Contacts of the helix formed by residues 132 - 140 (chain V) 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 V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1V THR 3.4 3.0 + - - -
2V THR* 4.5 1.8 - - - -
3V ILE 5.1 0.2 - - - -
127V ILE* 3.2 29.1 + - - +
128V GLY* 3.4 34.3 - - - -
129V GLY 2.9 21.3 + - - -
131V GLY* 1.3 78.9 - - - +
133V SER* 1.3 66.0 + - - +
135V ILE* 3.1 24.8 + - - +
136V TYR* 5.3 2.3 + - - -
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Residues in contact with SER 133 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133H SER* 4.5 3.1 - - - -
134H TYR* 3.7 30.0 - - - -
129V GLY 5.1 1.0 + - - -
130V SER* 4.7 7.4 + - - -
131V GLY 3.3 1.4 - - - -
132V SER* 1.3 82.1 + - - +
134V TYR* 1.3 75.1 + - - +
136V TYR* 3.1 38.0 + - - +
33b LEU* 5.0 5.5 - - - +
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Residues in contact with TYR 134 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133H SER* 3.7 25.1 - - - -
134H TYR 3.9 3.8 - - - +
136H TYR* 3.8 27.5 - + + +
137H GLY* 2.9 30.4 + - - +
32N SER* 3.8 10.9 + - - -
33N LEU* 3.6 34.0 - - + +
130V SER 3.7 14.5 + - - -
131V GLY* 3.3 21.8 - - - +
132V SER 3.2 0.2 - - - -
133V SER* 1.3 81.9 - - - +
135V ILE* 1.3 59.6 + - - +
136V TYR 3.5 0.2 + - - -
162V LEU 5.0 1.3 - - - +
163V ALA* 3.6 23.3 - - - +
166V ARG* 3.8 13.7 - - + -
167V ASP* 3.7 28.5 - - + -
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Residues in contact with ILE 135 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137H GLY* 5.0 0.9 - - - -
2V THR* 3.4 31.0 - - + -
4V MET* 4.5 1.8 - - + -
127V ILE* 4.0 22.4 - - + -
132V SER* 3.1 17.9 + - - +
134V TYR* 1.3 76.4 - - - +
136V TYR* 1.4 64.1 + - - +
137V GLY 3.2 0.4 - - - -
138V TYR* 2.8 22.6 + - + +
139V VAL* 3.2 27.3 + - + -
159V ALA* 3.9 23.1 - - + +
160V LEU* 4.2 10.8 - - + -
162V LEU* 6.3 0.9 - - - -
163V ALA* 3.3 23.3 - - + +
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Residues in contact with TYR 136 (chain V).
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* 3.8 23.3 - + + -
162H LEU 5.8 1.6 - - - +
166H ARG* 3.5 43.8 + - + -
127V ILE* 3.3 34.3 + - + +
132V SER* 5.3 2.2 + - - -
133V SER* 3.1 40.8 + - - +
134V TYR 3.3 0.4 - - - -
135V ILE* 1.4 74.1 - - - +
137V GLY* 1.3 62.5 + - - +
138V TYR 3.1 1.4 + - - -
139V VAL* 3.1 12.9 + - + +
140V ASP* 2.7 28.3 + - - +
33b LEU* 3.6 41.1 - - + +
35b ARG* 3.9 15.4 + - - +
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Residues in contact with GLY 137 (chain V).
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 2.9 22.6 + - - -
135H ILE* 5.0 0.7 - - - -
138H TYR* 3.7 29.6 - - - +
162H LEU* 4.0 18.9 - - - +
134V TYR 4.4 0.6 + - - -
135V ILE 3.0 0.8 + - - -
136V TYR* 1.3 75.7 - - - +
138V TYR* 1.3 58.0 + - - +
140V ASP* 4.6 1.8 - - - -
141V ALA* 3.6 21.5 + - - +
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Residues in contact with TYR 138 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137H GLY* 3.7 24.9 - - - +
138H TYR* 4.9 2.7 - + - +
141H ALA* 4.5 9.9 - - + -
135V ILE* 2.8 13.0 + - + +
137V GLY* 1.3 77.9 - - - +
139V VAL* 1.3 61.1 + - - +
140V ASP 3.5 0.2 - - - -
141V ALA* 4.2 1.6 - - - +
142V THR* 3.1 35.5 + - - +
155V PHE* 3.6 35.4 + + - -
158V ASN* 3.9 19.1 + - + +
159V ALA* 3.6 35.7 - - + -
162V LEU* 3.7 24.7 - - + -
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Residues in contact with VAL 139 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4V MET* 3.4 33.4 - - + -
125V PHE* 3.5 39.0 - - + -
127V ILE* 5.0 6.5 - - + -
135V ILE* 3.2 24.3 + - + +
136V TYR* 3.1 9.6 + - + +
138V TYR* 1.3 77.0 - - + +
140V ASP* 1.3 69.2 + - - +
142V THR* 3.1 1.6 + - - -
143V TYR* 3.1 26.1 + - + +
155V PHE* 3.8 16.9 - - + -
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Residues in contact with ASP 140 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162H LEU* 4.8 16.7 - - + +
165H GLU* 6.4 2.0 - - + -
166H ARG* 3.4 37.3 + - - +
125V PHE* 4.0 14.6 - - - -
136V TYR* 2.7 32.2 + - - +
137V GLY* 5.2 0.9 - - - +
139V VAL* 1.3 80.1 - - - +
141V ALA* 1.3 55.4 + - - +
142V THR 3.3 2.7 + - - -
143V TYR* 4.4 10.7 + - - +
37b ARG* 3.9 14.0 + - - +
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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