Contacts of the helix formed by residues 66 - 78 (chain F) in PDB entry 3JSX
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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64F ASN* 3.0 35.9 + - - +
65F PHE* 1.3 101.0 + - - +
67F TYR* 1.3 64.8 + - - +
68F PRO* 3.4 11.6 - - + -
69F ALA* 3.6 12.5 + - + -
70F GLU* 2.9 30.3 + - + +
15H THR* 5.0 2.0 - - - +
601H FAD 2.7 41.1 + - - +
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Residues in contact with TYR 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F ILE* 3.7 27.9 - - + +
51F SER* 3.8 11.4 - - - -
54F ASP* 2.8 46.2 + - + +
55F ILE* 4.5 2.7 - - + -
65F PHE* 4.1 32.4 + + + -
66F GLN* 1.3 68.6 - - - +
68F PRO* 1.4 70.0 - - + +
71F SER* 2.4 61.1 + - - -
80F LEU* 5.5 0.2 - - - +
84F ILE* 4.3 1.0 - - - +
117F GLU 4.3 3.8 - - - -
118F ARG 4.2 3.1 + - - -
121F ILE* 3.5 24.1 - - + +
601H FAD 4.4 19.7 - - + -
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Residues in contact with PRO 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66F GLN* 3.5 11.7 - - + -
67F TYR* 1.4 100.1 - - + +
69F ALA* 1.3 61.2 + - - +
71F SER* 2.9 11.7 + - - +
72F VAL* 3.0 21.7 - - + +
126F TYR* 5.5 6.7 - - - +
128F TYR* 5.3 8.5 - - - +
601H FAD 3.7 39.5 - - + +
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Residues in contact with ALA 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66F GLN* 3.6 15.0 + - + +
67F TYR 3.4 0.2 - - - -
68F PRO* 1.3 79.0 - - - +
70F GLU* 1.3 56.6 + - + +
72F VAL* 3.1 7.6 + - - +
73F LEU* 2.7 36.6 + - - +
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Residues in contact with GLU 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F ILE* 4.1 7.7 - - + +
59F LEU* 3.8 7.5 - - - +
60F LYS* 2.8 34.1 + - - +
61F ASP* 2.8 36.4 + - - +
65F PHE* 3.5 36.3 - - + -
66F GLN* 2.9 31.3 + - + +
67F TYR 3.9 1.1 - - - +
69F ALA* 1.3 76.1 - - + +
71F SER* 1.3 54.0 + - - +
73F LEU* 3.5 9.4 - - - +
74F ALA* 2.6 35.1 + - - +
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Residues in contact with SER 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55F ILE* 4.5 4.9 - - - +
67F TYR* 2.4 64.6 + - - -
68F PRO* 2.9 10.7 + - - +
70F GLU* 1.3 71.2 - - - +
72F VAL* 1.3 53.8 + - - +
74F ALA* 3.2 9.8 + - - +
75F TYR* 2.6 33.8 + - - +
80F LEU* 3.9 6.3 - - - +
121F ILE* 3.7 20.8 - - - +
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Residues in contact with VAL 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68F PRO* 3.0 21.4 + - + +
69F ALA* 3.1 5.9 + - - +
71F SER* 1.3 73.9 - - - +
73F LEU* 1.3 64.4 + - - +
75F TYR* 3.0 9.2 + - - +
76F LYS* 3.0 33.7 + - - +
121F ILE* 4.1 2.0 - - + -
122F GLY* 3.8 29.8 - - - +
123F GLU* 3.7 31.6 - - + +
126F TYR* 5.2 2.7 - - - +
128F TYR* 6.2 3.8 - - + -
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Residues in contact with LEU 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B LYS* 5.4 8.1 - - - +
59F LEU 5.8 0.2 - - - -
60F LYS* 3.9 35.4 - - + +
69F ALA 2.7 19.9 + - - +
70F GLU* 3.5 9.6 - - - +
72F VAL* 1.3 73.1 - - - +
74F ALA* 1.3 66.7 + - - +
76F LYS* 3.0 20.6 + - + -
77F GLU* 3.1 45.3 + - + +
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Residues in contact with ALA 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F ILE* 3.6 31.0 - - + -
70F GLU 2.6 22.5 + - - +
71F SER 3.3 6.1 - - - +
73F LEU* 1.3 74.1 - - - +
75F TYR* 1.3 63.6 + - - +
77F GLU* 3.6 2.3 + - - -
78F GLY* 3.3 3.5 + - - -
79F HIS* 3.0 37.4 + - - +
80F LEU* 3.6 16.2 + - + -
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Residues in contact with TYR 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F SER 2.6 17.6 + - - +
72F VAL* 3.0 11.8 + - - +
74F ALA* 1.3 76.9 - - - +
76F LYS* 1.3 69.7 + - + +
77F GLU 3.6 0.2 + - - -
78F GLY* 3.7 7.7 + - - -
80F LEU* 3.7 16.4 - - + +
88F GLN* 3.9 18.4 - - - -
92F GLU* 4.9 4.2 + - - -
121F ILE* 4.2 5.8 - - + -
122F GLY 3.9 4.0 - - - -
123F GLU* 3.9 33.8 + - + -
124F PHE* 3.5 46.4 - + + +
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Residues in contact with LYS 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72F VAL* 3.0 22.9 + - + +
73F LEU* 3.0 14.3 + - + +
75F TYR* 1.3 89.3 - - + +
77F GLU* 1.3 62.1 + - + +
78F GLY 3.3 1.4 + - - -
123F GLU* 3.0 43.0 + - + -
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Residues in contact with GLU 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58F LYS* 5.5 6.4 + - - -
73F LEU* 3.1 45.6 + - + +
74F ALA* 5.1 0.7 - - - -
76F LYS* 1.3 78.4 - - + +
78F GLY* 1.3 62.8 + - - +
79F HIS* 3.1 36.0 + - + +
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Residues in contact with GLY 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56F THR* 4.9 1.4 - - - +
74F ALA 3.3 4.5 + - - -
75F TYR 3.7 6.1 + - - -
76F LYS 3.3 4.4 + - - -
77F GLU* 1.3 80.4 - - - +
79F HIS* 1.3 65.5 + - - +
80F LEU* 3.6 3.1 - - - +
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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