Contacts of the helix formed by residues 81 - 90 (chain E) in PDB entry 4P9U
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 HIS 81 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58E ASP* 3.0 58.1 + - + -
60E TRP* 4.4 4.0 - - - -
78E SER* 4.3 0.2 - - - -
79E GLY* 3.0 23.4 + - - -
80E LEU* 1.3 76.3 - - - +
82E ILE* 1.3 94.3 + - + +
83E LEU 3.0 4.4 + - - -
84E ASP* 3.2 19.8 + - - +
85E THR* 4.0 7.6 + - - -
207E GLY* 4.0 12.9 + - - +
210E LYS* 5.9 4.1 - - + +
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Residues in contact with ILE 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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60E TRP* 3.8 25.8 - - + -
74E PHE* 4.6 2.9 - - + -
75E MET* 3.6 36.1 - - + +
78E SER* 3.6 27.4 - - - +
79E GLY 3.1 14.1 - - - +
81E HIS* 1.3 102.3 + - + +
83E LEU* 1.3 60.8 + - + +
84E ASP 3.1 0.4 - - - -
85E THR* 3.1 7.7 + - - -
86E LEU* 2.8 38.6 + - + +
203F LEU* 3.6 22.2 - - + -
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Residues in contact with LEU 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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75E MET* 5.7 1.3 - - + -
80E LEU* 3.7 15.0 + - + +
81E HIS 3.0 1.4 + - - -
82E ILE* 1.3 79.9 - - + +
84E ASP* 1.3 61.3 + - - +
86E LEU* 4.4 4.7 - - + -
87E MET* 3.3 24.9 + - - +
97E ILE* 3.7 29.2 - - + +
100E ASP* 5.7 2.9 - - + +
208E LEU* 3.6 18.6 - - + -
211E LEU* 3.8 18.8 - - + -
199F GLN* 3.4 30.5 - - + +
200F ILE* 3.4 36.8 - - + -
203F LEU* 4.6 11.9 - - + -
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Residues in contact with ASP 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 LEU 5.0 0.2 + - - -
81E HIS 3.2 11.0 + - - +
82E ILE 3.1 0.4 - - - -
83E LEU* 1.3 77.0 - - - +
85E THR* 1.3 67.0 + - - +
87E MET* 3.1 23.3 + - - +
88E THR* 3.6 1.9 + - - +
210E LYS* 3.3 55.6 - - + +
211E LEU* 3.3 13.7 + - + +
214E ARG* 3.0 39.0 + - - +
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Residues in contact with THR 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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17E ILE* 4.3 17.9 - - + +
60E TRP* 4.3 12.9 - - + -
81E HIS* 4.3 9.9 + - - -
82E ILE* 3.1 13.6 + - - +
84E ASP* 1.3 80.2 + - - +
86E LEU* 1.3 58.8 + - - +
88E THR* 3.1 18.1 + - + +
89E LEU* 2.9 48.4 + - + +
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Residues in contact with LEU 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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21E TRP* 3.6 36.8 - - + -
60E TRP* 5.1 2.7 - - + -
74E PHE* 4.6 8.7 - - + -
75E MET* 3.6 32.3 - - + -
82E ILE* 2.8 34.8 + - + +
83E LEU* 3.8 4.0 - - - +
85E THR* 1.3 79.5 - - - +
87E MET* 1.3 55.4 + - - +
89E LEU* 4.2 10.1 - - + -
90E ASP* 2.5 45.5 + - + +
97E ILE* 3.6 19.3 - - + -
199F GLN* 5.4 4.3 - - - +
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Residues in contact with MET 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 LEU 3.3 17.0 + - - +
84E ASP 3.1 12.9 + - - +
86E LEU* 1.3 78.4 - - - +
88E THR* 1.3 56.1 + - - +
90E ASP 4.6 2.0 - - - -
91E ALA* 3.4 17.3 - - - -
94E ALA* 3.6 37.2 - - + +
97E ILE* 3.8 17.9 - - + -
98E VAL* 4.1 9.0 - - + -
211E LEU* 3.7 16.6 - - + -
214E ARG* 3.4 22.0 - - - +
215E VAL* 5.5 0.4 - - + -
274E PHE* 3.5 36.3 - - + -
275E THR* 3.3 22.8 - - + +
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Residues in contact with THR 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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18E GLU* 5.7 0.7 - - - +
84E ASP* 3.6 1.9 + - - +
85E THR* 3.1 27.0 + - + +
87E MET* 1.3 77.7 - - - +
89E LEU* 1.3 67.0 + - + +
91E ALA* 4.8 3.9 - - - +
214E ARG* 4.4 6.7 - - - +
275E THR* 3.1 29.9 + - - +
276E GLU* 3.2 18.9 - - - -
277E ASP* 4.1 9.1 + - + +
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Residues in contact with LEU 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E ILE* 3.7 17.5 - - + -
18E GLU* 3.8 31.6 - - + +
21E TRP* 3.1 59.6 + - + -
60E TRP* 4.4 9.9 - - + -
85E THR* 2.9 39.2 + - + +
86E LEU* 4.0 8.5 - - + +
88E THR* 1.3 88.0 - - + +
90E ASP* 1.3 57.6 + - - +
91E ALA 3.6 1.3 - - - -
92E GLU* 4.0 6.6 - - - +
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Residues in contact with ASP 90 (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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21E TRP* 3.4 33.1 - - + -
86E LEU* 2.5 30.7 + - + +
87E MET 4.1 0.7 - - - +
89E LEU* 1.3 75.0 - - - +
91E ALA* 1.3 55.3 + - - +
92E GLU* 2.4 33.7 - - - +
93E ASN* 3.0 46.2 + - + +
94E ALA* 3.3 8.5 + - - -
97E ILE* 5.0 2.8 - - + +
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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