Contacts of the helix formed by residues 189 - 198 (chain A) in PDB entry 5FDK
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 TYR 189 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A LEU* 5.1 5.4 - - + -
42A THR* 4.7 5.8 - - - -
43A ASN* 2.8 27.6 + - - -
46A TYR* 3.5 25.5 + + - -
52A ALA* 6.5 1.3 - - + -
54A ILE* 3.8 16.2 - - + +
98A ILE* 5.2 3.8 - - + -
100A PHE* 4.1 22.6 - + - -
135A PHE* 4.1 12.1 - + + -
137A ILE* 4.0 24.2 - - + -
146A PHE* 4.7 6.7 - - + -
179A ILE* 4.5 9.9 - - + -
187A ILE* 3.5 19.6 - - + +
188A ASP* 1.3 76.2 - - - +
190A ILE* 1.3 80.0 + - + +
192A ILE* 2.9 19.2 + - - +
193A ILE* 3.1 32.7 + - + +
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Residues in contact with ILE 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A TYR* 3.0 35.9 + - + +
51A ILE* 5.2 0.7 - - + -
52A ALA* 5.8 1.8 - - + -
93A TYR* 4.2 26.9 + - + -
189A TYR* 1.3 87.5 - - + +
191A SER* 1.3 51.0 + - - +
192A ILE 3.1 0.2 - - - -
193A ILE* 3.6 12.4 - - + +
194A GLU* 2.7 36.8 + - - +
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Residues in contact with SER 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A SER* 5.0 3.5 + - - -
188A ASP* 2.7 42.8 + - - +
190A ILE* 1.3 76.7 - - - +
192A ILE* 1.3 63.5 + - - +
194A GLU* 4.1 7.2 - - - +
195A GLN* 2.9 43.0 + - - +
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Residues in contact with ILE 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A PHE* 3.7 32.8 - - + -
177A TYR* 4.3 19.1 - - + -
178A PRO 4.0 16.6 - - - +
179A ILE* 4.5 23.1 - - + -
180A SER 5.8 0.7 - - - +
188A ASP 4.5 3.4 - - - +
189A TYR* 2.9 10.7 + - - +
191A SER* 1.3 84.5 + - - +
193A ILE* 1.3 60.9 + - - +
194A GLU 2.9 1.3 - - - -
195A GLN* 3.0 22.6 + - + +
196A LEU* 2.8 37.3 + - + +
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Residues in contact with ILE 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A TYR* 5.2 8.1 - - + -
98A ILE* 4.7 12.3 - - + -
133A ILE* 3.5 41.1 - - + -
135A PHE* 3.7 22.2 - - + -
146A PHE* 4.2 16.2 - - + -
189A TYR* 3.1 40.1 + - + +
190A ILE* 3.7 9.6 - - + +
192A ILE* 1.3 76.3 - - - +
194A GLU* 1.3 56.6 + - - +
196A LEU* 4.9 0.4 - - - -
197A TYR* 3.0 34.9 + - + +
198A PHE* 3.6 8.4 - - + -
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Residues in contact with GLU 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A TYR* 2.3 39.1 + - - +
94A LYS* 3.0 19.6 + - - -
190A ILE 2.7 18.6 + - - +
191A SER* 4.1 8.7 - - - +
193A ILE* 1.3 73.6 - - - +
195A GLN* 1.3 54.8 + - + +
196A LEU 2.8 15.2 + - - -
198A PHE* 3.1 57.4 + - - +
199A SER 3.7 1.3 - - - +
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Residues in contact with GLN 195 (chain A).
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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191A SER* 2.9 32.0 + - - +
192A ILE* 3.0 25.0 + - + +
194A GLU* 1.3 78.4 - - + +
196A LEU* 1.3 57.6 + - + +
199A SER 4.3 11.5 - - - +
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Residues in contact with LEU 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A PHE* 5.9 2.7 - - + -
177A TYR* 5.7 12.1 - - + +
192A ILE* 2.8 23.2 + - + +
193A ILE* 4.9 0.2 - - - -
194A GLU 2.8 4.0 + - - -
195A GLN* 1.3 80.1 - - - +
197A TYR* 1.3 72.8 + - + +
198A PHE 3.6 1.6 - - - -
199A SER* 5.2 2.4 + - - -
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Residues in contact with TYR 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A LYS* 3.4 11.4 + - - -
131A ASP* 5.1 7.2 - - - -
132A GLY 4.7 4.0 - - - -
133A ILE* 4.0 40.5 - - + -
146A PHE* 5.3 4.9 - + - -
148A GLU* 2.2 45.8 + - - -
193A ILE* 3.0 20.3 + - + +
196A LEU* 1.3 88.4 - - + +
198A PHE* 1.3 78.0 + - + +
199A SER 3.9 2.5 + - - -
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Residues in contact with PHE 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A TYR* 4.1 11.9 - + - -
94A LYS* 3.5 40.2 - - + +
96A ARG* 4.3 13.0 - - + -
133A ILE* 3.7 31.0 - - + -
193A ILE* 3.6 12.3 - - + -
194A GLU* 3.1 43.4 + - - +
196A LEU 5.2 0.2 - - - -
197A TYR* 1.3 85.4 - - + +
199A SER* 1.3 71.8 + - - +
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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