Contacts of the helix formed by residues 69 - 79 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ASP* 4.9 2.5 - - - +
67C TRP* 3.9 23.3 + - + -
68C ASP* 1.3 75.4 - - - +
70C GLU* 1.3 66.8 + - - +
71C ASN* 2.8 19.2 + - - +
72C VAL* 3.0 31.1 + - + +
73C HIS* 3.0 16.3 + - - -
329C TYR* 2.9 30.7 + - - -
330C GLU* 4.7 0.5 - - - +
333C ARG* 4.4 9.7 + - - -
427C ARG* 5.1 4.5 - - - +
44D GLN* 5.9 0.7 - - - -
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Residues in contact with GLU 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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68C ASP 4.2 1.0 + - - -
69C ASP* 1.3 70.5 + - - +
71C ASN* 1.3 63.1 + - - +
73C HIS* 3.1 13.6 + - + +
74C LYS* 2.8 64.0 + - + +
74E LYS* 4.5 14.2 + - - -
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Residues in contact with ASN 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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39B ASP* 3.5 16.8 + - - +
40B ASP* 3.0 27.7 + - - +
43B PHE* 3.8 28.4 - - + +
69C ASP* 2.8 8.9 + - - +
70C GLU* 1.3 76.4 - - - +
72C VAL* 1.3 57.8 + - - +
74C LYS* 3.4 15.6 + - - +
75C LEU* 2.9 36.2 + - - +
329C TYR* 3.0 33.4 + - + +
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Residues in contact with VAL 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ILE* 4.0 13.5 - - + -
69C ASP* 3.0 22.5 + - + +
71C ASN* 1.3 76.5 - - - +
73C HIS* 1.3 64.4 + - + +
75C LEU* 3.3 6.2 + - - +
76C MET* 2.8 24.5 + - + +
281C PRO* 3.7 31.2 - - + -
326C ALA* 4.1 11.4 - - + -
329C TYR* 3.7 19.7 - - + -
330C GLU* 3.5 24.7 - - - +
427C ARG* 5.9 0.9 - - - +
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Residues in contact with HIS 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ASP* 2.4 42.8 + - - +
80B ILE* 3.5 37.1 - - + +
68C ASP* 2.7 33.0 + - + +
69C ASP 3.0 30.2 + - - -
70C GLU* 3.3 12.8 - - + +
72C VAL* 1.3 76.2 - - + +
74C LYS* 1.3 57.9 + - + +
76C MET* 3.3 2.9 + - - +
77C ASP* 2.9 31.2 + - - +
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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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70A GLU* 5.0 14.8 + - - -
43B PHE* 3.8 34.5 - - + -
70C GLU* 2.8 53.4 + - + +
71C ASN* 3.8 12.3 + - - +
73C HIS* 1.3 68.8 - - + +
75C LEU* 1.3 67.4 + - - +
77C ASP* 3.1 6.4 + - - +
78C LEU* 2.9 31.6 + - + +
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Residues in contact with LEU 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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43B PHE* 3.5 25.1 - - + -
46B ILE* 4.1 23.3 - - + -
47B ASN 4.5 4.7 - - - +
50B LEU* 4.5 3.8 - - + +
71C ASN 2.9 22.3 + - - +
72C VAL* 3.8 3.8 - - - +
74C LYS* 1.3 75.8 - - - +
76C MET* 1.3 62.7 + - - +
78C LEU* 3.5 14.7 + - + +
79C SER* 2.8 29.9 + - - -
322C GLY* 5.4 1.1 - - - +
325C ILE* 4.1 21.3 - - + +
326C ALA* 4.4 9.2 - - + +
329C TYR* 3.5 44.2 - - + -
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Residues in contact with MET 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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76B MET* 6.2 4.0 - - + -
80B ILE* 4.0 31.2 - - + -
320B PRO* 6.1 1.1 - - + -
72C VAL* 2.8 26.4 + - + +
73C HIS* 3.8 4.3 - - - +
75C LEU* 1.3 74.3 - - - +
77C ASP* 1.3 57.7 + - - +
79C SER* 3.0 19.8 + - - -
80C ILE* 3.3 12.8 + - - +
281C PRO* 4.1 10.3 - - + -
282C LEU 5.3 0.2 - - - +
320C PRO* 6.1 2.9 - - + -
322C GLY* 3.3 35.6 - - - +
323C GLN* 3.6 33.0 - - + +
326C ALA* 4.8 1.1 - - + -
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Residues in contact with ASP 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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73B HIS* 2.7 59.9 + - - +
76B MET* 6.1 0.2 - - - +
77B ASP* 5.1 10.2 - - + +
73C HIS 2.9 17.4 + - - +
74C LYS* 3.1 7.9 + - - +
76C MET* 1.3 78.5 - - - +
78C LEU* 1.4 62.6 + - - +
79C SER 3.4 0.7 + - - -
80C ILE* 3.7 10.2 - - - +
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Residues in contact with LEU 78 (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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43B PHE* 4.7 5.8 - - + -
47B ASN* 3.2 28.5 - - - +
50B LEU* 4.6 10.3 - - + -
74C LYS* 2.9 26.6 + - + +
75C LEU* 3.8 22.7 - - + +
77C ASP* 1.4 73.6 + - - +
79C SER* 1.3 60.0 + - - +
80C ILE* 3.5 2.6 + - - +
81C ASN* 4.9 1.6 + - - +
82C LYS* 3.5 20.2 - - - +
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Residues in contact with SER 79 (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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50B LEU* 4.4 2.8 - - - +
75C LEU 2.8 20.1 + - - -
76C MET 3.0 4.9 + - - -
78C LEU* 1.3 78.5 - - - +
80C ILE* 1.3 66.7 + - - +
81C ASN 3.0 3.6 - - - -
82C LYS* 2.8 37.1 + - - +
320C PRO* 4.2 7.6 - - - +
322C GLY* 3.4 27.6 - - - -
325C ILE* 3.5 20.4 - - - +
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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