Contacts of the helix formed by residues 136 - 150 (chain A) in PDB entry 3LRA
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 GLY 136 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A LEU* 3.2 10.5 - - - +
135A HIS* 1.3 80.7 - - - +
137A ALA* 1.3 59.6 + - - +
138A ALA 3.4 1.8 - - - -
139A ALA* 3.7 12.2 + - - +
140A LEU* 3.0 27.5 + - - +
177A ASP* 3.6 5.2 - - - -
181A GLN* 4.8 1.1 - - - -
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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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134A LEU* 3.4 6.2 - - + +
136A GLY* 1.3 71.9 - - - +
138A ALA* 1.3 55.7 + - - +
140A LEU* 3.2 6.0 + - - +
141A ALA* 2.7 37.1 + - - +
173A LEU* 3.7 24.5 - - + +
176A HIS* 3.6 18.4 - - + +
177A ASP* 2.7 18.0 + - - +
229A LEU* 4.8 1.0 - - + +
232A VAL* 3.9 19.3 - - + -
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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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137A ALA* 1.3 77.4 - - - +
139A ALA* 1.3 61.4 + - - +
141A ALA* 3.5 3.3 + - - +
142A ASP* 3.0 28.0 + - - +
170A LYS 5.5 0.7 - - - +
173A LEU* 3.9 27.9 - - + +
174A SER* 4.4 7.4 - - - +
177A ASP* 2.9 19.5 + - - +
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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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136A GLY* 3.7 14.6 + - - +
137A ALA 3.2 0.2 - - - -
138A ALA* 1.3 75.1 - - - +
140A LEU* 1.3 58.0 + - - +
142A ASP* 2.6 31.9 + - - +
143A ASP* 2.9 21.4 + - - +
177A ASP* 4.4 0.4 + - - -
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Residues in contact with LEU 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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134A LEU* 4.1 21.5 - - + -
136A GLY 3.0 15.4 + - - +
137A ALA* 3.3 4.3 - - - +
139A ALA* 1.3 78.2 - - - +
141A ALA* 1.3 64.6 + - - +
143A ASP* 2.9 21.6 + - + +
144A LEU* 2.9 15.4 + - + +
225A LYS* 4.0 38.4 - - + +
228A ALA* 4.0 13.5 - - + +
229A LEU* 3.7 41.5 - - + +
232A VAL* 4.6 3.4 - - + -
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Residues in contact with ALA 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 2.7 11.9 + - - +
138A ALA 3.6 4.5 - - - +
140A LEU* 1.3 72.2 - - - +
142A ASP* 1.3 56.5 + - - +
144A LEU* 3.9 2.1 - - - +
145A ALA* 3.1 28.8 + - - +
164A LEU* 3.9 17.2 - - + +
173A LEU* 3.2 35.4 - - + -
229A LEU* 4.4 21.8 - - + -
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Residues in contact with ASP 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 ALA* 3.0 18.2 + - - +
139A ALA* 2.6 20.8 + - - +
141A ALA* 1.3 73.9 - - - +
143A ASP* 1.3 63.2 + - - +
144A LEU 3.2 0.2 - - - -
145A ALA* 3.5 5.6 + - - +
146A GLU* 3.1 24.1 + - - +
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Residues in contact with ASP 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* 2.9 22.0 + - - +
140A LEU* 2.9 11.1 + - - +
142A ASP* 1.3 78.6 - - - +
144A LEU* 1.3 61.9 + - - +
146A GLU* 3.4 6.7 + - - +
147A GLU* 3.2 27.5 + - - +
225A LYS* 3.9 26.6 + - + +
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Residues in contact with LEU 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 LEU* 2.9 15.0 + - + +
141A ALA* 3.9 3.4 - - - +
143A ASP* 1.3 77.7 - - - +
145A ALA* 1.3 57.6 + - - +
147A GLU* 3.2 7.8 + - - +
148A LEU* 3.0 49.4 + - + +
160A LEU* 4.9 1.8 - - + -
164A LEU* 4.5 8.1 - - + -
212A LEU* 4.2 17.5 - - + -
225A LYS* 4.0 20.5 - - + +
226A LEU* 3.1 37.5 - - + -
229A LEU* 3.6 36.8 - - + -
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Residues in contact with ALA 145 (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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141A ALA 3.1 19.4 + - - +
142A ASP* 3.5 7.2 + - - +
144A LEU* 1.3 74.8 - - - +
146A GLU* 1.3 62.6 + - - +
148A LEU 4.1 0.7 - - - -
149A GLN* 3.2 27.7 + - - +
161A LEU* 3.4 31.0 - - + +
164A LEU* 4.0 11.9 - - + -
165A SER* 6.0 1.8 - - - +
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Residues in contact with GLU 146 (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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142A ASP 3.1 17.4 + - - +
143A ASP* 3.6 7.4 - - - +
144A LEU 3.1 0.2 - - - -
145A ALA* 1.3 75.0 - - - +
147A GLU* 1.3 71.1 + - + +
149A GLN* 2.9 33.9 + - - +
150A ASN* 2.6 47.1 + - - +
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Residues in contact with GLU 147 (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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143A ASP 3.2 10.1 + - - +
144A LEU* 3.4 10.0 - - - +
146A GLU* 1.3 84.1 - - + +
148A LEU* 1.3 60.1 + - + +
150A ASN* 2.9 26.1 + - - +
151A LYS* 3.2 17.1 + - + +
221A VAL* 4.9 1.4 - - + +
223A PRO* 2.8 34.7 - - - +
225A LYS* 3.1 32.5 - - - +
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Residues in contact with LEU 148 (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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144A LEU* 3.0 33.0 + - + +
145A ALA 4.4 0.2 - - - +
147A GLU* 1.3 79.3 - - + +
149A GLN* 1.3 61.7 + - - +
151A LYS* 3.2 24.6 + - - +
157A ILE* 3.7 34.7 - - + +
160A LEU* 3.7 31.6 - - + -
161A LEU* 3.9 23.6 - - + -
164A LEU* 5.3 0.7 - - + -
215A LEU* 4.4 14.8 - - + -
221A VAL* 3.5 32.3 - - + -
226A LEU* 4.8 0.4 - - + -
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Residues in contact with GLN 149 (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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145A ALA* 3.2 19.8 + - - +
146A GLU* 2.9 37.4 + - - +
148A LEU* 1.3 73.8 - - - +
150A ASN* 1.3 63.8 + - - +
151A LYS 3.0 15.2 + - - +
153A LEU* 5.8 3.1 - - - -
157A ILE* 5.2 0.9 - - - -
161A LEU* 3.9 18.3 - - + +
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Residues in contact with ASN 150 (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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146A GLU* 2.6 36.2 + - - +
147A GLU* 2.9 13.9 + - - +
149A GLN* 1.3 84.5 - - - +
151A LYS* 1.3 68.6 + - - +
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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