Contacts of the helix formed by residues 82 - 92 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257I GLU* 3.1 39.3 + - - -
394I ARG* 3.4 30.4 + - - +
79J SER* 4.1 10.9 + - - +
80J TYR 3.3 1.6 - - - -
81J ALA* 1.3 79.4 - - - +
83J PHE* 1.3 76.4 + + - +
84J GLY* 2.7 34.6 + - - -
85J ILE* 3.4 14.7 + - + +
86J HIS* 3.8 10.5 + - - -
145J ILE* 5.0 0.4 - - - -
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Residues in contact with PHE 83 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235I LYS* 6.1 0.4 - - - -
239I TRP* 3.6 16.4 - + - -
250I ILE* 3.8 28.3 - - + -
253I VAL* 4.5 15.0 - - + -
254I ALA* 4.0 35.2 - - + -
257I GLU* 3.3 32.1 - - + -
259I LEU* 6.5 1.6 - - + -
81J ALA 3.6 4.0 + - - -
82J HIS* 1.3 84.8 - + - +
84J GLY* 1.3 63.5 + - - +
85J ILE 3.7 0.2 - - - -
86J HIS* 3.6 6.0 + - - +
87J GLU* 3.1 39.8 + - - -
145J ILE* 4.7 11.4 - - + -
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Residues in contact with GLY 84 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82J HIS* 2.7 21.8 + - - -
83J PHE* 1.3 89.6 - - - +
85J ILE* 1.3 61.8 + - - -
86J HIS 3.2 1.1 - - - -
87J GLU* 3.5 9.4 - - - +
88J GLU* 3.3 18.9 + - - +
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Residues in contact with ILE 85 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79J SER 4.3 8.3 - - - +
80J TYR* 3.9 33.9 - - + +
82J HIS* 3.4 12.6 + - + +
84J GLY* 1.3 75.7 - - - +
86J HIS* 1.3 82.4 + - + +
88J GLU* 3.4 17.9 + - + +
89J MET* 3.3 39.4 + - + +
334J HIS* 5.7 3.1 - - + -
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Residues in contact with HIS 86 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239I TRP* 5.2 0.7 - - + -
250I ILE* 6.3 0.2 - - + -
80J TYR* 2.9 41.4 + + + -
82J HIS 3.8 6.3 + - - -
83J PHE* 3.6 9.1 + - - +
84J GLY 3.2 0.2 - - - -
85J ILE* 1.3 86.6 - - + +
87J GLU* 1.3 65.3 + - - +
89J MET* 3.2 10.6 + - - +
90J LEU* 2.8 33.3 + - + +
121J GLY* 3.9 8.6 - - - -
122J THR* 3.7 41.3 - - + -
145J ILE* 3.7 17.1 - - + +
401J SAH 3.8 29.9 + - + +
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Residues in contact with GLU 87 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235I LYS* 3.0 38.4 + - - +
238I TRP* 4.2 7.2 - - + -
239I TRP* 3.8 29.6 + - + -
83J PHE* 3.1 36.8 + - - +
84J GLY* 3.5 11.8 - - - +
85J ILE 3.4 0.2 - - - -
86J HIS* 1.3 76.4 - - - +
88J GLU* 1.3 64.0 + - - +
90J LEU* 3.3 0.7 + - - +
91J LYS* 2.6 66.8 + - + +
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Residues in contact with GLU 88 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84J GLY 3.3 9.2 + - - +
85J ILE* 3.6 21.9 - - + +
86J HIS 3.2 0.8 - - - -
87J GLU* 1.3 79.7 - - - +
89J MET* 1.3 64.1 + - + +
91J LYS* 3.4 5.6 + - - +
92J ASP* 3.2 20.8 + - - +
189J TYR* 4.5 8.9 + - - -
332J TYR* 4.4 7.9 + - - +
334J HIS* 3.5 38.1 - - + +
336J LYS* 5.1 5.0 + - - -
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Residues in contact with MET 89 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80J TYR* 4.1 19.3 - - + +
85J ILE* 3.3 25.3 + - + +
86J HIS* 3.2 15.6 + - - +
88J GLU* 1.3 80.0 - - - +
90J LEU* 1.3 63.3 + - - +
92J ASP* 3.4 8.7 + - - +
95J ARG* 3.0 37.0 + - - +
96J THR* 3.1 3.8 + - - -
185J GLU* 3.6 21.1 - - - +
187J MET 5.2 1.8 - - - +
334J HIS* 4.1 27.8 - - + +
401J SAH 3.6 44.0 - - - +
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Residues in contact with LEU 90 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238I TRP* 3.8 26.0 - - + -
239I TRP* 4.4 9.2 - - + -
242I VAL* 4.2 15.9 - - + -
243I TYR* 2.6 34.0 + - + -
247I MET* 4.6 2.5 - - + -
86J HIS* 2.8 27.2 + - + +
89J MET* 1.3 78.1 - - - +
91J LYS* 1.3 56.3 + - - +
92J ASP 3.2 1.0 + - - -
95J ARG* 4.4 6.3 - - - +
96J THR* 3.3 12.9 + - + -
122J THR* 4.2 24.0 - - + +
124J ILE* 3.8 42.8 - - + -
401J SAH 4.7 2.7 - - - +
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Residues in contact with LYS 91 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234I PHE* 3.1 62.6 + - + -
235I LYS* 4.3 1.0 - - - +
238I TRP* 3.5 37.9 - - + +
243I TYR* 4.5 1.8 - - - -
87J GLU* 2.6 52.9 + - + +
88J GLU* 3.9 5.4 - - - +
90J LEU* 1.3 72.8 - - - +
92J ASP* 1.3 59.7 + - - +
93J GLU* 3.0 19.0 + - - +
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Residues in contact with ASP 92 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88J GLU 3.2 12.9 + - - +
89J MET 3.4 11.4 - - - +
90J LEU 3.1 1.7 - - - -
91J LYS* 1.3 72.7 - - - +
93J GLU* 1.3 56.3 + - - +
94J VAL* 3.2 20.4 + - - +
95J ARG* 3.2 18.6 + - + +
96J THR* 2.9 31.7 + - - -
332J TYR* 3.8 9.3 - - + +
333J THR* 3.5 14.5 - - - -
334J HIS* 3.1 44.1 + - + +
335J TRP* 4.0 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