Contacts of the helix formed by residues 75 - 83 (chain E) in PDB entry 5B6N
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 SER 75 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E ILE 4.0 0.6 + - - -
74E ASP* 1.3 74.5 + - - +
76E VAL* 1.3 66.9 + - - +
77E GLU* 3.1 16.9 + - - +
78E ASP* 3.0 33.0 + - - +
79E HIS* 3.0 15.6 + - - -
104E ASP* 3.9 8.0 + - - -
106E ARG* 2.9 37.1 + - - +
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Residues in contact with VAL 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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17E ASN* 3.7 18.4 - - + +
18E THR 3.2 30.3 - - - +
19E THR* 5.0 4.7 - - + -
75E SER* 1.3 75.9 + - - +
77E GLU* 1.3 74.8 + - - +
79E HIS* 3.1 22.6 + - + +
80E LEU* 3.1 17.7 + - + +
104E ASP* 3.5 29.9 + - + +
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Residues in contact with GLU 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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75E SER* 3.6 15.6 + - - +
76E VAL* 1.3 88.0 - - - +
78E ASP* 1.3 66.5 + - - +
80E LEU* 3.8 8.1 + - - +
81E ALA* 3.4 21.7 + - - +
106E ARG* 5.5 1.1 - - - +
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Residues in contact with ASP 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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41E ARG* 5.2 2.6 + - - -
42E ASP* 4.4 3.4 - - - +
43E PHE* 3.9 22.1 - - + -
74E ASP* 3.5 24.0 - - - +
75E SER* 3.0 29.9 + - - +
77E GLU* 1.3 79.9 - - - +
79E HIS* 1.3 66.8 + - - +
80E LEU 3.1 0.2 - - - -
81E ALA* 3.1 4.3 + - - -
82E TRP* 2.8 27.1 + - - +
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Residues in contact with HIS 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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18E THR 5.2 0.7 - - - -
19E THR* 4.8 9.2 - - + +
42E ASP* 2.8 31.4 + - - -
72E SER* 3.2 18.4 - - - -
74E ASP* 3.3 21.3 + - + -
75E SER 3.0 6.8 + - - -
76E VAL* 3.2 19.7 - - + +
78E ASP* 1.3 73.2 - - - +
80E LEU* 1.3 54.7 + - - +
82E TRP* 3.2 5.1 + - - +
83E SER* 2.3 39.4 + - - +
102E ILE* 3.2 47.5 - - + +
103E ILE 2.7 24.9 + - - -
104E ASP* 4.0 0.6 + - - -
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Residues in contact with LEU 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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19E THR* 5.4 13.5 - - + +
76E VAL* 3.1 14.8 + - + +
77E GLU* 4.0 9.2 - - - +
79E HIS* 1.3 81.3 - - - +
81E ALA* 1.3 62.9 + - + +
82E TRP 3.0 0.2 - - - -
83E SER* 3.1 22.7 + - - -
84E LYS* 3.3 18.7 - - - +
96E GLU* 3.2 46.6 - - + +
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Residues in contact with ALA 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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43E PHE* 4.2 13.5 - - + -
77E GLU 3.4 13.5 + - - +
78E ASP* 3.1 5.2 + - - +
80E LEU* 1.3 83.7 - - + +
82E TRP* 1.3 58.1 + - - +
84E LYS* 3.2 29.4 - - + +
85E ASP* 3.7 11.4 - - - +
213F SER* 5.1 2.4 - - - -
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Residues in contact with TRP 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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39E HIS* 3.5 22.7 - + - -
42E ASP* 3.9 16.4 - - + -
43E PHE* 3.0 52.8 - + + +
44E THR 4.4 1.6 - - - -
47E CSD 3.7 18.2 - - - -
48E THR* 3.3 23.7 + - - -
51E LEU* 3.5 24.9 - - + -
78E ASP 2.8 18.3 + - - +
79E HIS* 3.4 3.6 - - - +
81E ALA* 1.3 76.0 - - - +
83E SER* 1.3 55.7 + - - +
84E LYS 3.0 4.9 - - - -
85E ASP* 2.7 27.8 + - + +
86E ILE* 2.8 43.9 + - + +
102E ILE* 4.4 11.9 - - + -
217F TYR* 3.3 20.0 + - - -
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Residues in contact with SER 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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19E THR* 5.1 6.0 - - - +
79E HIS* 2.3 26.2 + - - +
80E LEU* 3.1 9.4 + - - -
82E TRP* 1.3 76.0 - - - +
84E LYS* 1.3 56.2 + - - +
86E ILE* 3.9 13.1 - - - +
87E ASN* 3.1 27.5 + - - +
96E GLU* 3.3 20.7 + - - -
98E LEU* 3.3 31.7 - - - +
102E ILE* 4.2 4.3 - - - +
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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