Contacts of the helix formed by residues 82 - 92 (chain N) 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 N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257M GLU* 3.1 39.7 + - - -
394M ARG* 3.5 28.2 + - - +
79N SER* 3.6 11.6 + - - +
80N TYR 3.2 1.2 - - - -
81N ALA* 1.3 78.7 - - - +
83N PHE* 1.3 83.3 + + - +
84N GLY* 2.8 25.3 + - - -
85N ILE* 3.5 14.5 + - + +
86N HIS* 3.6 14.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 83 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235M LYS 6.0 0.2 - - - -
239M TRP* 3.5 22.6 - + - -
250M ILE* 3.7 28.5 - - + -
253M VAL* 4.3 16.6 - - + -
254M ALA* 3.9 35.9 - - + -
257M GLU* 3.4 33.4 - - + -
259M LEU* 6.3 2.5 - - + -
81N ALA 3.5 3.4 + - - -
82N HIS* 1.3 86.6 + + - +
84N GLY* 1.3 63.5 + - - +
86N HIS* 3.6 6.5 + - - +
87N GLU* 3.1 35.0 + - - -
145N ILE* 4.7 11.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 84 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82N HIS* 2.8 17.9 + - - -
83N PHE* 1.3 93.8 - - - +
85N ILE* 1.3 63.1 + - - -
86N HIS 3.2 2.0 - - - -
87N GLU* 3.2 9.5 + - - +
88N GLU* 3.1 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 85 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79N SER 4.3 6.3 - - - +
80N TYR* 3.9 35.7 - - + +
82N HIS* 3.5 13.4 + - + +
84N GLY* 1.3 75.7 - - - +
86N HIS* 1.3 81.2 + - + +
88N GLU* 3.3 20.0 + - - +
89N MET* 3.3 40.0 + - + +
334N HIS* 5.8 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 86 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239M TRP* 5.1 1.3 - - + -
250M ILE* 6.3 0.2 - - + -
80N TYR* 2.9 35.3 + + - -
82N HIS 3.6 10.1 + - - -
83N PHE* 3.6 8.3 + - - +
84N GLY 3.2 0.2 - - - -
85N ILE* 1.3 82.6 - - + +
87N GLU* 1.3 59.9 + - - +
89N MET* 3.2 10.7 + - - +
90N LEU* 2.8 39.5 + - + +
121N GLY* 3.9 9.4 - - - -
122N THR* 3.8 40.1 + - + -
145N ILE* 3.6 17.1 - - + +
401N SAH 3.6 35.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 87 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235M LYS* 3.1 36.4 + - - +
238M TRP* 4.0 6.7 - - + -
239M TRP* 3.6 39.4 + - + -
83N PHE* 3.1 26.6 + - - +
84N GLY* 3.3 11.5 - - - +
86N HIS* 1.3 75.1 - - - +
88N GLU* 1.3 64.1 + - - +
90N LEU* 3.8 0.2 - - - -
91N LYS* 2.6 68.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 88 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84N GLY 3.1 9.1 + - - +
85N ILE* 3.5 22.1 - - + +
86N HIS 3.2 0.4 - - - -
87N GLU* 1.3 80.8 - - - +
89N MET* 1.3 63.9 + - - +
91N LYS* 3.5 5.4 + - - +
92N ASP* 3.3 19.8 + - - +
189N TYR* 4.6 9.6 + - - -
332N TYR* 4.4 8.4 + - - +
334N HIS* 3.7 37.0 - - + +
336N LYS* 5.1 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 89 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80N TYR* 4.2 19.7 - - + +
85N ILE* 3.3 25.1 + - + +
86N HIS* 3.2 14.7 + - - +
88N GLU* 1.3 80.3 - - + +
90N LEU* 1.3 62.9 - - - +
92N ASP* 3.4 9.0 + - - +
95N ARG* 2.9 36.7 + - - +
96N THR* 3.1 2.9 + - - -
185N GLU* 3.5 23.3 - - - +
187N MET 5.1 2.2 - - - +
334N HIS* 4.1 27.4 - - + +
401N SAH 3.7 40.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 90 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238M TRP* 3.7 26.0 - - + -
239M TRP* 4.3 9.6 - - + -
242M VAL* 4.1 16.8 - - + -
243M TYR* 2.6 35.4 + - + -
247M MET* 4.6 2.5 - - + -
86N HIS* 2.8 29.2 + - + +
89N MET* 1.3 74.0 - - - +
91N LYS* 1.3 56.1 - - - +
95N ARG* 4.4 6.3 - - - +
96N THR* 3.2 11.1 + - + -
122N THR* 4.0 25.8 - - + +
124N ILE* 3.8 42.6 - - + -
401N SAH 4.9 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 91 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234M PHE* 2.9 61.5 + - + -
235M LYS* 4.3 0.6 - - - +
238M TRP* 3.3 43.1 - - + +
243M TYR* 4.5 0.9 - - - -
87N GLU* 2.6 50.9 + - + +
88N GLU* 4.1 4.3 - - - +
90N LEU* 1.3 73.4 - - - +
92N ASP* 1.3 60.4 + - - +
93N GLU* 3.0 20.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 92 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88N GLU 3.3 12.4 + - - +
89N MET 3.5 11.9 - - - +
90N LEU 3.2 1.9 - - - -
91N LYS* 1.3 72.9 - - - +
93N GLU* 1.3 58.1 + - - +
94N VAL* 3.3 19.2 + - - +
95N ARG* 3.4 16.3 + - + +
96N THR* 3.0 28.8 + - - -
332N TYR* 4.0 10.5 - - + +
333N THR* 3.4 15.3 - - - -
334N HIS* 2.9 47.1 + - + +
335N TRP* 4.1 0.5 - - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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