Contacts of the helix formed by residues 82 - 92 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257G GLU* 3.0 41.8 + - - -
394G ARG* 3.6 26.3 + - - +
79H SER* 3.9 11.6 + - - +
80H TYR 3.2 1.6 - - - -
81H ALA* 1.3 78.1 - - - +
83H PHE* 1.3 82.0 + + - +
84H GLY* 2.7 26.4 + - - -
85H ILE* 3.3 15.8 + - + +
86H HIS* 3.6 12.7 + - - -
145H ILE* 4.9 0.2 - - - -
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Residues in contact with PHE 83 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235G LYS* 5.9 0.4 - - + -
239G TRP* 3.5 17.3 - + - -
250G ILE* 3.6 29.4 - - + -
253G VAL* 4.2 17.7 - - + -
254G ALA* 3.7 38.8 - - + -
257G GLU* 3.3 33.4 - - + -
259G LEU* 6.3 2.9 - - + -
81H ALA 3.6 4.4 + - - -
82H HIS* 1.3 85.0 - + - +
84H GLY* 1.3 75.8 + - - +
86H HIS* 3.4 6.0 + - - +
87H GLU* 3.1 41.9 + - - -
145H ILE* 4.7 11.0 - - + -
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Residues in contact with GLY 84 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82H HIS* 2.7 17.5 + - - -
83H PHE* 1.3 96.8 - - - +
85H ILE* 1.3 61.4 + - - -
87H GLU* 3.3 9.8 - - - +
88H GLU* 3.2 18.9 + - - +
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Residues in contact with ILE 85 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79H SER 4.2 15.0 - - - +
80H TYR* 3.9 26.5 - - + +
82H HIS* 3.3 13.5 + - + +
84H GLY* 1.3 73.2 - - - +
86H HIS* 1.3 85.0 + - + +
88H GLU* 3.1 27.0 + - + +
89H MET* 3.2 33.1 + - + +
189H TYR* 6.2 0.2 - - - +
334H HIS* 5.8 2.9 - - + -
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Residues in contact with HIS 86 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239G TRP* 5.1 1.3 - - + -
250G ILE* 6.0 0.2 - - + -
80H TYR* 2.8 38.7 + + + -
82H HIS 3.6 9.9 + - - -
83H PHE* 3.4 8.5 + - - +
84H GLY 3.3 0.4 - - - -
85H ILE* 1.3 80.7 - - + +
87H GLU* 1.3 55.9 + - - +
89H MET* 3.2 11.6 + - - +
90H LEU* 2.7 44.7 + - + +
121H GLY* 3.9 10.0 - - - -
122H THR* 3.7 39.3 - - + -
145H ILE* 3.5 18.2 - - + +
401H SAH 3.8 29.7 + - + +
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Residues in contact with GLU 87 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235G LYS* 3.3 36.6 + - - +
238G TRP* 4.0 7.9 - - + -
239G TRP* 3.6 38.2 + - + -
83H PHE* 3.1 26.3 + - - +
84H GLY* 3.3 12.4 - - - +
86H HIS* 1.3 76.4 - - - +
88H GLU* 1.3 63.9 + - - +
90H LEU 3.2 0.3 + - - -
91H LYS* 2.6 68.9 + - + +
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Residues in contact with GLU 88 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84H GLY 3.2 7.8 + - - +
85H ILE* 3.1 23.9 + - + +
87H GLU* 1.3 81.2 - - - +
89H MET* 1.3 61.7 + - + +
91H LYS* 3.5 5.4 + - - +
92H ASP* 3.3 20.4 + - - +
189H TYR* 4.7 9.5 + - - -
332H TYR* 4.3 9.3 + - - +
334H HIS* 3.6 38.2 - - + +
336H LYS* 5.0 5.4 + - - -
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Residues in contact with MET 89 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80H TYR* 4.1 20.2 - - + +
85H ILE* 3.2 26.1 + - + +
86H HIS* 3.5 14.6 - - - +
88H GLU* 1.3 77.5 - - - +
90H LEU* 1.3 62.7 + - - +
92H ASP* 3.2 11.3 + - - +
95H ARG* 3.1 37.3 + - - +
96H THR* 3.1 4.2 + - - -
185H GLU* 3.5 24.2 - - - +
187H MET 5.3 2.0 - - - +
334H HIS* 4.1 25.6 - - + +
401H SAH 3.5 39.9 - - - +
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Residues in contact with LEU 90 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238G TRP* 3.7 27.3 - - + -
239G TRP* 4.3 4.3 - - + -
242G VAL* 3.9 17.5 - - + -
243G TYR* 2.6 36.0 + - - -
247G MET* 4.3 7.6 - - + -
86H HIS 2.7 29.8 + - - +
89H MET* 1.3 73.5 - - - +
91H LYS* 1.3 55.2 + - - +
92H ASP 3.4 0.5 + - - -
95H ARG* 4.2 7.4 - - - +
96H THR* 3.4 9.9 + - + -
122H THR* 4.1 26.0 - - + +
124H ILE* 3.7 42.6 - - + -
401H SAH 4.6 2.2 - - - +
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Residues in contact with LYS 91 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234G PHE* 2.9 63.6 + - + -
235G LYS* 4.5 0.6 - - - +
238G TRP* 3.4 42.2 - - + +
243G TYR* 4.3 1.6 - - - -
87H GLU* 2.6 49.6 + - + +
88H GLU* 4.1 4.9 - - - +
90H LEU* 1.3 74.4 - - - +
92H ASP* 1.3 58.3 + - - +
93H GLU* 2.9 18.8 + - - +
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Residues in contact with ASP 92 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243G TYR* 4.0 1.3 - - - -
88H GLU 3.3 11.3 + - - +
89H MET 3.2 12.7 + - - +
90H LEU 3.2 0.6 - - - -
91H LYS* 1.3 71.6 - - - +
93H GLU* 1.3 62.7 + - - +
94H VAL* 3.3 12.8 + - - +
95H ARG* 3.2 24.9 + - + +
96H THR* 3.0 24.6 + - - -
332H TYR* 4.1 9.1 - - + +
333H THR* 3.5 14.2 - - - -
334H HIS* 2.9 46.5 + - + +
335H TRP* 4.1 0.7 - - - -
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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