Contacts of the helix formed by residues 66 - 77 (chain C) in PDB entry 2FBW
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 GLN 66 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64C PRO 4.3 0.2 + - - -
65C GLU* 1.3 82.8 + - - +
67C PHE* 1.3 67.6 + - - +
68C PRO* 3.4 12.3 - - + -
69C HIS* 3.2 15.2 + - + +
70C TYR* 3.3 10.4 - - - -
85D TYR* 6.1 1.0 - - - -
89D TYR* 2.8 29.4 + - - +
90D ASP* 3.1 19.7 + - - +
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Residues in contact with PHE 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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56C PHE* 4.2 20.6 - + - -
65C GLU 4.0 0.2 + - - -
66C GLN* 1.3 72.3 - - - +
68C PRO* 1.3 71.9 - - + +
69C HIS 3.0 1.4 + - - -
70C TYR* 3.1 23.3 + + + +
71C VAL* 3.2 35.2 + - + +
86D PHE* 3.8 22.7 - + + -
90D ASP* 3.0 19.2 + - - +
91D VAL* 4.4 5.4 - - + -
96D ALA* 3.5 40.2 - - + -
99D MET* 4.2 9.2 - - + -
100D LEU* 4.4 18.2 - - + -
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Residues in contact with PRO 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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66C GLN* 3.5 11.9 - - + -
67C PHE* 1.3 94.5 - - + +
69C HIS* 1.3 55.4 + - - +
71C VAL* 3.7 2.7 - - + +
72C ALA* 3.0 29.1 + - - +
90D ASP* 3.7 10.1 - - - +
91D VAL* 3.9 17.7 - - + -
99D MET* 3.5 32.2 - - + +
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Residues in contact with HIS 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 GLU* 3.7 42.9 + - + +
66C GLN* 3.2 15.4 + - + +
67C PHE 3.0 1.0 + - - -
68C PRO* 1.3 78.0 - - - +
70C TYR* 1.3 74.4 + + - +
72C ALA* 3.2 8.1 + - - +
73C VAL* 3.0 50.7 + - + +
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Residues in contact with TYR 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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63C LEU* 3.6 28.0 - - + +
64C PRO* 3.4 17.7 - - - +
65C GLU* 3.2 52.2 + - + +
66C GLN 3.3 11.2 - - - -
67C PHE* 3.1 13.9 + + + +
69C HIS* 1.3 85.1 - + - +
71C VAL* 1.3 66.2 + - + +
73C VAL* 3.4 7.9 + - + +
74C VAL* 3.1 31.6 + - + +
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Residues in contact with VAL 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 PHE* 3.2 49.1 + - + +
68C PRO* 3.7 8.7 - - + +
69C HIS 3.3 0.2 - - - -
70C TYR* 1.3 77.0 - - + +
72C ALA* 1.3 61.9 + - - +
74C VAL* 3.4 6.1 + - - +
75C LYS* 3.1 43.7 + - + +
99D MET* 3.8 36.8 - - + +
100D LEU* 4.8 3.1 - - + +
103D ILE* 4.3 10.7 - - + +
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Residues in contact with ALA 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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68C PRO 3.0 17.6 + - - +
69C HIS* 3.5 6.5 - - - +
71C VAL* 1.3 74.8 - - - +
73C VAL* 1.3 66.0 + - + +
75C LYS* 3.2 10.0 + - - +
76C SER* 3.0 24.0 + - - -
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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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69C HIS* 3.0 44.0 + - + +
70C TYR* 3.8 9.6 - - + +
71C VAL 3.4 0.2 - - - -
72C ALA* 1.3 76.3 - - + +
74C VAL* 1.3 64.1 + - + +
76C SER* 2.5 26.5 + - - +
77C LEU* 3.4 17.5 + - + +
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Residues in contact with VAL 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 TYR* 3.1 20.0 + - + +
71C VAL* 3.8 4.5 - - - +
73C VAL* 1.3 80.4 - - + +
75C LYS* 1.3 61.8 + - - +
77C LEU* 3.1 19.7 + - + -
78C SER 4.0 0.3 + - - -
79C LEU* 3.5 26.1 + - + +
84C ILE* 5.8 0.4 - - + -
103D ILE* 3.7 36.5 - - + +
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Residues in contact with LYS 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 VAL* 3.1 34.1 + - + +
72C ALA* 3.2 8.3 + - - +
74C VAL* 1.3 75.2 - - - +
76C SER* 1.3 61.8 + - - +
78C SER* 3.3 15.9 + - - -
99D MET* 6.1 0.8 - - - +
102D SER* 2.9 49.7 + - - -
103D ILE* 3.9 20.2 - - + +
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Residues in contact with SER 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 ALA 3.0 12.4 + - - -
73C VAL* 2.5 27.2 + - - +
75C LYS* 1.3 75.3 - - - +
77C LEU* 1.3 69.5 + - - +
78C SER* 3.2 7.7 + - - -
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Residues in contact with LEU 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 VAL* 3.5 24.5 - - + +
74C VAL* 3.1 9.7 + - + +
76C SER* 1.3 80.9 - - - +
78C SER* 1.3 70.3 + - - +
79C LEU* 3.3 31.4 + - + +
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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