Contacts of the helix formed by residues 132 - 140 (chain H) in PDB entry 5A0Q
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 SER 132 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1H THR 3.4 2.8 + - - -
2H THR* 4.5 1.8 - - - -
3H ILE 5.1 0.2 - - - -
127H ILE* 3.2 29.2 + - - +
128H GLY* 3.4 34.3 - - - -
129H GLY 2.9 21.7 + - - -
131H GLY* 1.3 78.3 - - - +
133H SER* 1.3 66.6 + - - +
134H TYR 3.2 0.2 - - - -
135H ILE* 3.1 23.8 + - - +
136H TYR* 5.3 2.7 + - - -
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Residues in contact with SER 133 (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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129H GLY 5.1 1.2 + - - -
130H SER* 4.7 7.8 + - - -
131H GLY 3.3 1.2 - - - -
132H SER* 1.3 80.5 + - - +
134H TYR* 1.3 75.4 + - - +
136H TYR* 3.1 38.1 + - - +
33N LEU* 5.0 5.7 - - - +
133V SER* 4.5 2.7 - - - -
134V TYR* 3.7 29.1 - - - -
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Residues in contact with TYR 134 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130H SER 3.7 14.2 + - - -
131H GLY* 3.3 21.1 - - - +
132H SER 3.2 0.4 - - - -
133H SER* 1.3 83.0 - - - +
135H ILE* 1.3 59.3 + - - +
136H TYR 3.5 0.7 + - - -
162H LEU 5.0 1.3 - - - +
163H ALA* 3.6 22.7 - - - +
166H ARG* 3.8 14.1 - - + -
167H ASP* 3.7 29.7 + - + -
133V SER* 3.7 25.6 - - - -
134V TYR 3.9 3.6 - - - +
136V TYR* 3.8 25.8 - + + -
137V GLY* 2.9 30.0 + - - +
32b SER* 3.8 11.4 + - - -
33b LEU* 3.6 33.3 - - + +
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Residues in contact with ILE 135 (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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2H THR* 3.4 30.5 - - + -
4H MET* 4.5 1.3 - - + -
127H ILE* 4.0 22.0 - - + -
132H SER* 3.1 17.8 + - - +
134H TYR* 1.3 76.1 - - - +
136H TYR* 1.4 64.7 + - - +
137H GLY 3.2 0.4 - - - -
138H TYR* 2.8 22.4 + - + +
139H VAL* 3.2 27.1 + - + -
159H ALA* 3.9 21.8 - - + +
160H LEU* 4.2 11.4 - - + -
162H LEU* 6.3 1.1 - - + -
163H ALA* 3.3 23.8 - - + +
137V GLY* 5.0 1.6 - - - -
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Residues in contact with TYR 136 (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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127H ILE* 3.3 35.2 + - + +
132H SER* 5.3 2.2 + - - -
133H SER* 3.1 40.6 + - - +
134H TYR 3.3 0.2 - - - -
135H ILE* 1.4 74.6 - - - +
137H GLY* 1.3 61.2 + - - +
138H TYR 3.1 1.4 + - - -
139H VAL* 3.1 12.8 + - + +
140H ASP* 2.7 28.3 + - - +
33N LEU* 3.6 40.6 - - + +
35N ARG* 3.9 16.3 + - - +
134V TYR* 3.8 23.8 - + + -
162V LEU 5.8 1.8 - - - +
166V ARG* 3.5 43.8 + - + -
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Residues in contact with GLY 137 (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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134H TYR 4.4 0.2 + - - -
135H ILE 3.0 1.0 + - - -
136H TYR* 1.3 75.2 - - - +
138H TYR* 1.3 57.5 + - - +
140H ASP* 4.6 1.1 - - - -
141H ALA* 3.6 21.7 + - - +
134V TYR 2.9 21.4 + - - -
135V ILE* 5.0 1.1 - - - -
138V TYR* 3.7 28.1 - - - +
162V LEU* 4.0 19.4 - - - +
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Residues in contact with TYR 138 (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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135H ILE* 2.8 13.2 + - + +
137H GLY* 1.3 76.6 - - - +
139H VAL* 1.3 61.4 + - - +
141H ALA* 4.2 2.4 - - - -
142H THR* 3.1 34.6 + - - +
154H GLN 5.3 0.2 - - - -
155H PHE* 3.6 35.5 + + - -
158H ASN* 3.9 18.7 + - + +
159H ALA* 3.6 35.2 - - + -
162H LEU* 3.7 24.9 - - + -
137V GLY* 3.7 25.8 - - - +
138V TYR* 4.9 2.5 - + - +
141V ALA* 4.5 9.2 - - + -
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Residues in contact with VAL 139 (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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4H MET* 3.4 33.7 - - + -
125H PHE* 3.5 38.8 - - + -
127H ILE* 5.0 7.0 - - + -
135H ILE* 3.2 24.9 + - + +
136H TYR* 3.1 9.6 + - + +
138H TYR* 1.3 76.0 - - + +
140H ASP* 1.3 69.9 + - - +
142H THR* 3.1 2.1 + - - -
143H TYR* 3.1 26.7 + - + +
155H PHE* 3.8 17.2 - - + -
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Residues in contact with ASP 140 (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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125H PHE* 4.0 14.2 - - - -
136H TYR* 2.7 32.2 + - - +
137H GLY* 5.2 1.1 - - - +
139H VAL* 1.3 81.0 - - - +
141H ALA* 1.3 55.3 + - - +
142H THR 3.3 2.7 + - - -
143H TYR* 4.4 10.5 + - - +
37N ARG* 3.9 13.8 + - - +
162V LEU* 4.8 16.3 - - + +
165V GLU* 6.4 2.7 - - + -
166V ARG* 3.4 36.8 + - - +
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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