Contacts of the helix formed by residues 132 - 139 (chain A) in PDB entry 2WOE
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 132 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A LEU* 4.7 1.8 - - - +
128A ALA 3.5 4.3 - - - -
129A ALA* 3.4 13.2 + - - +
130A MET 3.6 0.6 - - - -
131A ARG* 1.3 76.5 - - - +
133A LEU* 1.3 65.7 - - - +
134A PRO* 3.4 1.1 - - - -
135A ALA* 3.1 16.7 - - - +
136A ALA* 3.2 11.2 - - - -
150A VAL* 3.7 13.1 - - + -
153A GLN* 3.4 20.6 + - - -
167A CYS* 3.4 49.6 - - - +
170A LEU* 5.3 6.7 - - + -
171A GLY* 5.4 3.4 - - - +
253A MET* 5.8 2.5 - - - -
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Residues in contact with LEU 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ALA* 3.5 22.7 - - + +
14A PHE* 3.4 48.7 - - + +
17A LEU* 4.6 11.9 - - + -
65A SER* 5.3 0.9 - - - +
130A MET 5.3 0.6 + - - -
131A ARG 3.3 0.8 - - - -
132A CYS* 1.3 77.9 + - - +
134A PRO* 1.3 72.3 - - + +
136A ALA* 3.0 6.3 + - - +
137A LEU* 2.9 45.9 + - + +
174A VAL* 4.0 17.3 - - + -
253A MET* 3.8 27.4 - - + -
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Residues in contact with PRO 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PHE* 4.2 12.6 - - + -
65A SER* 3.2 33.9 - - - +
68A LEU* 4.1 3.1 - - + -
69A GLY* 3.7 24.7 - - - +
72A LEU* 3.6 7.9 - - + +
131A ARG 3.2 16.4 - - - +
132A CYS 3.5 0.9 - - - -
133A LEU* 1.3 95.0 - - + +
135A ALA* 1.3 55.7 + - - +
137A LEU* 3.7 2.8 - - + +
138A ALA* 2.9 31.9 + - - +
287A LEU* 3.8 17.8 - - + +
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Residues in contact with ALA 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A LEU* 4.3 12.5 - - + +
72A LEU* 3.7 15.8 - - + +
78A LEU* 6.1 0.7 - - + -
132A CYS 3.1 10.3 - - - -
134A PRO* 1.3 79.0 - - - +
136A ALA* 1.3 59.2 + - - +
138A ALA* 3.7 1.1 + - - +
139A THR* 2.9 30.7 + - - +
146A LEU* 4.3 0.3 - - - +
149A TRP* 4.3 11.0 - - + +
150A VAL* 3.7 34.8 - - + +
153A GLN* 4.6 2.2 - - + -
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Residues in contact with ALA 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A CYS 3.2 8.9 - - - -
133A LEU* 3.0 11.0 + - - +
135A ALA* 1.3 77.9 - - - +
137A LEU* 1.3 62.9 + - - +
139A THR* 3.3 5.5 + - - -
140A LEU* 3.5 3.0 + - - +
146A LEU* 3.8 11.5 - - + +
150A VAL* 4.5 0.2 - - - +
171A GLY* 4.0 26.0 - - - +
174A VAL* 3.9 26.0 - - + -
175A HIS* 2.9 24.8 + - + -
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Residues in contact with LEU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ALA* 4.0 27.4 - - + +
14A PHE* 4.2 19.5 - - + -
133A LEU* 2.9 43.6 + - + +
134A PRO* 3.2 4.2 + - + +
136A ALA* 1.3 77.3 - - - +
138A ALA* 1.3 61.4 + - - +
139A THR 3.2 1.2 + - - -
140A LEU* 3.2 24.0 - - + +
174A VAL* 4.4 1.3 - - + -
178A ILE* 3.4 32.5 - - + -
284A VAL* 4.7 8.5 - - + +
287A LEU* 3.8 26.9 - - + +
288A LEU* 5.3 2.7 - - + +
291A ALA* 3.3 10.4 - - - +
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Residues in contact with ALA 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A LEU* 4.2 6.5 - - + -
134A PRO 2.9 16.4 + - - +
135A ALA 3.7 2.4 + - - +
136A ALA 3.3 0.2 - - - -
137A LEU* 1.3 75.9 - - - +
139A THR* 1.3 57.1 + - - +
140A LEU 3.6 0.7 - - - -
142A HIS* 2.8 23.0 + - - -
149A TRP* 3.8 21.8 - - + -
287A LEU* 3.9 19.7 - - + +
290A LEU* 3.8 19.2 - - + +
291A ALA* 3.5 10.9 + - - +
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Residues in contact with THR 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A ALA 2.9 18.6 + - - +
137A LEU 3.2 0.6 - - - -
138A ALA* 1.3 76.7 - - - +
140A LEU* 1.3 66.0 + - - +
141A GLY 3.2 2.9 - - - -
142A HIS* 3.0 34.2 + - + -
143A PRO 3.1 2.8 - - - -
145A ASP* 3.7 25.6 - - + +
146A LEU* 3.6 14.2 - - - +
149A TRP* 3.4 34.3 - - + -
175A HIS* 3.2 22.3 + - - -
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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