Contacts of the helix formed by residues 168 - 174 (chain d) in PDB entry 5OOM
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 CYS 168 (chain d).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150U TRP* 3.4 36.8 - - - -
164d VAL* 3.5 20.6 - - + -
165d THR* 3.3 5.9 + - - +
166d GLU 3.2 0.4 - - - -
167d HIS* 1.3 80.2 - - - +
169d PHE* 1.3 63.2 + - - +
170d PRO 3.5 0.7 - - - -
171d ASP* 3.5 5.9 + - - -
172d MET* 3.2 22.7 + - - +
261d MET* 3.3 21.3 - - - +
262d HIS 3.2 20.4 - - - +
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Residues in contact with PHE 169 (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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97V TYR* 5.4 1.1 - - - -
108V MET* 3.5 25.1 - - + -
157d HIS* 3.3 35.4 - + + -
160d LEU* 3.6 39.0 - - + -
161d HIS* 3.4 40.4 - + + +
164d VAL* 3.8 12.8 - - + +
165d THR 2.9 17.8 + - - +
166d GLU* 4.3 5.4 - - - -
168d CYS* 1.3 77.4 - - - +
170d PRO* 1.3 57.5 - - + +
172d MET* 3.5 1.9 - - - +
173d THR* 2.6 48.8 + - + +
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Residues in contact with PRO 170 (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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97V TYR* 3.9 25.4 - - + +
105V ARG* 3.7 26.5 - - - +
106V GLY 5.7 1.1 - - - +
107V THR* 5.7 1.6 - - - -
108V MET* 3.9 18.2 - - + +
166d GLU 3.3 20.9 - - - +
167d HIS 4.1 6.5 - - - +
168d CYS 3.8 1.1 - - - -
169d PHE* 1.3 91.7 - - + +
171d ASP* 1.3 58.9 + - - +
172d MET 3.1 0.2 + - - -
173d THR* 3.8 5.2 - - - +
174d TRP* 2.8 35.3 + - + +
175d ASP 4.7 0.2 + - - -
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Residues in contact with ASP 171 (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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148U PRO* 6.1 0.5 - - - +
149U SER* 5.7 1.6 + - - -
150U TRP* 3.6 35.1 + - + +
105V ARG* 3.5 19.3 + - - +
167d HIS* 4.2 19.0 - - + +
168d CYS* 3.5 8.5 + - - +
169d PHE 3.4 0.4 - - - -
170d PRO* 1.3 79.7 - - - +
172d MET* 1.3 57.1 + - - +
174d TRP 4.9 0.2 - - - -
175d ASP* 5.3 7.8 + - - +
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Residues in contact with MET 172 (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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148U PRO* 5.7 2.4 - - - +
150U TRP* 3.6 43.5 - - + +
151U PHE* 5.4 1.0 - - - -
148d ALA 4.7 9.2 - - - +
149d HIS* 4.9 5.6 - - + -
152d LEU* 3.7 37.9 - - + +
160d LEU* 4.8 7.2 - - + -
164d VAL* 4.0 32.3 - - - -
168d CYS* 3.2 17.7 + - - +
169d PHE* 3.5 6.3 - - - +
170d PRO 3.1 0.4 - - - -
171d ASP* 1.3 79.9 - - - +
173d THR* 1.3 68.7 + - + +
174d TRP 3.7 0.7 - - - -
175d ASP 5.4 0.4 - - - -
176d ILE* 3.7 20.8 - - - +
261d MET* 4.6 9.6 - - + -
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Residues in contact with THR 173 (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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97V TYR* 5.5 0.9 + - - -
152d LEU* 4.0 7.6 - - + -
157d HIS* 4.0 20.2 - - + -
160d LEU* 3.7 29.6 - - + -
169d PHE* 2.6 42.0 + - + +
170d PRO* 3.8 2.6 - - - +
172d MET* 1.3 89.1 - - + +
174d TRP* 1.3 65.5 + - - +
175d ASP 3.6 1.1 - - - -
176d ILE* 3.4 18.0 - - - +
177d LYS* 3.7 9.2 + - - +
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Residues in contact with TRP 174 (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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97V TYR* 3.3 37.9 - + - -
100V LYS* 3.8 25.8 - - - -
105V ARG* 3.6 34.5 - - + +
170d PRO* 2.8 21.4 + - + +
172d MET 3.7 0.2 - - - -
173d THR* 1.3 77.9 + - - +
175d ASP* 1.3 86.9 + - - +
177d LYS* 3.2 36.6 + - + +
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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