Contacts of the helix formed by residues 149 - 161 (chain A) in PDB entry 3L82
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 THR 149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A LEU* 4.4 20.9 - - + +
140A ALA 4.9 1.1 - - - -
142A PHE* 5.7 0.9 - - - -
147A ARG 4.1 5.2 - - - +
148A ILE* 1.3 77.5 - - - +
150A PRO* 1.3 76.0 - - - +
151A LEU* 4.1 4.5 + - - +
152A GLU* 2.9 39.8 + - - +
153A SER* 3.0 19.4 + - - -
180A ALA* 5.1 4.2 + - - +
184A CYS* 5.3 1.1 - - - -
192A GLU* 4.0 27.4 - - - +
196A VAL* 4.5 10.1 - - + +
199A ARG* 4.6 0.2 - - - +
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Residues in contact with PRO 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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131A ARG* 3.8 17.1 - - + +
134A ALA 3.5 21.1 - - - +
135A GLY* 4.4 5.8 - - - +
137A THR 3.6 23.1 - - - +
138A LEU* 4.2 9.2 - - + +
140A ALA* 3.8 20.0 - - + +
142A PHE* 4.3 23.3 - - + -
149A THR* 1.3 88.9 - - - +
151A LEU* 1.3 58.5 + - - +
153A SER* 3.1 9.2 + - - -
154A ALA* 2.9 27.0 + - - +
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Residues in contact with LEU 151 (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 ILE* 4.2 25.8 - - + -
135A GLY* 4.1 27.1 + - - +
149A THR* 3.3 4.0 + - - +
150A PRO* 1.3 79.0 - - - +
152A GLU* 1.3 63.2 + - - +
154A ALA* 3.3 3.4 + - + +
155A LEU* 3.0 23.2 + - - +
176A ILE* 3.7 12.8 - - + +
179A GLN* 3.7 17.3 - - + +
180A ALA* 3.6 42.4 - - + +
183A VAL* 4.1 17.3 - - + -
233A TYR* 4.6 4.3 - - + -
236A MSE 4.4 15.3 - - + -
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Residues in contact with GLU 152 (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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147A ARG 3.7 0.2 - - - +
148A ILE* 3.6 15.9 - - + +
149A THR* 2.9 38.8 + - - +
151A LEU* 1.3 77.4 - - - +
153A SER* 1.3 60.4 + - - +
155A LEU* 3.5 11.1 + - - +
156A MSE 3.2 28.2 + - + +
180A ALA* 4.9 3.4 - - + -
196A VAL* 3.7 24.5 - - + +
199A ARG* 2.9 54.2 + - - +
200A ILE* 4.6 11.1 - - + +
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Residues in contact with SER 153 (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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131A ARG* 3.1 22.7 + - - -
142A PHE* 3.9 8.8 - - - +
143A GLU* 3.0 23.0 + - - -
148A ILE* 3.8 3.8 - - - +
149A THR 3.0 12.4 + - - -
150A PRO* 3.1 13.2 + - - -
152A GLU* 1.3 75.3 - - - +
154A ALA* 1.3 63.6 + - - +
156A MSE 3.2 20.4 + - - +
157A ILE* 3.2 24.6 + - - +
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Residues in contact with ALA 154 (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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128A PHE* 3.7 15.9 - - + -
131A ARG* 3.8 17.7 - - + +
132A ILE* 3.8 29.2 - - + -
150A PRO 2.9 13.7 + - - +
151A LEU* 3.3 11.9 + - + +
153A SER* 1.3 77.3 - - - +
155A LEU* 1.3 57.7 + - - +
157A ILE* 3.3 4.6 + - - +
158A TRP* 2.9 28.8 + - - +
176A ILE* 4.9 3.1 - - + -
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Residues in contact with LEU 155 (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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151A LEU 3.0 16.8 + - - +
152A GLU* 3.7 8.3 - - - +
153A SER 3.2 0.2 - - - -
154A ALA* 1.3 78.3 - - - +
156A MSE 1.3 60.9 + - + +
158A TRP* 3.4 7.3 + - + +
159A GLY* 3.2 18.0 + - - -
173A GLN* 3.9 36.0 + - + +
176A ILE* 3.9 17.4 - - + +
177A LYS* 3.8 37.0 - - + -
200A ILE* 4.5 24.0 - - + -
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Residues in contact with MSE 156 (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 GLU* 3.6 25.4 - - + +
148A ILE* 3.5 29.6 - - + -
152A GLU* 3.2 8.1 - - - +
153A SER* 3.2 31.4 + - - +
155A LEU* 1.3 77.8 - - + +
157A ILE* 1.3 65.1 + - + +
159A GLY* 3.1 11.6 + - - -
160A SER* 3.4 14.0 + - - -
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Residues in contact with ILE 157 (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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124A TYR* 3.5 35.4 - - + +
127A GLN* 3.9 27.8 - - + +
128A PHE* 4.0 12.6 - - + +
131A ARG* 3.6 41.1 - - + +
143A GLU* 4.9 3.8 - - - +
153A SER* 3.2 17.4 + - - +
154A ALA* 3.6 5.8 - - - +
156A MSE 1.3 78.7 - - + +
158A TRP* 1.3 57.1 + - - +
160A SER* 3.0 22.4 + - - -
161A ILE* 3.3 14.2 + - + +
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Residues in contact with TRP 158 (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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128A PHE* 3.6 39.5 - + + -
154A ALA 2.9 17.2 + - - +
155A LEU* 3.8 9.2 - - + +
156A MSE 3.2 0.2 - - - -
157A ILE* 1.3 76.9 - - - +
159A GLY* 1.3 61.7 + - - +
160A SER 3.4 0.5 + - - -
161A ILE* 3.6 22.6 + - + +
168A LEU* 6.2 0.2 - - + -
169A HIS* 3.2 88.6 + + - -
172A ILE* 3.7 29.9 - - + +
173A GLN* 4.2 22.7 - - + -
176A ILE* 4.8 2.7 - - + -
243A TYR* 3.7 51.8 - + - -
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Residues in contact with GLY 159 (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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155A LEU 3.2 9.5 + - - -
156A MSE 3.1 9.7 + - - -
158A TRP* 1.3 79.6 - - - +
160A SER* 1.3 57.1 + - - +
161A ILE 3.5 2.9 + - - +
169A HIS* 5.0 4.0 + - - -
173A GLN* 5.1 9.6 - - - -
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Residues in contact with SER 160 (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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124A TYR* 3.7 36.2 + - - -
156A MSE 3.4 9.7 + - - -
157A ILE* 3.0 13.6 + - - -
159A GLY* 1.3 79.6 - - - +
161A ILE* 1.3 62.7 + - - +
162A GLU* 3.3 3.5 + - - +
346B HIS* 5.0 7.6 - - - -
349B HIS* 5.8 4.3 - - - -
351B ASN* 5.0 8.5 + - - -
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Residues in contact with ILE 161 (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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121A ARG* 4.1 20.0 - - + +
124A TYR* 3.8 40.8 - - + +
125A ILE* 4.3 13.9 - - + +
128A PHE* 4.4 3.8 - - + -
157A ILE* 3.3 17.9 + - + +
158A TRP* 3.6 34.8 + - + +
159A GLY 3.5 3.3 - - - +
160A SER* 1.3 76.3 - - - +
162A GLU* 1.3 74.1 + - - +
163A LYS* 3.2 3.3 + - - +
169A HIS* 3.7 18.8 - - + +
243A TYR* 4.1 17.0 - - + +
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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