Contacts of the helix formed by residues 74 - 89 (chain E) in PDB entry 3F0D
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 74 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37E SER* 5.2 10.1 + - - -
38E ASP* 4.0 11.8 - - - +
75E SER* 1.3 64.4 + - - +
76E ARG* 3.0 16.1 + - - +
77E ALA* 2.8 48.4 + - + +
78E LEU* 3.1 20.8 + - - +
80E ARG* 4.5 3.3 + - - -
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Residues in contact with SER 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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37E SER* 5.6 1.4 - - - -
38E ASP* 2.4 38.0 + - - -
40E ASP* 3.7 16.9 - - - +
43E LEU* 3.9 16.1 - - - +
44E HIS* 3.0 26.6 + - - -
47E THR* 5.1 0.9 + - - -
74E ASP* 1.3 72.5 + - - +
76E ARG* 1.3 57.4 + - - +
78E LEU* 3.4 12.5 + - - +
79E LEU* 2.9 27.5 + - - +
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Residues in contact with ARG 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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24E GLY* 4.0 22.5 + - - -
43E LEU* 3.5 19.5 - - + -
74E ASP* 3.0 11.7 + - - +
75E SER* 1.3 76.0 - - - +
77E ALA* 1.3 65.7 + - - +
79E LEU* 3.2 3.4 + - - +
80E ARG* 2.9 42.0 + - - +
117E ASN* 3.4 40.9 + - + +
120E ALA* 4.4 8.9 - - - +
121E ASP* 2.8 41.2 + - - +
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Residues in contact with ALA 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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74E ASP* 2.8 29.7 + - + +
76E ARG* 1.3 73.3 - - - +
78E LEU* 1.3 60.2 + - + +
80E ARG* 3.3 25.1 + - - +
81E GLU* 3.0 28.5 + - - +
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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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37E SER* 6.3 3.6 - - - -
44E HIS* 4.9 12.3 - - + +
47E THR* 4.8 10.0 - - + +
51E PHE* 5.7 0.2 - - - -
74E ASP 3.1 17.5 + - - +
75E SER* 3.6 18.8 - - - +
76E ARG 3.2 0.2 - - - -
77E ALA* 1.3 76.9 - - + +
79E LEU* 1.3 57.4 + - - +
81E GLU* 3.2 8.4 + - + +
82E CYS* 2.8 29.1 + - - +
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Residues in contact with LEU 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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43E LEU* 4.0 27.8 - - + +
46E ILE* 4.0 19.1 - - + -
47E THR* 3.4 23.5 + - - +
50E LEU* 4.1 8.1 - - + -
75E SER 2.9 17.2 + - - +
76E ARG* 3.2 6.5 + - - +
78E LEU* 1.3 76.4 - - - +
80E ARG* 1.3 62.7 + - - +
82E CYS* 3.4 4.8 + - + +
83E ALA* 3.0 22.7 + - - +
118E ILE* 4.4 12.6 - - + -
121E ASP* 3.8 24.7 - - + +
122E LEU* 3.8 26.5 - - + -
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Residues in contact with ARG 80 (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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74E ASP* 4.5 4.2 + - - -
76E ARG* 2.9 40.0 + - - +
77E ALA* 3.5 29.0 - - - +
79E LEU* 1.3 77.9 - - - +
81E GLU* 1.3 59.8 + - - +
83E ALA* 3.3 3.5 + - - +
84E SER* 3.1 21.8 + - - -
120E ALA 5.7 0.2 - - - -
121E ASP* 3.0 50.4 + - + +
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Residues in contact with GLU 81 (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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51E PHE* 5.5 0.7 - - + -
77E ALA 3.0 17.3 + - - +
78E LEU* 3.6 11.0 - - + +
80E ARG* 1.3 73.3 - - - +
82E CYS* 1.3 66.4 + - - +
84E SER* 3.1 14.9 + - - -
85E ARG* 3.0 66.4 + - + +
88E GLN* 5.8 0.2 - - - +
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Residues in contact with CYS 82 (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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47E THR* 3.8 25.1 - - + -
50E LEU* 3.7 37.5 - - - -
51E PHE* 3.8 34.6 - - + -
78E LEU 2.8 17.8 + - - +
79E LEU* 3.4 10.5 - - - +
81E GLU* 1.3 73.2 - - - +
83E ALA* 1.3 62.7 + - - +
85E ARG* 3.1 2.8 + - - +
86E VAL* 2.9 29.6 + - - +
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Residues in contact with ALA 83 (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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79E LEU 3.0 14.1 + - - +
80E ARG 3.6 8.3 - - - +
81E GLU 3.3 0.4 - - - -
82E CYS* 1.3 76.5 - - - +
84E SER* 1.3 61.7 + - - +
86E VAL* 3.4 8.3 + - - +
87E ALA* 3.0 23.4 + - - +
93E ILE* 4.7 8.8 - - + +
121E ASP 4.0 10.8 - - - +
122E LEU* 3.8 28.5 - - + +
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Residues in contact with SER 84 (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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80E ARG 3.1 13.0 + - - -
81E GLU* 3.1 24.8 + - - -
83E ALA* 1.3 78.0 - - - +
85E ARG* 1.3 56.3 + - - +
87E ALA* 3.3 6.7 + - - +
88E GLN* 2.9 45.2 + - - +
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Residues in contact with ARG 85 (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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51E PHE* 4.3 17.7 - - + -
56E LEU* 3.8 9.2 - - + +
81E GLU* 3.0 41.9 + - + +
82E CYS* 3.5 7.6 - - - +
84E SER* 1.3 74.1 - - - +
86E VAL* 1.3 64.4 + - - +
88E GLN* 3.3 28.7 + - - +
89E ALA* 3.0 24.3 + - - +
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Residues in contact with VAL 86 (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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50E LEU* 4.1 25.4 - - + +
51E PHE* 4.7 1.1 - - + +
54E ALA* 4.3 11.0 - - + -
56E LEU* 4.1 11.0 - - + -
82E CYS* 2.9 34.0 + - - +
83E ALA* 3.7 7.4 - - - +
84E SER 3.3 0.2 - - - -
85E ARG* 1.3 74.2 - - - +
87E ALA* 1.3 63.7 + - - +
89E ALA* 3.3 9.1 + - - +
90E GLY 3.5 0.5 + - - -
91E PHE* 3.2 39.8 + - + +
93E ILE* 4.4 19.5 - - + -
156E VAL* 4.8 6.5 - - + -
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Residues in contact with ALA 87 (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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83E ALA 3.0 13.8 + - - +
84E SER* 3.6 10.1 - - - +
86E VAL* 1.3 77.9 - - - +
88E GLN* 1.3 57.6 + - + +
90E GLY* 2.9 20.4 + - - -
91E PHE 3.6 13.4 + - - +
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Residues in contact with GLN 88 (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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84E SER* 2.9 32.2 + - - +
85E ARG* 3.3 38.9 + - - +
87E ALA* 1.3 75.8 - - + +
89E ALA* 1.3 59.7 + - - +
90E GLY* 3.1 1.3 + - - -
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Residues in contact with ALA 89 (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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56E LEU* 3.9 27.6 - - + -
85E ARG 3.0 16.3 + - - +
86E VAL 3.7 5.8 - - - +
87E ALA 3.1 0.6 - - - -
88E GLN* 1.3 75.6 - - - +
90E GLY* 1.3 57.8 + - - +
91E PHE* 3.7 24.3 - - + -
158E ARG* 5.4 3.8 - - - -
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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