR 3.3 23.7 - - - -
78C PRO* 3.4 9.0 - - - +
80C ALA* 4.1 12.3 - - - +
81C ARG* 3.9 26.2 + - + +
87C PHE* 4.0 9.2 - - + -
110C MET 5.3 0.2 - - - -
111C SER* 2.9 40.8 + - - +
112C GLY 4.6 3.0 - - - +
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Residues in contact with GLU 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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71C SER 3.0 11.7 + - - +
72C LEU* 3.1 35.3 - - - +
74C LYS* 1.3 79.7 - - - +
76C VAL* 1.3 59.6 + - + +
78C PRO* 4.2 9.4 - - - +
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Residues in contact with VAL 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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56C LEU* 3.9 40.2 - - + -
58C ILE* 6.3 0.4 - - + -
72C LEU 3.5 13.5 - - - +
73C VAL 3.1 7.7 + - - +
75C GLU* 1.3 80.9 - - + +
77C TYR* 1.3 78.7 + - + +
78C PRO* 3.5 7.1 - - - +
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Residues in contact with TYR 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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34C THR* 3.7 32.2 + - + -
54C SER* 4.3 20.1 + - - -
56C LEU* 4.7 9.9 - - + +
73C VAL* 2.9 26.9 + - + +
74C LYS* 3.3 8.4 - - - +
76C VAL* 1.3 100.8 - - + +
78C PRO* 1.3 65.9 - - - +
79C GLU* 3.2 4.9 - - + +
80C ALA* 3.0 28.2 + - + +
137C ILE* 5.1 5.6 - - + -
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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