Contacts of the helix formed by residues 137 - 145 (chain Z) 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 Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11Z ASP* 4.2 6.1 - - - +
12Z ASN 4.1 14.2 + - - +
74Z GLY* 5.0 5.5 + - - -
106Z THR* 3.8 22.7 + - - +
107Z GLU* 3.0 34.3 + - - +
108Z ALA* 3.4 11.4 - - - +
109Z PRO* 4.8 6.8 - - + +
135Z ALA 4.6 0.4 - - - -
136Z ILE* 1.3 72.2 - - - +
138Z ALA* 1.3 58.2 + - - +
140Z LEU* 2.9 24.4 + - - +
141Z SER* 3.1 11.3 + - - -
154Z ASP* 4.0 16.4 - - - +
339Z VAL* 4.0 21.6 - - + +
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Residues in contact with ALA 138 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109Z PRO* 5.0 2.9 - - + +
136Z ILE* 3.6 3.3 - - + +
137Z GLN* 1.3 75.0 - - - +
139Z VAL* 1.3 62.7 + - + +
141Z SER* 3.2 3.0 + - - -
142Z LEU* 2.9 21.1 + - - +
152Z VAL* 3.3 33.1 - - + +
154Z ASP* 4.1 8.7 + - + +
163Z VAL* 3.4 44.6 - - + -
165Z ILE* 3.7 3.4 - - + -
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Residues in contact with VAL 139 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135Z ALA* 6.1 0.7 - - + -
136Z ILE* 3.3 39.5 - - + +
137Z GLN 3.0 0.4 + - - -
138Z ALA* 1.3 78.1 - - + +
140Z LEU* 1.3 62.3 + - + +
142Z LEU* 3.5 3.3 + - - +
143Z TYR* 3.3 23.9 + - + +
165Z ILE* 3.5 25.8 - - + -
168Z GLY* 4.2 20.2 - - - +
170Z ALA* 3.9 15.9 - - + -
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Residues in contact with LEU 140 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104Z LEU* 4.4 1.1 - - + -
106Z THR* 3.4 33.9 - - + -
135Z ALA* 3.6 28.5 - - + -
136Z ILE 3.2 8.4 + - - +
137Z GLN 2.9 6.2 + - - +
139Z VAL* 1.3 75.6 - - + +
141Z SER* 1.3 67.5 + - - +
143Z TYR* 3.9 4.9 - - + +
144Z ALA* 3.1 24.8 + - - +
338Z SER 4.3 0.9 - - - -
339Z VAL* 3.3 27.8 - - + +
342Z GLY* 3.4 6.9 - - - +
343Z GLY* 3.8 21.3 - - - +
346Z LEU* 3.7 23.8 - - + -
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Residues in contact with SER 141 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137Z GLN 3.1 7.4 + - - -
138Z ALA* 3.2 11.9 + - - -
140Z LEU* 1.3 81.1 - - - +
142Z LEU* 1.3 62.9 + - - +
144Z ALA* 3.3 10.6 + - - +
145Z SER* 3.4 10.7 + - - -
152Z VAL* 4.3 5.8 - - - -
298Z VAL* 4.5 6.5 - - - +
300Z SER* 3.0 31.7 + - - -
338Z SER* 3.2 14.1 + - - -
339Z VAL* 3.1 27.5 + - - +
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Residues in contact with LEU 142 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138Z ALA 2.9 16.7 + - - +
139Z VAL* 3.8 4.9 - - - +
140Z LEU 3.3 0.2 - - - -
141Z SER* 1.3 75.6 - - - +
143Z TYR* 1.3 59.2 + - - +
145Z SER* 2.9 26.2 + - - -
147Z ARG* 3.4 27.4 + - + +
148Z THR* 3.6 33.9 - - - +
149Z THR 3.8 2.7 - - - +
150Z GLY* 3.8 23.8 - - - +
152Z VAL* 3.8 15.9 - - + +
165Z ILE* 3.9 20.6 - - + -
298Z VAL* 3.7 29.8 - - + -
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Residues in contact with TYR 143 (chain Z).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139Z VAL* 3.3 17.0 - - + +
140Z LEU* 3.9 6.1 - - + +
142Z LEU* 1.3 79.0 - - - +
144Z ALA* 1.3 58.7 + - - +
146Z GLY* 2.9 28.4 + - - -
147Z ARG 3.4 14.1 - - - +
148Z THR* 5.0 11.0 - - + -
342Z GLY* 3.7 14.8 - - - -
345Z ILE* 3.5 34.1 - - + +
346Z LEU* 3.8 30.5 - - + +
349Z LEU* 4.2 17.7 - - - +
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Residues in contact with ALA 144 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140Z LEU 3.1 18.8 + - - +
141Z SER 3.4 6.3 - - - +
143Z TYR* 1.3 76.2 - - - +
145Z SER* 1.3 56.4 + - - +
146Z GLY 3.2 3.3 + - - -
334Z GLU* 5.2 7.4 - - - +
338Z SER* 3.5 17.3 - - - +
341Z ILE* 4.3 11.2 - - + +
342Z GLY* 3.5 21.8 - - - +
345Z ILE* 4.4 13.2 - - - +
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Residues in contact with SER 145 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141Z SER 3.4 8.0 + - - -
142Z LEU 2.9 12.0 + - - -
144Z ALA* 1.3 73.9 - - - +
146Z GLY* 1.3 54.2 + - - +
147Z ARG* 3.0 45.3 + - - -
298Z VAL* 3.5 21.9 - - - +
330Z ILE* 5.0 2.7 - - - -
332Z PRO* 4.7 17.7 - - - -
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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