Contacts of the helix formed by residues 82 - 92 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79M SER* 4.1 10.7 + - - +
80M TYR 3.2 2.6 - - - -
81M ALA* 1.3 77.0 - - - +
83M PHE* 1.3 76.4 + + - +
84M GLY* 2.6 35.6 + - - -
85M ILE* 3.2 15.4 + - + +
86M HIS* 3.8 9.7 + - - -
257N GLU* 3.2 39.9 + - - -
394N ARG* 3.7 26.1 + - - +
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Residues in contact with PHE 83 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81M ALA 3.6 5.0 + - - -
82M HIS* 1.3 86.9 + + - +
84M GLY* 1.3 63.3 + - - +
86M HIS* 3.5 8.7 + - - +
87M GLU* 3.1 40.4 + - - -
145M ILE* 4.7 12.8 - - + +
235N LYS* 5.9 0.7 - - + -
239N TRP* 3.6 14.5 - + - -
250N ILE* 3.7 28.0 - - + -
253N VAL* 4.4 16.6 - - + -
254N ALA* 4.0 35.0 - - + -
257N GLU* 3.3 32.5 - - + -
259N LEU* 6.4 2.2 - - + -
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Residues in contact with GLY 84 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82M HIS* 2.6 20.8 + - - -
83M PHE* 1.3 90.9 - - - +
85M ILE* 1.3 62.7 + - - -
86M HIS 3.1 2.0 - - - -
87M GLU* 3.4 9.2 + - - +
88M GLU* 3.3 19.4 + - - +
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Residues in contact with ILE 85 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79M SER 4.4 7.4 - - - +
80M TYR* 3.8 35.2 - - + +
82M HIS* 3.2 11.3 + - + +
84M GLY* 1.3 76.4 - - - +
86M HIS* 1.3 81.4 + - + +
88M GLU* 3.5 19.8 + - + +
89M MET* 3.4 38.5 + - + +
189M TYR* 6.1 0.7 - - - +
334M HIS* 5.8 2.9 - - + -
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Residues in contact with HIS 86 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80M TYR* 2.8 36.8 + + - -
82M HIS 3.8 5.9 + - - -
83M PHE* 3.5 8.9 + - - +
84M GLY 3.1 0.4 - - - -
85M ILE* 1.3 86.9 - - + +
87M GLU* 1.3 60.9 + - - +
89M MET* 3.2 10.9 + - - +
90M LEU* 2.8 39.7 + - + +
121M GLY* 3.9 8.6 - - - -
122M THR* 3.9 41.7 - - + -
145M ILE* 3.7 17.9 - - + +
401M SAH 3.6 34.2 + - + +
239N TRP* 5.1 0.7 - - + -
250N ILE* 6.3 0.2 - - + -
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Residues in contact with GLU 87 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83M PHE* 3.1 27.6 + - - +
84M GLY* 3.4 11.5 - - - +
86M HIS* 1.3 75.7 - - - +
88M GLU* 1.3 62.8 + - - +
90M LEU* 3.8 0.5 - - - +
91M LYS* 2.7 66.2 + - + +
235N LYS* 3.1 36.3 + - - +
238N TRP* 4.2 7.1 - - + -
239N TRP* 3.6 38.1 + - + -
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Residues in contact with GLU 88 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84M GLY 3.3 8.6 + - - +
85M ILE* 3.6 22.4 - - + +
86M HIS 3.2 0.6 - - - -
87M GLU* 1.3 79.3 - - - +
89M MET* 1.3 62.9 + - + +
91M LYS* 3.4 5.8 + - - +
92M ASP* 3.2 21.1 + - - +
189M TYR* 4.5 10.6 + - - -
332M TYR* 4.5 8.1 + - - +
334M HIS* 3.6 39.1 - - + +
336M LYS* 5.2 4.5 + - - -
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Residues in contact with MET 89 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80M TYR* 4.2 19.1 - - + +
85M ILE* 3.4 24.8 + - + +
86M HIS* 3.2 15.3 + - - +
88M GLU* 1.3 75.1 - - - +
90M LEU* 1.3 66.0 + - + +
92M ASP* 3.4 8.8 + - - +
95M ARG* 3.0 37.6 + - - +
96M THR* 3.1 3.5 + - - -
185M GLU* 3.4 24.2 - - - +
187M MET 5.1 2.5 - - - +
334M HIS* 4.0 26.9 - - + +
401M SAH 3.6 41.1 - - - +
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Residues in contact with LEU 90 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86M HIS 2.8 26.9 + - - +
89M MET* 1.3 78.5 - - - +
91M LYS* 1.3 55.5 + - - +
92M ASP 3.1 1.1 + - - -
95M ARG* 4.5 6.1 - - - +
96M THR* 3.3 7.2 + - + -
122M THR* 4.1 25.1 - - + +
124M ILE* 3.8 42.4 - - + -
401M SAH 4.8 2.0 - - - +
238N TRP* 3.7 26.7 - - + -
239N TRP* 4.3 10.1 - - + -
242N VAL* 4.0 17.5 - - + -
243N TYR* 2.5 37.4 + - + -
247N MET* 4.4 2.5 - - + -
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Residues in contact with LYS 91 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87M GLU* 2.7 53.1 + - + +
88M GLU* 4.0 4.5 - - - +
89M MET 3.3 0.2 - - - -
90M LEU* 1.3 72.7 - - - +
92M ASP* 1.3 59.8 + - - +
93M GLU* 3.0 19.0 + - - +
234N PHE* 3.0 62.6 + - + -
235N LYS* 4.4 0.8 - - - +
238N TRP* 3.5 40.4 - - + +
243N TYR* 4.4 1.8 - - - -
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Residues in contact with ASP 92 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88M GLU 3.2 11.7 + - - +
89M MET 3.4 11.9 - - - +
90M LEU 3.1 1.8 - - - -
91M LYS* 1.3 72.2 - - - +
93M GLU* 1.3 57.0 + - - +
94M VAL* 3.2 12.0 + - - +
95M ARG* 2.9 28.7 + - + +
96M THR* 3.0 28.6 + - - -
332M TYR* 4.2 9.2 - - + +
333M THR* 3.5 12.4 - - - -
334M HIS* 2.9 45.9 + - + +
335M TRP* 3.9 0.9 - - - -
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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