Contacts of the helix formed by residues 82 - 92 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257C GLU* 3.2 39.6 + - - -
394C ARG* 3.6 25.3 + - - +
79D SER* 4.0 11.6 + - - +
80D TYR 3.3 1.8 - - - -
81D ALA* 1.3 77.8 - - - +
83D PHE* 1.3 74.8 + + - +
84D GLY* 2.5 38.8 + - - -
85D ILE* 3.3 15.1 + - + +
86D HIS* 3.8 9.8 + - - -
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Residues in contact with PHE 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235C LYS* 5.9 1.3 - - + -
239C TRP* 3.5 23.8 - + - -
250C ILE* 3.6 28.9 - - + -
253C VAL* 4.4 16.4 - - + -
254C ALA* 3.8 37.2 - - + -
257C GLU* 3.4 29.4 - - + -
259C LEU* 6.3 2.9 - - + -
81D ALA 3.6 4.7 + - - -
82D HIS* 1.3 83.4 + + - +
84D GLY* 1.3 64.2 + - - +
86D HIS* 3.4 6.0 + - - +
87D GLU* 3.1 35.9 + - - -
145D ILE* 4.7 11.9 - - + +
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Residues in contact with GLY 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D HIS* 2.5 23.5 + - - -
83D PHE* 1.3 91.1 - - - +
85D ILE* 1.3 61.4 + - - -
86D HIS 3.2 1.1 - - - -
87D GLU* 3.4 10.2 - - - +
88D GLU* 3.3 18.5 + - - +
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Residues in contact with ILE 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D SER 4.3 7.0 - - - +
80D TYR* 3.8 35.4 - - + -
82D HIS* 3.3 12.6 + - + +
84D GLY* 1.3 76.6 - - - +
86D HIS* 1.3 81.5 + - + +
88D GLU* 3.3 18.0 + - - +
89D MET* 3.3 40.2 + - + +
334D HIS* 5.7 3.8 - - + -
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Residues in contact with HIS 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239C TRP* 5.1 1.1 - - + -
80D TYR* 2.8 36.9 + - + -
82D HIS 3.8 7.3 + - - -
83D PHE* 3.4 7.8 + - - +
85D ILE* 1.3 82.8 - - + +
87D GLU* 1.3 68.0 + - - +
89D MET* 3.7 12.5 - - - +
90D LEU* 2.8 35.0 + - + +
121D GLY* 3.9 8.4 - - - -
122D THR* 3.9 38.4 - - + -
145D ILE* 3.7 18.2 - - + +
401D SAH 3.6 33.5 + - + +
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Residues in contact with GLU 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235C LYS* 3.1 37.3 + - - +
238C TRP* 4.2 8.1 - - + -
239C TRP* 3.8 31.9 + - + -
83D PHE* 3.1 32.0 + - - +
84D GLY* 3.4 12.5 - - - +
86D HIS* 1.3 76.0 - - - +
88D GLU* 1.3 63.7 + - - +
90D LEU* 3.8 0.7 - - - +
91D LYS* 2.7 62.9 + - + +
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Residues in contact with GLU 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D GLY 3.3 7.8 + - - +
85D ILE* 3.3 22.7 + - + +
86D HIS 3.2 0.6 - - - -
87D GLU* 1.3 79.5 - - - +
89D MET* 1.3 63.6 + - + +
91D LYS* 3.5 5.8 + - - +
92D ASP* 3.3 19.9 + - - +
189D TYR* 4.9 8.6 + - - -
332D TYR* 4.3 10.2 + - - +
334D HIS* 3.7 34.1 - - + +
336D LYS* 5.1 5.4 + - - -
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Residues in contact with MET 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D TYR* 4.1 19.1 - - + +
85D ILE* 3.3 25.0 + - + +
86D HIS* 3.3 15.5 + - - +
88D GLU* 1.3 78.2 - - - +
90D LEU* 1.3 64.6 + - + +
92D ASP* 3.3 9.5 + - - +
95D ARG* 3.0 37.6 + - - +
96D THR* 3.2 4.0 + - - -
185D GLU* 3.5 23.8 - - - +
187D MET 5.2 2.2 - - - +
334D HIS* 4.1 26.2 - - + +
401D SAH 3.7 39.7 - - - +
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Residues in contact with LEU 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C TRP* 3.8 25.1 - - + -
239C TRP* 4.4 8.5 - - + -
242C VAL* 4.0 17.3 - - + -
243C TYR* 2.6 39.8 + - + -
247C MET* 4.4 2.5 - - + -
86D HIS* 2.8 26.5 + - + +
87D GLU 3.8 2.5 - - - +
89D MET* 1.3 76.7 - - + +
91D LYS* 1.3 56.2 + - - +
92D ASP 3.1 0.9 + - - -
95D ARG* 4.4 6.3 - - - +
96D THR* 3.3 7.4 + - + -
122D THR* 4.1 25.1 - - + +
124D ILE* 3.9 41.5 - - + -
401D SAH 4.6 2.2 - - - +
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Residues in contact with LYS 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234C PHE* 2.9 63.0 + - + -
238C TRP* 3.5 43.7 - - + +
243C TYR* 4.3 2.5 - - - -
87D GLU* 2.7 47.6 + - + +
88D GLU* 4.0 5.2 - - - +
90D LEU* 1.3 73.0 - - - +
92D ASP* 1.3 58.7 + - - +
93D GLU* 3.0 18.0 + - - +
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Residues in contact with ASP 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D GLU 3.3 11.5 + - - +
89D MET 3.3 11.4 + - - +
90D LEU 3.1 1.7 - - - -
91D LYS* 1.3 72.0 - - - +
93D GLU* 1.3 58.1 + - - +
94D VAL* 3.3 12.1 + - - +
95D ARG* 3.1 25.4 + - + +
96D THR* 2.9 31.4 + - - -
332D TYR* 4.0 9.8 - - + +
333D THR* 3.3 14.3 - - - -
334D HIS* 3.0 43.7 + - + +
335D TRP* 4.0 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