Contacts of the helix formed by residues 133 - 144 (chain A) in PDB entry 3WOO
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 VAL 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A THR* 4.0 17.7 - - + +
132A ASP* 1.3 77.1 - - - +
134A THR* 1.3 64.2 + - - +
135A LYS 3.4 1.8 - - - -
136A ASP* 3.5 11.8 + - + +
137A ALA* 3.0 20.8 + - - +
158A PHE* 4.3 12.8 - - + -
162A LEU* 4.0 27.8 - - + -
176A LEU* 3.7 29.8 - - + -
185A TYR* 2.9 18.1 + - + +
187A LEU* 4.3 9.9 - - + +
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Residues in contact with THR 134 (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 ASP* 2.6 24.4 + - - -
133A VAL* 1.3 76.7 - - - +
135A LYS* 1.3 64.9 + - - +
137A ALA* 3.4 0.9 + - - +
138A LYS* 2.9 59.1 + - + +
183A ASN 3.5 11.7 - - - +
184A THR* 3.4 14.1 - - - +
185A TYR* 2.8 29.1 + - + +
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Residues in contact with LYS 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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133A VAL 3.4 0.2 - - - -
134A THR* 1.3 80.1 - - - +
136A ASP* 1.3 66.7 + - - +
138A LYS* 3.8 6.1 - - - +
139A ALA* 3.1 29.0 + - + +
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Residues in contact with ASP 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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133A VAL* 3.5 13.4 + - + +
134A THR 3.3 0.2 - - - -
135A LYS* 1.3 81.4 + - - +
137A ALA* 1.3 66.4 + - - +
139A ALA* 3.4 6.5 + - - +
140A ALA* 2.9 24.9 + - - +
158A PHE* 3.8 21.0 - - + -
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Residues in contact with ALA 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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133A VAL 3.0 18.7 + - - +
134A THR 3.8 0.2 - - - +
136A ASP* 1.3 77.5 - - - +
138A LYS* 1.3 64.4 + - - +
140A ALA* 3.2 4.7 + - - +
141A ILE* 3.2 25.8 + - - +
155A LEU* 4.8 2.9 - - + +
158A PHE* 3.6 28.1 - - + -
185A TYR* 3.6 37.5 - - + -
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Residues in contact with LYS 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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134A THR* 2.9 37.0 + - + +
135A LYS* 3.8 6.1 - - - +
136A ASP 3.3 0.2 - - - -
137A ALA* 1.3 78.8 - - - +
139A ALA* 1.3 56.8 + - - +
141A ILE* 3.4 13.1 + - + +
142A ALA* 2.9 28.2 + - - +
182A GLY 4.0 13.0 - - - +
183A ASN* 2.9 35.7 + - - +
185A TYR* 4.7 9.6 - - + -
554A PRO* 6.2 0.7 - - - -
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Residues in contact with ALA 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 LYS* 3.1 18.4 + - + +
136A ASP* 3.6 8.5 - - - +
138A LYS* 1.3 73.8 - - - +
140A ALA* 1.3 64.5 + - - +
142A ALA* 3.9 6.1 - - - +
143A ALA* 3.0 24.6 + - - +
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Residues in contact with ALA 140 (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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136A ASP 2.9 14.8 + - - +
137A ALA 3.2 9.1 + - - +
139A ALA* 1.3 76.6 - - - +
141A ILE* 1.3 63.3 + - + +
143A ALA* 3.5 12.2 + - - +
144A ALA 3.7 2.9 + - - -
154A ALA* 3.5 23.2 - - + +
155A LEU* 5.4 0.2 - - - -
158A PHE* 3.8 32.5 - - + -
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Residues in contact with ILE 141 (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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137A ALA 3.2 16.4 + - - +
138A LYS* 3.6 15.7 - - + +
140A ALA* 1.3 74.4 - - - +
142A ALA* 1.3 70.2 + - - +
144A ALA* 3.2 19.2 + - - +
145A GLY 4.2 1.9 + - - +
151A ARG* 3.6 32.0 + - + +
154A ALA* 4.6 5.6 - - - -
155A LEU* 4.2 31.2 - - + +
185A TYR* 3.5 28.7 - - + +
550A LEU* 4.7 15.7 - - + +
551A ALA* 6.3 0.2 - - - -
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Residues in contact with ALA 142 (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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138A LYS 2.9 17.0 + - - +
139A ALA* 3.9 7.9 - - - +
140A ALA 3.4 0.2 - - - -
141A ILE* 1.3 80.5 - - - +
143A ALA* 1.3 63.4 + - - +
144A ALA 3.0 1.6 + - - -
145A GLY* 3.0 15.1 + - - +
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Residues in contact with ALA 143 (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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139A ALA 3.0 17.6 + - - +
140A ALA* 3.7 8.5 - - - +
141A ILE 3.2 0.4 - - - -
142A ALA* 1.3 75.9 - - - +
144A ALA* 1.3 58.6 + - - +
145A GLY* 3.2 1.5 + - - -
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Residues in contact with ALA 144 (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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140A ALA 3.7 2.8 + - - -
141A ILE 3.2 13.4 + - - +
142A ALA 3.0 1.4 + - - -
143A ALA* 1.3 76.8 - - - +
145A GLY* 1.3 62.5 + - - +
146A ASP 3.8 0.7 + - - -
147A ASP* 4.3 4.0 + - - +
150A ALA* 3.7 21.3 - - + +
151A ARG* 3.6 35.7 - - + +
154A ALA* 3.9 10.1 - - + +
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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