Contacts of the helix formed by residues 82 - 92 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79K SER* 4.1 12.3 + - - +
80K TYR 3.2 1.8 - - - -
81K ALA* 1.3 78.1 - - - +
83K PHE* 1.3 71.2 + + - +
84K GLY* 2.6 39.2 + - - -
85K ILE* 3.4 15.0 + - + +
86K HIS* 3.7 11.8 + - - -
145K ILE* 4.8 0.2 - - - -
257L GLU* 3.1 38.9 + - - -
394L ARG* 3.5 27.5 + - - +
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Residues in contact with PHE 83 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81K ALA 3.6 4.2 + - - -
82K HIS* 1.3 81.7 - + - +
84K GLY* 1.3 65.5 + - - +
86K HIS* 3.5 7.1 + - - +
87K GLU* 3.1 42.3 + - - -
145K ILE* 4.7 11.6 - - + +
239L TRP* 3.7 13.4 - + - -
250L ILE* 3.8 28.9 - - + -
253L VAL* 4.3 19.1 - - + -
254L ALA* 3.9 31.6 - - + -
257L GLU* 3.0 40.2 - - + -
259L LEU* 6.3 2.9 - - + -
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Residues in contact with GLY 84 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82K HIS* 2.6 22.9 + - - -
83K PHE* 1.3 89.4 - - - +
85K ILE* 1.3 63.6 + - - -
86K HIS 3.2 1.3 - - - -
87K GLU* 3.4 8.7 - - - +
88K GLU* 3.2 18.7 + - - +
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Residues in contact with ILE 85 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79K SER 4.2 7.6 - - - +
80K TYR* 3.8 35.4 - - + +
82K HIS* 3.4 12.4 + - + +
84K GLY* 1.3 75.9 - - - +
86K HIS* 1.3 81.0 + - + +
88K GLU* 3.3 19.8 + - + +
89K MET* 3.2 38.5 + - + +
189K TYR* 6.2 0.2 - - - +
334K HIS* 5.8 3.4 - - + -
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Residues in contact with HIS 86 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80K TYR* 2.8 41.4 + + + -
82K HIS 3.7 6.3 + - - -
83K PHE* 3.5 8.5 + - - +
84K GLY 3.2 0.4 - - - -
85K ILE* 1.3 83.7 - - + +
87K GLU* 1.3 55.9 + - - +
89K MET* 3.0 12.1 + - - +
90K LEU* 2.7 43.7 + - + +
121K GLY* 3.9 9.2 - - - -
122K THR* 3.9 40.2 - - + -
145K ILE* 3.7 16.9 - - + +
401K SAH 3.6 31.2 + - + +
239L TRP* 5.2 0.7 - - + -
250L ILE* 6.3 0.2 - - + -
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Residues in contact with GLU 87 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83K PHE* 3.1 31.5 + - - +
84K GLY* 3.4 12.0 - - - +
86K HIS* 1.3 75.0 - - - +
88K GLU* 1.3 62.8 + - - +
90K LEU* 3.9 0.5 - - - +
91K LYS* 2.7 68.0 + - + +
235L LYS* 2.9 35.7 + - - +
238L TRP* 4.2 6.7 - - + -
239L TRP* 3.5 36.4 + - + -
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Residues in contact with GLU 88 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84K GLY 3.2 8.6 + - - +
85K ILE* 3.5 22.2 - - + +
86K HIS 3.2 0.8 - - - -
87K GLU* 1.3 81.3 - - - +
89K MET* 1.3 61.9 + - + +
91K LYS* 4.0 5.1 - - - +
92K ASP* 3.3 20.8 + - - +
189K TYR* 4.8 10.0 + - - -
332K TYR* 4.1 10.7 + - - +
334K HIS* 3.5 36.7 - - + +
336K LYS* 5.0 5.0 + - - -
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Residues in contact with MET 89 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80K TYR* 4.0 20.2 - - + +
85K ILE* 3.2 24.1 + - + +
86K HIS* 3.0 15.3 + - - +
88K GLU* 1.3 77.3 - - - +
90K LEU* 1.3 62.9 + - - +
92K ASP* 3.4 11.2 + - - +
95K ARG* 2.9 38.9 + - - +
96K THR* 3.1 3.1 + - - -
185K GLU* 3.5 23.1 - - - +
187K MET 5.2 2.0 - - - +
334K HIS* 4.2 23.8 - - + +
401K SAH 3.7 44.2 - - - +
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Residues in contact with LEU 90 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86K HIS* 2.7 29.9 + - + +
87K GLU 3.9 0.2 - - - +
89K MET* 1.3 74.8 - - - +
91K LYS* 1.3 53.3 + - - +
95K ARG* 4.3 7.0 - - - +
96K THR* 3.3 9.9 + - + -
122K THR* 4.0 25.8 - - + +
124K ILE* 3.7 42.4 - - + -
401K SAH 4.5 2.2 - - - +
238L TRP* 3.7 26.2 - - + -
239L TRP* 4.4 9.4 - - + -
242L VAL* 4.1 12.1 - - + -
243L TYR* 2.6 36.4 + - - -
247L MET* 4.4 7.2 - - + -
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Residues in contact with LYS 91 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87K GLU* 2.7 51.7 + - + +
88K GLU* 4.1 5.6 - - - +
90K LEU* 1.3 72.9 - - - +
92K ASP* 1.3 59.2 + - - +
93K GLU* 2.9 18.9 + - - +
234L PHE* 2.8 65.7 + - + -
235L LYS* 4.2 0.2 - - - +
238L TRP* 3.5 39.2 - - + +
243L TYR* 4.3 1.3 - - - -
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Residues in contact with ASP 92 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88K GLU 3.3 12.2 + - - +
89K MET 3.4 12.6 - - - +
90K LEU 3.1 1.9 - - - -
91K LYS* 1.3 73.3 - - - +
93K GLU* 1.3 62.3 + - - +
94K VAL* 3.3 11.6 + - - +
95K ARG* 3.2 25.5 + - + +
96K THR* 3.0 25.1 + - - -
332K TYR* 4.1 9.3 - - + +
333K THR* 3.6 13.9 - - - -
334K HIS* 2.9 47.2 + - + +
335K TRP* 4.0 0.3 - - - -
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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