Contacts of the helix formed by residues 197 - 208 (chain o) in PDB entry 5JPQ
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 GLU 197 (chain o).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78o ASN* 4.9 5.7 + - - -
82o LYS* 3.6 38.7 + - - +
195o ILE 4.0 3.7 + - - +
196o GLY* 1.3 70.0 - - - -
198o ASP* 1.3 61.5 + - - +
199o TYR 3.4 1.1 - - - -
200o THR* 3.7 19.2 - - + +
201o LYS* 3.1 38.7 + - + +
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Residues in contact with ASP 198 (chain o).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192o LYS* 4.9 0.9 - - - +
193o ASN* 4.1 23.3 - - - +
196o GLY* 2.6 15.5 + - - +
197o GLU* 1.3 75.3 - - - +
199o TYR* 1.3 74.5 + - + +
201o LYS* 3.3 11.4 + - - +
202o LYS* 3.2 27.2 + - - +
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Residues in contact with TYR 199 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177o PHE* 3.6 25.8 - + + -
178o ILE* 5.0 6.5 - - + -
181o GLU* 2.9 45.8 + - + +
185o LEU* 3.5 9.7 - - - +
190o PHE* 4.2 5.5 - + - -
193o ASN* 3.0 52.7 + - + +
194o LEU* 4.2 19.5 - - + -
196o GLY 3.6 2.5 + - - +
198o ASP* 1.3 80.7 - - + +
200o THR* 1.3 65.2 + - - +
201o LYS 3.1 1.8 - - - -
202o LYS* 3.7 7.0 - - + -
203o ILE* 2.9 35.8 + - + +
218o ILE* 4.5 16.4 - - + -
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Residues in contact with THR 200 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85o ARG* 6.0 0.3 + - - -
196o GLY 4.7 1.3 + - - -
197o GLU* 3.6 24.7 + - + +
198o ASP 3.3 0.2 - - - -
199o TYR* 1.3 78.6 - - - +
201o LYS* 1.3 61.4 + - + +
204o GLU* 3.1 31.8 + - + +
216o ILE* 3.8 43.4 + - + +
217o THR* 5.6 0.9 - - - -
218o ILE* 5.9 3.3 - - - +
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Residues in contact with LYS 201 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197o GLU* 3.1 29.4 - - + +
198o ASP* 3.3 9.2 + - - +
199o TYR 3.1 0.4 - - - -
200o THR* 1.3 78.5 - - + +
202o LYS* 1.3 65.7 + - + +
204o GLU* 3.2 18.1 - - - +
205o LYS* 3.0 27.8 + - + +
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Residues in contact with LYS 202 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10562 U 5.0 0.8 - - - -
10572 U 3.5 21.8 + - - -
10582 U 3.8 15.4 + - - -
177o PHE* 4.0 32.1 - - + -
198o ASP 3.2 15.0 + - - +
199o TYR* 3.4 6.5 + - + +
201o LYS* 1.3 79.8 - - + +
203o ILE* 1.3 62.1 - - - +
205o LYS* 2.9 25.7 + - + +
206o GLU* 3.2 20.9 + - + +
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Residues in contact with ILE 203 (chain o).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142o THR* 3.8 20.9 - - + -
174o ILE* 3.5 46.9 - - + -
177o PHE* 4.3 21.7 - - + -
178o ILE* 5.1 3.6 - - + -
199o TYR* 2.9 24.0 + - + +
202o LYS* 1.3 75.3 - - - +
204o GLU* 1.3 57.0 + - - +
205o LYS 3.2 0.2 + - - -
206o GLU* 3.3 7.9 + - + +
207o THR* 2.9 41.1 + - - +
213o LEU* 5.0 1.8 - - + -
216o ILE* 3.7 27.6 - - + -
218o ILE* 6.3 1.3 - - + -
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Residues in contact with GLU 204 (chain o).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10552 U 3.9 23.8 + - - +
147o LYS* 5.5 4.5 + - - -
200o THR* 3.1 20.2 + - + +
201o LYS* 3.2 22.3 - - - +
203o ILE* 1.3 80.4 - - - +
205o LYS* 1.3 58.0 + - + +
207o THR* 4.5 3.1 - - - +
208o LYS* 3.2 26.1 + - + +
213o LEU* 5.2 8.1 - - - +
216o ILE* 3.9 12.3 - - + +
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Residues in contact with LYS 205 (chain o).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10552 U 1.0 80.5 + - - +
10562 U 0.5 141.0 + - - +
10572 U 4.3 0.8 + - - -
10582 U 3.3 1.8 - - - +
10642 G 2.2 37.6 + - - -
201o LYS* 3.0 18.8 + - + +
202o LYS* 2.9 17.9 + - + +
204o GLU* 1.3 75.1 - - - +
206o GLU* 1.3 59.5 + - - +
208o LYS* 3.2 1.2 - - - +
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Residues in contact with GLU 206 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10562 U 3.2 26.3 - - - +
10572 U 3.7 9.6 + - - -
10652 A 3.1 14.4 + - - -
173o LYS* 2.9 60.3 + - + +
174o ILE* 6.5 1.8 - - + -
177o PHE* 5.4 19.7 - - + +
202o LYS* 3.2 24.6 + - + +
203o ILE* 4.0 7.0 - - - +
205o LYS* 1.3 76.9 - - - +
207o THR* 1.3 59.7 + - - +
209o ASN* 4.2 2.5 - - - +
210o ILE* 4.9 0.2 - - - +
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Residues in contact with THR 207 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10652 A 1.4 34.6 + - - +
10662 C 2.4 9.4 - - - +
170o ILE* 3.3 28.7 - - + +
173o LYS* 5.5 1.4 - - - +
174o ILE* 4.6 1.0 - - - +
203o ILE* 2.9 28.0 + - - +
204o GLU* 4.2 4.0 - - - +
206o GLU* 1.3 75.9 - - - +
208o LYS* 1.3 48.8 + - - +
209o ASN 2.7 1.1 - - - -
210o ILE* 2.6 4.4 + - - -
211o PHE 2.8 15.8 + - - +
213o LEU* 2.9 42.5 - - + +
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Residues in contact with LYS 208 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10542 U 3.5 3.8 - - - +
10552 U 1.1 147.7 + - + +
10562 U 2.0 22.4 - - - -
10642 G 2.6 20.2 - - - +
10652 A 1.5 63.2 - - + +
10662 C 1.1 87.8 - - - -
204o GLU* 3.2 12.5 + - + +
205o LYS 3.2 1.6 - - - +
207o THR* 1.3 64.6 - - - +
209o ASN 1.3 45.0 - - - +
212o PRO* 4.2 3.6 - - + -
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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