Contacts of the helix formed by residues 82 - 92 (chain E) in PDB entry 5DST
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 82 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79E SER* 3.9 12.3 + - - +
80E TYR 3.2 1.2 - - - -
81E ALA* 1.3 78.9 - - - +
83E PHE* 1.3 71.0 + + - +
84E GLY* 2.7 35.9 + - - -
85E ILE* 3.3 22.8 + - + +
86E HIS* 3.8 5.2 + - - -
145E ILE* 4.9 0.2 - - - -
257F GLU* 3.0 42.6 + - - -
394F ARG* 3.6 26.9 + - - +
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Residues in contact with PHE 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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81E ALA 3.5 4.6 + - - -
82E HIS* 1.3 82.0 - + - +
84E GLY* 1.3 64.9 + - - +
85E ILE 3.7 0.2 - - - -
86E HIS* 3.6 5.6 + - - +
87E GLU* 3.1 34.6 + - - -
145E ILE* 4.7 11.4 - - + -
235F LYS* 5.9 0.7 - - + -
239F TRP* 3.4 23.7 - + - -
250F ILE* 3.6 28.9 - - + +
253F VAL* 4.3 17.0 - - + -
254F ALA* 3.6 38.4 - - + -
257F GLU* 3.3 34.3 - - + -
259F LEU* 6.2 3.8 - - + -
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Residues in contact with GLY 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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82E HIS* 2.7 21.9 + - - -
83E PHE* 1.3 90.2 - - - +
85E ILE* 1.3 63.1 + - - -
86E HIS 3.2 1.3 - - - -
87E GLU* 3.4 9.6 - - - +
88E GLU* 3.2 19.6 + - - +
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Residues in contact with ILE 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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79E SER 4.3 6.3 - - - +
80E TYR* 3.8 35.2 - - + +
82E HIS* 3.3 14.5 + - + +
84E GLY* 1.3 76.0 - - - +
86E HIS* 1.3 79.4 + - + +
88E GLU* 3.4 19.6 + - - +
89E MET* 3.3 40.1 + - + +
189E TYR* 6.0 1.6 - - - +
334E HIS* 5.7 3.1 - - + -
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Residues in contact with HIS 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80E TYR* 2.9 32.7 + + - -
82E HIS 3.8 6.1 + - - -
83E PHE* 3.6 8.0 + - - +
84E GLY 3.2 0.2 - - - -
85E ILE* 1.3 84.9 - - + +
87E GLU* 1.3 55.9 + - - +
89E MET* 3.1 11.9 + - - +
90E LEU* 2.8 43.9 + - + +
121E GLY* 3.8 9.8 - - - -
122E THR* 3.7 28.9 - - + -
145E ILE* 3.6 18.8 - - + +
401E SAH 3.4 47.3 + - + +
239F TRP* 5.0 0.9 - - + -
250F ILE* 6.1 0.2 - - + -
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Residues in contact with GLU 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 PHE* 3.1 27.3 + - - +
84E GLY* 3.4 11.4 - - - +
86E HIS* 1.3 75.1 - - - +
88E GLU* 1.3 63.4 + - - +
91E LYS* 2.7 67.0 + - + +
235F LYS* 3.2 38.0 + - - +
238F TRP* 4.1 7.9 - - + -
239F TRP* 3.5 39.4 + - + -
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Residues in contact with GLU 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 GLY 3.2 9.3 + - - +
85E ILE* 3.5 22.9 - - + +
86E HIS 3.2 0.2 - - - -
87E GLU* 1.3 81.4 - - - +
89E MET* 1.3 62.4 + - + +
91E LYS* 3.5 5.3 + - - +
92E ASP* 3.3 18.5 + - - +
189E TYR* 4.7 10.2 + - - -
332E TYR* 4.3 9.7 + - - +
334E HIS* 3.7 35.7 - - + +
336E LYS* 5.1 5.2 + - - -
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Residues in contact with MET 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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80E TYR* 4.1 21.3 - - + +
85E ILE* 3.3 24.0 + - + +
86E HIS* 3.1 14.7 + - - +
88E GLU* 1.3 77.5 - - - +
90E LEU* 1.3 63.2 + - - +
92E ASP* 3.2 13.3 + - - +
95E ARG* 3.2 35.4 + - - +
96E THR* 3.2 2.4 + - - -
185E GLU* 3.4 24.5 - - - +
187E MET 5.2 1.3 - - - +
334E HIS* 4.0 26.9 - - + +
401E SAH 3.5 42.8 - - + +
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Residues in contact with LEU 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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86E HIS 2.8 30.1 + - - +
89E MET* 1.3 72.4 - - - +
91E LYS* 1.3 56.8 + - - +
95E ARG* 4.3 6.1 - - - +
96E THR* 3.3 11.0 + - + -
122E THR* 4.1 23.8 - - + +
124E ILE* 3.8 42.6 - - + -
401E SAH 4.4 4.5 - - - +
238F TRP* 3.7 25.8 - - + -
239F TRP* 4.2 9.4 - - + -
242F VAL* 4.0 17.0 - - + -
243F TYR* 2.6 36.0 + - + -
247F MET* 4.5 2.0 - - + -
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Residues in contact with LYS 91 (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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87E GLU* 2.7 50.0 + - + +
88E GLU* 4.0 4.5 - - - +
90E LEU* 1.3 72.5 - - - +
92E ASP* 1.3 60.4 + - - +
93E GLU* 3.0 18.3 + - - +
234F PHE* 3.1 59.7 + - + -
235F LYS* 4.5 1.2 - - - +
238F TRP* 3.4 46.4 - - + +
243F TYR* 4.4 1.8 - - - -
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Residues in contact with ASP 92 (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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88E GLU 3.3 10.9 + - - +
89E MET 3.2 13.0 + - - +
90E LEU 3.8 0.7 - - - -
91E LYS* 1.3 72.7 - - - +
93E GLU* 1.3 62.9 + - - +
94E VAL* 3.0 21.5 + - - +
95E ARG* 3.2 16.6 + - + +
96E THR* 3.0 26.9 + - - -
332E TYR* 4.0 10.5 - - + +
333E THR* 3.2 15.3 - - - -
334E HIS* 2.8 45.9 + - + +
335E TRP* 4.2 0.3 - - - -
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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