Contacts of the helix formed by residues 137 - 145 (chain V) in PDB entry 1O1F
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 GLN 137 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11V ASP* 4.2 7.5 - - - +
12V ASN 4.1 13.5 + - - +
74V GLY* 5.0 5.7 + - - -
106V THR* 3.8 21.6 + - - +
107V GLU* 3.0 33.8 + - - +
108V ALA* 3.4 11.7 - - - +
109V PRO* 4.8 6.1 - - + +
135V ALA 4.6 0.2 - - - -
136V ILE* 1.3 72.6 - - - +
138V ALA* 1.3 59.3 + - - +
140V LEU* 2.9 24.1 + - - +
141V SER* 3.1 11.4 + - - -
154V ASP* 4.0 16.4 - - - +
339V VAL* 4.0 21.2 - - + +
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Residues in contact with ALA 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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109V PRO* 5.0 3.1 - - + +
136V ILE* 3.6 3.3 - - + +
137V GLN* 1.3 76.2 - - - +
139V VAL* 1.3 61.8 + - + +
141V SER* 3.2 3.2 + - - -
142V LEU* 2.9 21.5 + - - +
152V VAL* 3.3 33.6 - - + +
154V ASP* 4.1 8.6 + - + +
163V VAL* 3.4 44.2 - - + -
165V ILE* 3.7 2.9 - - + -
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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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135V ALA* 6.1 0.9 - - + -
136V ILE* 3.3 39.7 - - + +
137V GLN 3.0 0.4 + - - -
138V ALA* 1.3 78.1 - - - +
140V LEU* 1.3 62.3 + - + +
142V LEU* 3.5 2.3 + - - +
143V TYR* 3.3 24.6 + - + +
165V ILE* 3.5 26.9 - - + -
168V GLY* 4.2 19.5 - - - +
170V ALA* 3.9 15.5 - - + -
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Residues in contact with LEU 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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104V LEU* 4.4 0.9 - - + -
106V THR* 3.4 33.9 - - + -
135V ALA* 3.6 28.5 - - + -
136V ILE 3.2 7.9 + - - +
137V GLN* 2.9 6.2 + - - +
139V VAL* 1.3 75.7 - - + +
141V SER* 1.3 66.7 + - - +
143V TYR* 4.4 5.4 - - + -
144V ALA* 3.1 25.3 + - - +
338V SER 4.3 0.9 - - - -
339V VAL* 3.3 27.4 - - + +
342V GLY* 3.4 7.2 - - - +
343V GLY* 3.8 21.3 - - - +
346V LEU* 3.7 23.8 - - + -
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Residues in contact with SER 141 (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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137V GLN 3.1 7.9 + - - -
138V ALA* 3.2 11.6 + - - -
140V LEU* 1.3 80.8 - - - +
142V LEU* 1.3 62.6 + - - +
144V ALA* 3.3 10.4 + - - +
145V SER* 3.4 10.9 + - - -
152V VAL* 4.3 5.8 - - - -
298V VAL* 4.5 6.1 - - - +
300V SER* 3.0 32.1 + - - -
338V SER* 3.2 14.5 + - - -
339V VAL* 3.1 27.4 + - - +
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Residues in contact with LEU 142 (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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138V ALA 2.9 16.8 + - - +
139V VAL* 3.8 5.2 - - - +
141V SER* 1.3 76.0 - - - +
143V TYR* 1.3 60.0 + - - +
145V SER* 2.9 26.2 + - - -
147V ARG* 3.4 27.7 + - + +
148V THR* 3.6 33.9 - - - +
149V THR 3.8 2.9 - - - +
150V GLY* 3.8 23.8 - - - +
152V VAL* 3.8 15.7 - - + +
165V ILE* 3.9 20.6 - - + -
298V VAL* 3.7 30.3 - - + -
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Residues in contact with TYR 143 (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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139V VAL* 3.3 17.2 + - + +
140V LEU* 3.9 6.1 - - + +
141V SER 3.3 0.2 - - - -
142V LEU* 1.3 78.4 - - - +
144V ALA* 1.3 58.6 + - - +
146V GLY* 2.9 28.0 + - - -
147V ARG 3.4 14.8 - - - +
148V THR* 5.0 11.0 - - + -
342V GLY* 3.7 15.5 - - - -
345V ILE* 3.5 33.4 - - + +
346V LEU* 3.8 30.1 - - + +
349V LEU* 4.2 17.8 - - - +
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Residues in contact with ALA 144 (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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140V LEU 3.1 19.0 + - - +
141V SER 3.4 6.1 - - - +
143V TYR* 1.3 76.3 - - - +
145V SER* 1.3 55.5 + - - +
146V GLY 3.2 3.1 + - - -
334V GLU* 5.2 7.4 - - - +
338V SER* 3.5 17.3 - - - +
341V ILE* 4.3 11.2 - - + +
342V GLY* 3.5 21.1 - - - +
345V ILE* 4.4 12.8 - - - +
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Residues in contact with SER 145 (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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141V SER 3.4 7.8 + - - -
142V LEU 2.9 12.0 + - - -
144V ALA* 1.3 75.8 - - - +
146V GLY* 1.3 54.3 + - - +
147V ARG* 3.0 45.8 + - - -
298V VAL* 3.5 21.5 - - - +
330V ILE* 5.0 2.9 - - - -
332V PRO* 4.7 17.5 - - - -
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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