Contacts of the helix formed by residues 82 - 92 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79I SER 3.8 11.4 + - - +
80I TYR 3.2 1.2 - - - -
81I ALA* 1.3 79.3 - - - +
83I PHE* 1.3 72.6 + + - +
84I GLY* 2.6 35.2 + - - -
85I ILE* 3.3 21.5 + - + +
86I HIS* 3.8 4.5 + - - -
257J GLU* 3.1 39.8 + - - -
394J ARG* 3.3 29.8 + - - +
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Residues in contact with PHE 83 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81I ALA 3.5 4.8 + - - -
82I HIS* 1.3 85.5 + + - +
84I GLY* 1.3 76.3 + - - +
86I HIS* 3.4 8.6 + - - +
87I GLU* 3.1 40.8 + - - -
145I ILE* 4.6 11.6 - - + +
235J LYS* 6.1 0.4 - - - -
239J TRP* 3.7 14.2 - + + -
250J ILE* 3.8 28.0 - - + -
253J VAL* 4.4 15.0 - - + -
254J ALA* 4.0 33.9 - - + -
257J GLU* 3.2 34.5 - - + -
259J LEU* 6.4 2.7 - - + -
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Residues in contact with GLY 84 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82I HIS* 2.6 19.5 + - - -
83I PHE* 1.3 91.0 - - - +
85I ILE* 1.3 61.8 + - - -
86I HIS 3.2 1.3 - - - -
87I GLU* 3.5 10.7 - - - +
88I GLU* 3.4 17.2 + - - +
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Residues in contact with ILE 85 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79I SER 4.3 6.5 - - - +
80I TYR* 3.8 35.2 - - + +
82I HIS* 3.3 12.4 + - + +
84I GLY* 1.3 75.6 - - - +
86I HIS* 1.3 81.0 + - + +
88I GLU* 3.3 25.5 + - + +
89I MET* 3.3 32.8 + - + +
334I HIS* 5.8 3.1 - - + -
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Residues in contact with HIS 86 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80I TYR* 2.9 38.6 + + + -
82I HIS 3.8 6.5 + - - -
83I PHE* 3.4 8.7 + - - +
84I GLY 3.2 0.4 - - - -
85I ILE* 1.3 84.2 - - + +
87I GLU* 1.3 60.9 + - - +
89I MET* 3.7 11.0 - - - +
90I LEU* 2.9 39.9 + - + +
121I GLY* 3.9 7.3 - - - -
122I THR* 3.8 39.5 - - + -
145I ILE* 3.5 19.3 - - + +
401I SAH 3.8 33.1 + - + +
239J TRP* 5.2 0.4 - - + -
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Residues in contact with GLU 87 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83I PHE* 3.1 36.7 + - - +
84I GLY* 3.5 11.4 - - - +
86I HIS* 1.3 77.0 - - - +
88I GLU* 1.3 63.0 + - - +
90I LEU* 3.4 0.5 + - - +
91I LYS* 2.7 67.5 + - + +
235J LYS* 3.1 36.5 + - - +
238J TRP* 4.1 7.9 - - + -
239J TRP* 3.7 30.9 + - + -
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Residues in contact with GLU 88 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84I GLY 3.4 8.0 + - - +
85I ILE* 3.3 22.0 + - + +
86I HIS 3.2 0.6 - - - -
87I GLU* 1.3 79.7 - - - +
89I MET* 1.3 61.9 + - + +
91I LYS* 3.5 4.1 + - - +
92I ASP* 3.1 20.8 + - - +
189I TYR* 4.7 10.3 + - - -
332I TYR* 4.4 8.8 + - - +
334I HIS* 3.4 39.8 - - + +
336I LYS* 5.1 5.0 + - - -
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Residues in contact with MET 89 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80I TYR* 4.1 19.5 - - + +
85I ILE* 3.3 25.1 + - + +
86I HIS* 3.2 17.1 + - - +
88I GLU* 1.3 75.5 - - - +
90I LEU* 1.3 63.9 + - - +
92I ASP* 3.3 9.2 + - - +
95I ARG* 2.8 38.4 + - - +
96I THR* 3.0 5.7 + - - -
185I GLU* 3.6 20.4 - - - +
187I MET 5.2 2.0 - - - +
334I HIS* 4.0 28.0 - - + +
401I SAH 3.5 44.0 - - - +
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Residues in contact with LEU 90 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86I HIS 2.9 26.7 + - - +
87I GLU 3.9 0.2 - - - +
89I MET* 1.3 75.0 - - - +
91I LYS* 1.3 60.3 + - - +
92I ASP 3.3 0.7 + - - -
95I ARG* 4.4 6.7 - - - +
96I THR* 3.3 7.8 + - + -
122I THR* 4.2 25.6 - - + +
124I ILE* 3.9 41.1 - - + -
401I SAH 4.5 2.5 - - - +
238J TRP* 3.8 27.6 - - + -
239J TRP* 4.3 10.1 - - + -
242J VAL* 4.1 15.7 - - + -
243J TYR* 2.6 38.5 + - + -
247J MET* 4.6 2.0 - - + -
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Residues in contact with LYS 91 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87I GLU* 2.7 52.7 + - + +
88I GLU* 3.8 4.7 - - - +
90I LEU* 1.3 74.7 - - - +
92I ASP* 1.3 58.2 + - - +
93I GLU* 2.9 17.6 + - - +
234J PHE* 3.1 62.2 + - + -
235J LYS* 4.5 0.6 - - - +
238J TRP* 3.5 40.6 - - + +
243J TYR* 4.6 1.6 - - - -
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Residues in contact with ASP 92 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88I GLU 3.1 11.9 + - - +
89I MET 3.4 11.0 - - - +
90I LEU 3.2 1.9 - - - -
91I LYS* 1.3 72.8 - - - +
93I GLU* 1.3 56.6 + - - +
94I VAL* 3.2 13.2 + - - +
95I ARG* 3.1 24.4 + - + +
96I THR* 3.0 29.6 + - - -
332I TYR* 4.0 10.1 - - + +
333I THR* 3.2 14.7 - - - -
334I HIS* 2.8 47.7 + - + +
335I TRP* 4.1 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