Contacts of the helix formed by residues 82 - 92 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79C SER* 3.9 11.9 + - - +
80C TYR 3.3 2.0 - - - -
81C ALA* 1.3 78.3 - - - +
83C PHE* 1.3 78.0 + + - +
84C GLY* 2.7 34.1 + - - -
85C ILE* 3.3 14.3 + - + +
86C HIS* 3.7 11.4 + - - -
257D GLU* 3.1 41.5 + - - -
394D ARG* 3.6 26.1 + - - +
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Residues in contact with PHE 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C ALA 3.5 4.4 + - - -
82C HIS* 1.3 85.7 - + - +
84C GLY* 1.3 76.4 + - - +
85C ILE 3.6 0.2 - - - -
86C HIS* 3.4 5.9 + - - +
87C GLU* 3.1 34.6 + - - -
145C ILE* 4.7 11.2 - - - -
235D LYS* 5.8 2.0 - - + -
239D TRP* 3.5 23.7 - + - -
250D ILE* 3.6 29.2 - - + -
253D VAL* 4.5 15.9 - - + -
254D ALA* 3.9 33.0 - - + -
257D GLU* 3.4 32.8 - - + -
259D LEU* 6.3 2.5 - - + -
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Residues in contact with GLY 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C HIS* 2.7 20.9 + - - -
83C PHE* 1.3 90.5 - - - +
85C ILE* 1.3 66.2 + - - -
86C HIS 3.1 1.3 - - - -
87C GLU* 3.1 16.2 + - - +
88C GLU* 3.2 12.0 + - - +
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Residues in contact with ILE 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C SER 4.1 8.3 - - - +
80C TYR* 3.8 34.8 - - + -
82C HIS* 3.3 14.3 + - + +
84C GLY* 1.3 74.9 - - - +
86C HIS* 1.3 81.2 + - + +
88C GLU* 3.2 18.5 + - - +
89C MET* 3.2 39.8 + - + +
334C HIS* 5.8 2.5 - - + -
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Residues in contact with HIS 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C TYR* 2.8 40.9 + + + -
82C HIS 3.7 7.1 + - - -
83C PHE* 3.4 8.3 + - - +
84C GLY 3.1 0.4 - - - -
85C ILE* 1.3 85.5 - - + +
87C GLU* 1.3 60.7 + - - +
89C MET* 3.3 11.8 + - - +
90C LEU* 2.8 38.9 + - + +
121C GLY* 3.9 9.3 - - - -
122C THR* 3.9 40.8 - - + -
145C ILE* 3.7 16.2 - - + +
401C SAH 3.6 29.3 + - + +
239D TRP* 5.2 1.1 - - + -
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Residues in contact with GLU 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C PHE* 3.1 25.9 + - - +
84C GLY* 3.1 11.9 + - - +
86C HIS* 1.3 75.4 - - - +
88C GLU* 1.3 57.0 + - - +
90C LEU* 3.4 1.0 + - - +
91C LYS* 2.7 71.9 + - + +
235D LYS* 3.2 35.7 + - - +
238D TRP* 4.0 12.8 - - + -
239D TRP* 3.5 35.9 + - + -
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Residues in contact with GLU 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C GLY 3.2 7.6 + - - +
85C ILE* 3.5 21.6 - - + +
86C HIS 3.2 0.2 - - - -
87C GLU* 1.3 79.9 - - - +
89C MET* 1.3 62.4 + - + +
91C LYS* 3.4 5.7 + - - +
92C ASP* 3.3 21.1 + - - +
189C TYR* 4.6 8.7 + - - -
332C TYR* 4.3 9.2 + - - +
334C HIS* 3.6 37.7 - - + +
336C LYS* 5.1 4.9 + - - -
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Residues in contact with MET 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C TYR* 4.1 18.8 - - + +
85C ILE* 3.2 26.3 + - + +
86C HIS* 3.6 15.9 - - - +
88C GLU* 1.3 78.0 - - - +
90C LEU* 1.3 62.2 + - - +
92C ASP* 3.3 9.5 - - - +
95C ARG* 2.9 38.3 + - - +
96C THR* 3.2 3.6 + - - -
185C GLU* 3.6 23.3 - - - +
187C MET 5.2 2.5 - - - +
334C HIS* 4.1 29.2 - - + +
401C SAH 3.6 39.9 - - + +
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Residues in contact with LEU 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C HIS* 2.8 26.7 + - + +
89C MET* 1.3 77.9 - - - +
91C LYS* 1.3 57.1 + - - +
92C ASP 3.1 1.5 + - - -
95C ARG* 4.4 7.9 - - - +
96C THR* 3.3 6.3 + - + -
122C THR* 4.0 25.6 - - + +
124C ILE* 3.7 42.2 - - + -
401C SAH 4.8 2.2 - - - +
238D TRP* 3.8 25.4 - - + -
239D TRP* 4.4 8.1 - - + -
242D VAL* 4.0 17.9 - - + -
243D TYR* 2.5 39.8 + - + -
247D MET* 4.5 2.0 - - + -
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Residues in contact with LYS 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C GLU* 2.7 52.9 + - + +
88C GLU* 4.0 4.7 - - - +
90C LEU* 1.3 72.9 - - - +
92C ASP* 1.3 59.8 + - - +
93C GLU* 3.0 19.2 + - - +
234D PHE* 3.0 58.9 + - + -
235D LYS* 4.5 0.4 - - - +
238D TRP* 3.5 41.7 - - + +
243D TYR* 4.4 1.6 - - - -
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Residues in contact with ASP 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C GLU 3.3 11.3 + - - +
89C MET 3.3 13.5 - - - +
90C LEU 3.9 0.7 - - - -
91C LYS* 1.3 73.0 - - - +
93C GLU* 1.3 62.5 + - - +
94C VAL* 3.3 11.4 + - - +
95C ARG* 3.0 27.2 + - + +
96C THR* 3.0 25.5 + - - -
332C TYR* 4.2 9.3 - - + +
333C THR* 3.5 12.4 - - - -
334C HIS* 2.8 46.3 + - + +
335C TRP* 4.1 0.2 - - - -
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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