Contacts of the helix formed by residues 82 - 92 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A SER* 3.7 13.2 + - - +
80A TYR 3.1 1.8 - - - -
81A ALA* 1.3 78.7 - - - +
83A PHE* 1.3 84.2 + + - +
84A GLY* 2.7 26.4 + - - -
85A ILE* 3.3 14.9 + - + +
86A HIS* 3.7 11.7 + - - -
145A ILE* 4.9 0.2 - - - -
257B GLU* 3.1 41.9 + - - -
394B ARG* 3.8 24.8 + - - +
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Residues in contact with PHE 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A ALA 3.4 4.8 + - - -
82A HIS* 1.3 85.7 + + - +
84A GLY* 1.3 77.2 + - - +
86A HIS* 3.4 6.0 + - - +
87A GLU* 3.1 34.4 + - - -
145A ILE* 4.7 11.7 - - + -
235B LYS* 5.8 1.3 - - + -
239B TRP* 3.4 22.6 - + - -
250B ILE* 3.5 28.5 - - + -
253B VAL* 4.2 18.4 - - + +
254B ALA* 3.7 39.3 - - + -
257B GLU* 3.4 31.6 - - + -
259B LEU* 6.2 4.3 - - + -
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Residues in contact with GLY 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A HIS* 2.7 20.8 + - - -
83A PHE* 1.3 93.6 - - - +
85A ILE* 1.3 62.2 + - - -
87A GLU* 3.3 9.0 - - - +
88A GLU* 3.3 19.1 + - - +
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Residues in contact with ILE 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A SER 4.4 6.3 - - - +
80A TYR* 3.7 40.8 - - + +
82A HIS* 3.3 13.2 + - + +
84A GLY* 1.3 75.3 - - - +
86A HIS* 1.3 75.5 + - + +
88A GLU* 3.3 19.3 + - + +
89A MET* 3.3 38.8 + - + +
189A TYR* 6.1 0.9 - - - +
334A HIS* 5.7 3.1 - - + -
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Residues in contact with HIS 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A TYR* 2.9 33.9 + + - -
82A HIS 3.7 8.7 + - - -
83A PHE* 3.4 8.5 + - - +
84A GLY 3.2 0.2 - - - -
85A ILE* 1.3 83.0 - - + +
87A GLU* 1.3 66.6 + - - +
89A MET* 3.0 12.1 + - - +
90A LEU* 2.8 33.6 + - + +
121A GLY* 3.8 10.7 - - - -
122A THR* 3.7 41.0 + - + -
145A ILE* 3.6 20.0 - - + +
401A SAH 3.6 32.8 + - + +
239B TRP* 4.9 1.3 - - + -
250B ILE* 5.9 0.2 - - + -
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Residues in contact with GLU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A PHE* 3.1 24.7 + - - +
84A GLY* 3.3 12.4 - - - +
86A HIS* 1.3 74.7 - - - +
88A GLU* 1.3 56.7 + - - +
90A LEU* 3.5 0.9 + - - +
91A LYS* 2.8 71.9 + - + +
235B LYS* 3.0 42.1 + - - +
238B TRP* 4.1 8.7 - - + -
239B TRP* 3.7 36.0 + - + -
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Residues in contact with GLU 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A GLY 3.3 9.1 + - - +
85A ILE* 3.6 21.3 - - + +
86A HIS 3.1 0.8 - - - -
87A GLU* 1.3 76.6 - - - +
89A MET* 1.3 66.1 + - + +
91A LYS* 3.5 5.6 + - - +
92A ASP* 3.2 20.6 + - - +
189A TYR* 4.8 9.8 + - - -
332A TYR* 4.2 9.8 + - - +
334A HIS* 3.4 38.5 - - + +
336A LYS* 5.2 4.2 + - - -
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Residues in contact with MET 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A TYR* 4.1 18.8 - - + +
85A ILE* 3.5 25.8 - - + +
86A HIS* 3.0 15.4 + - - +
88A GLU* 1.3 76.6 - - - +
90A LEU* 1.3 63.6 + - - +
92A ASP* 3.3 11.3 + - - +
95A ARG* 3.0 37.2 + - - +
96A THR* 3.2 3.1 + - - -
185A GLU* 3.5 24.9 - - - +
187A MET 5.1 2.0 - - - +
334A HIS* 4.0 26.9 - - + +
401A SAH 3.6 41.1 - - - +
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Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A HIS* 2.8 26.1 + - + +
89A MET* 1.3 79.3 - - + +
91A LYS* 1.3 55.1 + - - +
92A ASP 3.3 0.5 + - - -
95A ARG* 4.4 6.5 - - - +
96A THR* 3.3 5.5 + - + -
122A THR* 4.0 25.4 - - + +
124A ILE* 3.8 38.4 - - + -
401A SAH 4.6 2.2 - - - +
238B TRP* 3.7 26.9 - - + -
239B TRP* 4.3 8.3 - - + -
242B VAL* 3.8 22.9 - - + -
243B TYR* 2.6 41.3 + - + -
247B MET* 4.4 1.6 - - - -
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Residues in contact with LYS 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A GLU* 2.8 52.0 + - + +
88A GLU* 4.1 5.6 - - - +
90A LEU* 1.3 73.6 - - - +
92A ASP* 1.3 59.8 + - - +
93A GLU* 2.9 19.5 + - - +
234B PHE* 2.8 63.8 + - + -
235B LYS* 4.6 0.2 - - - +
238B TRP* 3.4 39.9 - - + +
243B TYR* 4.2 0.9 - - - -
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Residues in contact with ASP 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A GLU 3.2 11.9 + - - +
89A MET 3.3 11.9 - - - +
90A LEU 3.1 0.6 - - - -
91A LYS* 1.3 73.3 - - - +
93A GLU* 1.3 61.8 + - - +
94A VAL* 3.2 20.1 + - - +
95A ARG* 3.3 16.8 + - + +
96A THR* 3.0 27.4 + - - -
332A TYR* 4.0 9.5 - - + +
333A THR* 3.3 15.2 - - - -
334A HIS* 2.9 46.5 + - + +
335A TRP* 4.1 0.7 - - - -
243B TYR* 3.9 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