Contacts of the helix formed by residues 82 - 92 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79O SER 3.9 11.3 + - - +
80O TYR 3.3 1.4 - - - -
81O ALA* 1.3 78.6 - - - +
83O PHE* 1.3 90.4 + + - +
84O GLY* 2.6 36.9 + - - -
85O ILE* 3.4 14.6 + - + +
86O HIS* 3.7 11.3 + - - -
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Residues in contact with PHE 83 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81O ALA 3.6 4.2 + - - -
82O HIS* 1.3 99.4 + + - +
84O GLY* 1.3 64.6 + - - +
86O HIS* 3.4 8.3 + - - +
87O GLU* 3.1 44.1 + - + +
145O ILE* 4.7 12.5 - - + +
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Residues in contact with GLY 84 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82O HIS* 2.6 22.8 + - - -
83O PHE* 1.3 89.1 - - - +
85O ILE* 1.3 63.5 + - - -
86O HIS 3.1 1.6 - - - -
87O GLU* 3.4 8.7 + - - +
88O GLU* 3.3 18.2 + - - +
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Residues in contact with ILE 85 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79O SER 4.3 7.6 - - - +
80O TYR* 3.8 35.4 - - + +
82O HIS* 3.4 12.1 + - + +
84O GLY* 1.3 76.0 - - - +
86O HIS* 1.3 80.3 + - + +
88O GLU* 3.3 18.2 + - - +
89O MET* 3.3 39.9 + - + +
189O TYR* 6.1 0.4 - - - +
334O HIS* 5.8 3.1 - - + -
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Residues in contact with HIS 86 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80O TYR* 2.8 38.5 + + + -
82O HIS 3.7 7.5 + - - -
83O PHE* 3.4 8.5 + - - +
84O GLY 3.1 0.4 - - - -
85O ILE* 1.3 86.0 - - + +
87O GLU* 1.3 66.4 + - - +
89O MET* 3.1 13.3 + - - +
90O LEU* 2.9 32.3 + - + +
121O GLY* 4.1 5.9 - - - -
122O THR* 3.8 40.8 - - + -
145O ILE* 3.7 20.3 - - + +
401O SAH 3.7 28.0 + - + +
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Residues in contact with GLU 87 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83O PHE* 3.1 39.3 + - + +
84O GLY* 3.5 11.4 - - - +
86O HIS* 1.3 75.0 - - - +
88O GLU* 1.3 62.0 + - - +
90O LEU* 3.8 7.9 - - - +
91O LYS* 2.8 68.2 + - + +
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Residues in contact with GLU 88 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84O GLY 3.3 7.8 + - - +
85O ILE* 3.3 23.8 + - + +
86O HIS 3.1 0.8 - - - -
87O GLU* 1.3 77.7 - - - +
89O MET* 1.3 63.4 + - + +
91O LYS* 4.0 4.8 - - - +
92O ASP* 3.3 21.5 + - - +
189O TYR* 4.7 9.5 + - - -
332O TYR* 4.4 9.5 + - - +
334O HIS* 3.8 32.7 - - + +
336O LYS* 5.1 5.7 + - - -
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Residues in contact with MET 89 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80O TYR* 4.0 21.1 - - + +
85O ILE* 3.3 24.4 + - + +
86O HIS* 3.1 18.3 + - - +
88O GLU* 1.3 79.3 - - - +
90O LEU* 1.3 60.5 + - - +
92O ASP* 3.4 9.4 - - - +
95O ARG* 2.8 41.4 + - - +
96O THR* 3.1 5.0 + - - -
185O GLU* 3.4 24.7 - - - +
187O MET 5.1 2.5 - - - +
334O HIS* 4.1 26.2 - - + +
401O SAH 3.6 34.8 - - + +
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Residues in contact with LEU 90 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86O HIS* 2.9 27.8 + - + +
87O GLU* 3.8 6.5 - - - +
89O MET* 1.3 73.6 - - - +
91O LYS* 1.3 67.1 + - + +
92O ASP 3.3 2.3 + - - +
93O GLU* 4.5 2.3 + - - +
95O ARG* 4.3 7.2 - - - +
96O THR* 3.5 22.1 + - + +
122O THR* 4.1 25.8 - - + +
124O ILE* 3.8 44.6 - - + -
401O SAH 4.4 2.9 - - - +
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Residues in contact with LYS 91 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87O GLU* 2.8 55.4 + - + +
88O GLU* 4.1 4.9 - - - +
90O LEU* 1.3 75.0 - - + +
92O ASP* 1.3 60.3 + - - +
93O GLU* 2.8 21.3 + - - +
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Residues in contact with ASP 92 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88O GLU 3.3 13.1 + - - +
89O MET 3.4 12.8 - - - +
90O LEU 3.2 1.7 - - - -
91O LYS* 1.3 73.0 - - - +
93O GLU* 1.3 60.6 + - - +
94O VAL* 3.3 19.1 + - - +
95O ARG* 3.3 18.1 + - + +
96O THR* 3.0 25.1 + - - -
332O TYR* 3.9 10.2 - - + +
333O THR* 3.6 14.2 - - - -
334O HIS* 2.9 46.5 + - + +
335O TRP* 3.9 0.5 - - - -
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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