Contacts of the helix formed by residues 69 - 79 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44C GLN* 5.9 0.9 - - - -
67D TRP* 3.9 21.0 + - + -
68D ASP* 1.3 74.7 - - - +
70D GLU* 1.3 66.6 + - - +
71D ASN* 2.8 33.9 + - - +
72D VAL* 3.0 31.6 + - + +
73D HIS* 3.1 18.5 + - - -
329D TYR* 3.3 24.9 + - - -
330D GLU* 4.7 1.0 - - - +
333D ARG* 4.3 14.7 + - - -
427D ARG* 5.3 4.0 - - - +
39E ASP* 4.9 2.9 - - - +
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Residues in contact with GLU 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B LYS* 4.6 18.1 + - - -
68D ASP 4.2 0.8 + - - -
69D ASP* 1.3 73.6 + - - +
71D ASN* 1.3 65.9 + - - +
73D HIS* 3.1 12.4 + - + +
74D LYS* 3.0 48.0 + - + +
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Residues in contact with ASN 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D ASP* 2.8 9.9 + - - +
70D GLU* 1.3 76.6 - - - +
72D VAL* 1.3 61.4 + - - +
74D LYS* 3.3 18.4 + - - +
75D LEU* 3.0 29.2 + - - +
329D TYR* 2.9 37.9 + - + +
39E ASP* 3.9 14.6 + - - +
40E ASP* 3.0 27.9 + - - +
43E PHE* 3.9 24.4 - - + +
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Residues in contact with VAL 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D ASP* 3.0 22.7 + - + +
71D ASN* 1.3 73.9 - - - +
73D HIS* 1.3 66.2 + - - +
75D LEU* 3.3 6.3 + - - +
76D MET* 2.9 24.4 + - + +
279D LEU 5.9 0.2 - - - +
281D PRO* 4.0 18.8 - - + -
326D ALA* 3.9 22.2 - - + -
329D TYR* 3.6 21.5 - - + -
330D GLU* 3.5 24.0 - - - +
427D ARG* 6.0 0.7 - - - +
80E ILE* 4.1 13.5 - - + -
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Residues in contact with HIS 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D ASP* 2.8 33.2 + - + +
69D ASP 3.1 33.1 + - - -
70D GLU* 3.1 12.3 + - + +
72D VAL* 1.3 76.4 - - + +
74D LYS* 1.3 58.7 + - + +
76D MET* 4.0 2.1 - - - +
77D ASP* 3.0 30.9 + - - +
77E ASP* 2.5 42.0 + - - +
80E ILE* 3.6 33.5 - - + +
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Residues in contact with LYS 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D GLU* 3.0 44.8 + - + +
71D ASN* 3.7 19.4 + - - +
73D HIS* 1.3 75.2 - - + +
75D LEU* 1.3 60.7 + - - +
77D ASP* 3.3 6.3 + - - +
78D LEU* 2.9 37.5 + - + +
43E PHE* 3.8 34.4 - - + -
70F GLU* 4.8 18.0 + - - -
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Residues in contact with LEU 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D ASN 3.0 20.8 + - - +
72D VAL* 3.9 4.3 - - - +
74D LYS* 1.3 76.6 - - - +
76D MET* 1.3 58.0 + - - +
78D LEU* 3.4 8.7 + - + +
79D SER* 2.7 32.8 + - - -
322D GLY* 5.2 0.7 - - - -
325D ILE* 4.1 20.4 - - + +
326D ALA* 4.6 8.5 - - + +
329D TYR* 3.5 45.1 - - + -
43E PHE* 3.7 25.4 - - + -
46E ILE* 4.0 26.5 - - + -
47E ASN 4.7 3.4 - - - +
50E LEU* 4.2 10.3 - - + +
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Residues in contact with MET 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D VAL* 2.9 26.3 + - + +
73D HIS* 4.0 3.4 - - - +
75D LEU* 1.3 73.9 - - - +
77D ASP* 1.3 59.9 + - - +
79D SER* 2.8 23.2 + - - -
80D ILE* 3.2 12.1 + - - +
281D PRO* 3.9 13.5 - - + -
282D LEU 5.2 0.7 - - - +
320D PRO* 6.2 2.0 - - + -
322D GLY* 3.4 31.9 - - - +
323D GLN* 3.7 31.0 - - + +
326D ALA* 4.6 0.9 - - + -
76E MET* 6.1 5.2 - - + -
80E ILE* 4.0 34.1 - - + -
320E PRO* 6.0 0.9 - - + -
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Residues in contact with ASP 77 (chain D).
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 3.0 20.3 + - - +
74D LYS* 3.7 6.5 - - - +
76D MET* 1.3 77.3 - - - +
78D LEU* 1.3 60.8 + - - +
79D SER 3.0 0.9 + - - -
80D ILE* 3.5 20.1 - - - +
73E HIS* 2.6 50.2 + - - +
77E ASP* 5.2 10.2 - - + +
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Residues in contact with LEU 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D LYS* 2.9 27.2 + - + +
75D LEU* 3.6 21.5 - - + +
76D MET 3.3 0.2 - - - -
77D ASP* 1.3 76.3 - - - +
79D SER* 1.3 60.5 + - - +
80D ILE* 3.5 1.8 + - - +
81D ASN* 5.0 1.6 + - - +
82D LYS* 3.6 20.2 - - - +
43E PHE* 4.6 5.8 - - + -
47E ASN* 3.4 26.5 - - - +
50E LEU* 4.7 9.6 - - + -
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Residues in contact with SER 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D LEU 2.7 21.1 + - - -
76D MET 2.8 5.2 + - - -
78D LEU* 1.3 80.4 - - - +
80D ILE* 1.3 65.0 + - - +
81D ASN 3.0 4.9 + - - -
82D LYS* 3.0 32.5 + - - +
320D PRO* 4.1 7.5 - - - +
322D GLY* 3.4 27.7 + - - -
325D ILE* 3.4 20.8 - - - +
50E LEU* 4.8 0.9 - - - +
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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