Contacts of the helix formed by residues 191 - 195 (chain H) in PDB entry 2A2Q
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 191 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17H VAL* 4.7 2.0 - - + -
143H GLN* 3.5 44.9 - - - +
145H LEU 4.6 0.4 - - - -
146H ASP* 4.3 7.0 - - - -
147H ARG 4.8 0.9 - - - -
190H SER* 1.3 74.4 + - - +
192H LYS* 1.3 74.0 + - - +
193H GLY 3.4 0.7 - - - -
194H ASP* 2.8 29.0 + - - +
195H SER 3.6 2.8 + - - -
220H CYS* 2.0 47.3 - - + -
1016H PBZ 3.7 15.1 - - - -
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Residues in contact with LYS 192 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42H CYS* 5.3 1.0 - - - -
57H HIS* 5.0 0.2 + - - -
143H GLN* 3.7 18.2 - - - +
146H ASP* 6.0 0.7 - - - +
147H ARG* 6.1 6.3 - - + +
191H CYS* 1.3 77.5 - - - +
193H GLY* 1.3 56.2 + - - +
195H SER* 2.7 30.7 + - - -
220H CYS* 5.4 2.0 - - - -
1013H CL 3.4 29.4 - - + -
1016H PBZ 3.5 22.4 - - + +
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Residues in contact with GLY 193 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40H GLN* 4.2 13.7 + - - -
41H LEU 5.5 5.1 - - - -
42H CYS* 4.5 6.7 - - - -
43H GLY* 4.5 10.0 + - - -
141H TRP 4.4 2.3 + - - -
142H GLY* 3.5 20.7 + - - -
143H GLN* 2.8 24.5 + - - -
151H THR* 5.2 2.2 - - - -
192H LYS* 1.3 71.8 - - - +
194H ASP* 1.3 58.3 + - - +
195H SER* 3.3 1.1 - - - -
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Residues in contact with ASP 194 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H ILE* 2.9 34.6 + - - +
43H GLY* 4.6 2.7 + - - +
139H SER 4.2 10.1 - - - +
140H GLY* 3.3 17.1 - - - -
142H GLY* 2.8 27.2 + - - -
190H SER* 4.2 3.6 - - - -
191H CYS* 2.8 32.3 + - - +
193H GLY* 1.3 76.6 - - - +
195H SER* 1.3 67.3 + - - +
197H GLY* 2.9 19.1 + - - -
213H VAL* 3.2 17.0 - - + +
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Residues in contact with SER 195 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42H CYS* 3.4 9.7 - - - +
43H GLY 2.8 27.2 + - - -
57H HIS* 2.9 37.4 + - - -
58H CYS* 3.9 10.5 - - - -
191H CYS 3.6 2.2 + - - -
192H LYS 2.7 21.2 + - - -
193H GLY 3.3 0.6 - - - -
194H ASP* 1.3 76.2 - - - +
196H GLY* 1.3 58.9 + - - +
213H VAL* 3.4 9.0 - - - -
1016H PBZ 3.0 16.5 + - - -
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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