Contacts of the helix formed by residues 188 - 198 (chain D) 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 ASP 188 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46D TYR* 3.3 5.8 - - - +
179D ILE* 4.8 0.4 - - - +
180D SER* 3.3 39.7 + - - +
181D LEU 5.3 0.9 - - - +
182D GLY 5.5 0.7 - - - +
185D PRO* 3.0 44.3 - - - +
186D ARG 3.2 8.5 + - - -
187D ILE* 1.3 71.1 - - - +
189D TYR* 1.3 55.5 + - - +
190D ILE* 3.0 3.8 - - + -
191D SER* 2.3 49.8 + - - -
192D ILE* 3.2 6.9 + - - +
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Residues in contact with TYR 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D LEU* 3.9 23.0 - - + +
42D THR* 4.2 4.9 - - + -
43D ASN* 2.9 26.2 + - - -
46D TYR* 3.9 17.5 - + - -
54D ILE* 3.2 28.6 - - + +
89D TYR* 5.6 0.9 - - - -
98D ILE* 5.3 4.3 - - + -
100D PHE* 5.0 17.7 - - + +
146D PHE* 4.8 18.3 - + + -
179D ILE* 4.8 8.1 - - + -
187D ILE* 3.1 18.3 + - + -
188D ASP* 1.3 79.9 - - - +
190D ILE* 1.3 68.1 + - + +
192D ILE* 3.2 23.2 + - + +
193D ILE* 3.0 20.5 + - + +
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Residues in contact with ILE 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D TYR* 3.2 52.7 + - + +
51D ILE* 5.5 6.3 - - + -
52D ALA* 4.4 8.1 - - + -
54D ILE* 4.9 4.5 - - + -
93D TYR* 3.9 31.7 - - + +
188D ASP* 2.9 2.1 + - + +
189D TYR* 1.3 90.0 - - + +
191D SER* 1.3 69.0 + - - +
193D ILE* 2.9 9.9 + - - +
194D GLU* 2.8 24.6 + - - +
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Residues in contact with SER 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180D SER* 5.6 2.9 - - - -
188D ASP* 2.3 44.1 + - - -
190D ILE* 1.3 77.0 - - - +
192D ILE* 1.3 55.7 + - - -
194D GLU* 3.4 8.6 + - - +
195D GLN* 2.9 28.6 + - - +
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Residues in contact with ILE 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D PHE* 3.5 48.9 - - + -
177D TYR* 4.6 8.1 - - + -
178D PRO 4.1 6.7 - - - +
179D ILE* 3.6 27.6 - - + -
180D SER* 4.8 6.5 - - - +
188D ASP 3.9 3.1 - - - +
189D TYR* 3.3 22.0 - - - +
190D ILE 3.0 0.2 - - - -
191D SER* 1.3 75.9 - - - +
193D ILE* 1.3 58.8 + - - +
195D GLN* 2.7 33.4 + - + +
196D LEU* 3.0 27.7 + - + +
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Residues in contact with ILE 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D TYR* 5.6 7.0 - - + -
133D ILE* 5.2 9.6 - - + -
146D PHE* 5.4 7.1 - - + -
189D TYR* 3.0 11.9 + - + +
190D ILE* 2.9 12.4 + - + +
192D ILE* 1.3 77.7 - - - +
194D GLU* 1.3 54.2 + - - +
196D LEU* 5.0 1.3 - - - -
197D TYR* 2.7 58.3 + - + +
198D PHE* 3.3 9.3 - - + -
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Residues in contact with GLU 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D TYR* 2.8 30.2 + - - +
190D ILE 2.8 16.2 + - - +
191D SER* 3.5 8.5 - - - +
193D ILE* 1.3 77.1 - - - +
195D GLN* 1.3 63.4 + - - +
198D PHE* 3.0 69.3 + - - +
199D SER 3.6 0.9 - - - +
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Residues in contact with GLN 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D TYR* 6.0 3.4 - - - -
191D SER 2.9 14.2 + - - +
192D ILE* 2.7 20.7 + - - +
194D GLU* 1.3 77.7 - - - +
196D LEU* 1.3 68.1 + - + +
199D SER* 2.9 24.2 - - - +
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Residues in contact with LEU 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D PHE* 4.4 13.0 - - + -
148D GLU* 5.5 2.0 - - + +
177D TYR* 3.4 49.8 - - + +
192D ILE* 3.0 25.3 + - + +
193D ILE* 3.6 0.4 - - - -
195D GLN* 1.3 90.1 - - + +
197D TYR* 1.3 86.9 + - + +
198D PHE 3.7 0.2 - - - -
199D SER 5.3 1.1 - - - +
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Residues in contact with TYR 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D ARG* 5.1 11.1 + - - +
132D GLY 5.4 2.0 - - - -
133D ILE* 4.0 48.8 - - + +
134D CYS 4.7 1.0 + - - -
146D PHE* 4.7 8.3 - + - -
148D GLU* 2.2 34.6 + - - -
193D ILE* 2.7 28.7 + - + +
196D LEU* 1.3 98.0 - - + +
198D PHE* 1.3 82.8 + - + +
199D SER 3.9 1.3 - - - -
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Residues in contact with PHE 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D TYR* 3.7 28.0 - + + -
94D LYS* 4.3 16.4 - - + -
96D ARG* 6.0 4.7 - - + -
133D ILE* 6.0 6.3 - - + -
193D ILE* 3.3 26.9 - - + -
194D GLU* 3.0 44.5 + - - +
197D TYR* 1.3 97.3 - - + +
199D SER* 1.3 70.9 + - - +
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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