Contacts of the helix formed by residues 69 - 79 (chain E) in PDB entry 3FZ7
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 ASP 69 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39D ASP* 5.1 2.1 - - - +
67E TRP* 3.7 23.4 + - + -
68E ASP* 1.3 76.0 - - - +
70E GLU* 1.3 66.4 + - - +
71E ASN* 3.0 22.5 + - - +
72E VAL* 2.9 30.3 + - + +
73E HIS* 3.1 18.7 + - - -
329E TYR* 3.3 26.1 + - - -
330E GLU* 4.5 1.0 - - - +
333E ARG* 4.3 12.6 + - - -
427E ARG* 5.2 2.9 - - - +
44F GLN* 5.8 1.6 - - - -
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Residues in contact with GLU 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A LYS* 4.5 16.5 + - - -
68E ASP 4.2 1.0 + - - -
69E ASP* 1.3 74.0 + - - +
71E ASN* 1.3 60.1 + - - +
73E HIS* 3.2 11.7 + - + +
74E LYS* 2.8 60.0 + - + +
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Residues in contact with ASN 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D ASP* 3.6 17.8 + - - +
40D ASP* 2.8 29.6 + - - +
43D PHE* 3.8 22.7 - - + +
69E ASP* 3.0 6.4 + - - +
70E GLU* 1.3 80.7 - - - +
72E VAL* 1.3 56.7 + - - +
74E LYS* 3.2 19.6 + - - +
75E LEU* 3.0 34.2 + - - +
329E TYR* 3.0 36.7 + - + +
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Residues in contact with VAL 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D ILE* 4.0 13.0 - - + -
69E ASP* 2.9 22.8 + - + +
71E ASN* 1.3 72.8 - - - +
73E HIS* 1.3 56.6 + - + +
74E LYS 3.2 0.2 + - - -
75E LEU* 3.3 7.3 + - - +
76E MET* 2.7 35.4 + - + +
279E LEU 5.9 0.2 - - - +
281E PRO* 3.9 30.5 - - + -
326E ALA* 4.0 10.7 - - + +
329E TYR* 3.6 20.4 - - + -
330E GLU* 3.6 24.0 - - - +
427E ARG* 6.0 0.4 - - - +
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Residues in contact with HIS 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D ASP* 2.6 39.5 + - - +
80D ILE* 3.4 36.2 - - + +
68E ASP* 2.5 34.3 + - + +
69E ASP 3.1 33.2 + - - -
70E GLU* 3.4 13.2 - - + +
72E VAL* 1.3 76.4 - - + +
74E LYS* 1.3 57.2 + - + +
76E MET* 3.9 1.9 - - - +
77E ASP* 3.0 30.3 + - - +
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Residues in contact with LYS 74 (chain E).
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* 4.5 14.5 + - - -
43D PHE* 3.8 34.6 - - + -
70E GLU* 2.8 43.4 + - + +
71E ASN* 3.5 21.6 + - - +
72E VAL 3.1 0.2 - - - -
73E HIS* 1.3 75.1 - - + +
75E LEU* 1.3 60.7 + - - +
77E ASP* 3.5 5.3 + - - +
78E LEU* 3.0 35.5 + - + +
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Residues in contact with LEU 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D PHE* 3.6 26.2 - - + -
46D ILE* 3.9 26.0 - - + -
47D ASN 4.5 3.6 - - - +
50D LEU* 4.3 10.8 - - + -
71E ASN 3.0 20.5 + - - +
72E VAL* 3.8 4.5 - - - +
74E LYS* 1.3 73.0 - - - +
76E MET* 1.3 65.7 + - - +
78E LEU* 3.4 7.9 + - + +
79E SER* 2.7 29.1 + - - -
322E GLY 5.3 1.1 - - - -
325E ILE* 4.1 20.9 - - + +
326E ALA* 4.5 8.3 - - + +
329E TYR* 3.6 42.8 - - + -
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Residues in contact with MET 76 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D MET* 6.1 5.2 - - + -
80D ILE* 3.8 33.4 - - + -
320D PRO* 6.0 1.1 - - + -
72E VAL* 2.7 25.5 + - + +
73E HIS* 3.9 3.8 - - - +
75E LEU* 1.3 72.5 - - - +
77E ASP* 1.3 57.1 + - - +
79E SER* 2.9 20.4 + - - -
80E ILE* 3.3 12.0 + - - +
281E PRO* 4.0 11.4 - - + -
282E LEU 5.3 0.2 - - - +
320E PRO* 6.0 3.6 - - + -
322E GLY* 3.3 36.1 - - - +
323E GLN* 3.4 37.5 - - + +
326E ALA* 4.7 1.6 - - + -
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Residues in contact with ASP 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D HIS* 2.5 61.3 + - - +
76D MET* 6.1 0.3 - - - +
77D ASP* 5.2 9.7 - - + +
73E HIS 3.0 19.2 + - - +
74E LYS* 3.8 5.1 - - - +
75E LEU 3.3 0.2 - - - -
76E MET* 1.3 75.7 - - - +
78E LEU* 1.3 62.6 + - - +
79E SER 3.3 0.7 + - - -
80E ILE* 3.7 11.2 - - - +
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Residues in contact with LEU 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D PHE* 4.6 9.6 - - + -
47D ASN* 3.4 27.6 - - + +
50D LEU* 4.9 12.8 - - + -
74E LYS* 3.0 26.5 + - + +
75E LEU* 3.8 15.9 - - + +
76E MET 3.3 0.2 - - - -
77E ASP* 1.3 77.9 + - - +
79E SER* 1.3 60.4 + - - +
80E ILE* 3.6 1.9 + - - +
81E ASN* 5.0 1.2 + - - +
82E LYS* 3.8 14.3 - - - +
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Residues in contact with SER 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D LEU* 4.6 1.2 - - - +
75E LEU 2.7 20.7 + - - -
76E MET 2.9 5.5 + - - -
78E LEU* 1.3 79.2 - - - +
80E ILE* 1.3 62.2 + - - +
81E ASN 2.9 7.8 + - - -
82E LYS* 2.9 35.8 + - - +
320E PRO* 4.2 7.7 - - - +
322E GLY* 3.5 27.9 + - - -
325E ILE* 3.3 20.5 - - - +
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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