Contacts of the helix formed by residues 60 - 70 (chain C) in PDB entry 2BZN
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 60 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56C ASP 3.9 17.5 - - - +
57C THR 4.2 2.7 - - - -
58C VAL 2.9 14.1 + - - +
59C GLY* 1.3 77.0 - - - +
61C PHE* 1.3 60.9 + - - +
62C GLU* 3.5 9.7 + - - +
63C MET* 3.0 15.8 + - - +
64C ALA* 2.9 28.1 + - - +
74C THR* 4.0 2.0 - - - +
76C VAL* 5.4 1.1 - - - -
77C HIS* 4.3 2.7 - - + +
80C TYR* 3.2 14.4 - - - +
250C GLU 2.7 20.9 + - - +
252C GLY* 3.7 27.8 - - - +
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Residues in contact with PHE 61 (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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60C THR* 1.3 71.4 - - - +
62C GLU* 1.3 63.3 + - - +
64C ALA* 3.2 6.3 + - + +
65C LYS* 3.0 36.7 + - - +
76C VAL* 3.9 22.0 - - + -
80C TYR* 2.8 56.5 + + - +
84C GLN* 3.6 21.8 - - + -
85C TRP* 3.8 36.1 - + - -
88C PHE* 3.5 50.3 - + + -
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Residues in contact with GLU 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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60C THR* 3.5 16.5 - - - +
61C PHE* 1.3 82.0 + - - +
63C MET* 1.3 65.4 + - - +
65C LYS* 3.5 21.5 + - - +
66C VAL* 3.5 15.2 + - - +
80C TYR* 3.8 5.9 + - - -
249C SER 5.7 0.9 - - - +
250C GLU* 3.6 39.9 - - + +
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Residues in contact with MET 63 (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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52C ALA* 4.1 8.1 - - + -
58C VAL* 3.3 31.0 - - - +
60C THR* 3.0 14.6 + - - +
62C GLU* 1.3 75.7 - - - +
64C ALA* 1.3 66.2 + - - +
66C VAL* 3.1 3.6 + - - -
67C LEU* 2.9 58.9 + - + +
74C THR* 4.7 1.1 - - + +
245C LEU* 3.5 36.1 - - + +
250C GLU* 3.9 7.5 - - + +
251C SER* 3.7 24.5 - - - +
301C VAL* 3.8 22.7 - - + -
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Residues in contact with ALA 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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60C THR 2.9 13.5 + - - +
61C PHE* 3.2 11.6 + - + +
63C MET* 1.3 74.8 - - - +
65C LYS* 1.3 59.0 + - - +
67C LEU* 4.1 0.4 - - - +
68C CYS* 3.0 38.5 + - - -
74C THR* 3.4 28.4 + - + +
76C VAL* 5.5 1.1 - - + -
88C PHE* 4.3 15.9 - - + -
95C CYS* 4.6 3.6 - - + -
98C HIS 6.1 0.2 - - - +
99C LEU* 5.0 10.1 - - + -
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Residues in contact with LYS 65 (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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61C PHE* 3.0 24.4 + - - +
62C GLU* 3.7 22.1 + - - +
63C MET 3.2 0.4 - - - -
64C ALA* 1.3 76.9 - - - +
66C VAL* 1.3 62.2 + - + +
68C CYS* 4.0 0.2 - - - +
69C LYS* 2.7 39.8 + - - +
88C PHE* 4.0 14.4 - - + -
91C GLN* 5.7 3.0 + - - -
92C ASN* 3.4 37.3 + - - +
95C CYS* 4.1 5.2 - - - -
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Residues in contact with VAL 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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62C GLU 3.5 13.0 + - - +
63C MET 3.1 4.8 + - - +
65C LYS* 1.3 76.9 - - + +
67C LEU* 1.3 68.2 + - + +
69C LYS* 3.0 25.0 + - + +
70C PHE* 3.5 13.4 - - + -
250C GLU* 3.8 23.1 - - + +
301C VAL* 3.7 24.9 - - + -
302C GLU* 4.1 25.1 - - + +
305C ILE* 5.2 0.9 - - + -
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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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50C ILE* 6.3 0.2 - - + -
52C ALA* 3.6 32.5 - - + +
63C MET* 2.9 40.4 + - + +
64C ALA 4.1 2.5 - - - +
66C VAL* 1.3 79.0 - - - +
68C CYS* 1.3 56.2 + - - +
70C PHE* 2.9 22.7 + - - +
72C LEU* 3.0 49.8 + - + +
73C PHE 3.8 9.2 - - - +
74C THR* 3.8 13.0 - - - +
245C LEU* 4.4 6.3 - - + -
301C VAL* 4.3 4.9 - - + -
305C ILE* 4.1 22.7 - - + -
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Residues in contact with CYS 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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64C ALA* 3.0 24.5 + - - +
65C LYS 4.0 4.3 - - - +
67C LEU* 1.3 76.5 - - - +
69C LYS* 1.3 67.4 + - + +
70C PHE 3.0 0.2 - - - -
71C SER* 3.0 16.2 + - - +
72C LEU 4.0 11.4 + - - -
94C ASP 4.4 5.2 - - - +
95C CYS* 3.6 47.3 - - - -
98C HIS* 4.9 11.7 - - - -
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Residues in contact with LYS 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 LYS* 2.7 40.7 + - - +
66C VAL* 3.0 16.2 + - + +
68C CYS* 1.3 79.8 - - + +
70C PHE* 1.3 69.2 + - + +
71C SER* 3.9 0.7 + - - -
92C ASN* 5.5 2.6 - - - +
94C ASP* 6.2 1.4 - - - +
95C CYS* 4.2 14.6 - - - -
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Residues in contact with PHE 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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48C VAL* 3.6 10.0 - - - +
66C VAL* 3.5 24.5 - - + -
67C LEU* 2.9 9.1 + - - +
69C LYS* 1.3 86.6 - - + +
71C SER* 1.3 70.6 + - - +
72C LEU* 3.4 22.3 + - + +
302C GLU* 4.2 19.5 - - + -
305C ILE* 3.7 22.0 - - + -
306C ARG* 3.9 50.5 - - + -
309C LEU* 4.3 14.6 - - + +
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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