Contacts of the helix formed by residues 146 - 166 (chain A) in PDB entry 3LRB
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 MET 146 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A HIS* 5.6 2.2 - - + -
139A LEU* 3.1 51.1 - - + +
142A VAL* 3.3 23.6 - - + +
143A GLY* 3.2 20.5 - - - +
144A PRO 2.6 5.9 + - - -
145A LYS* 1.3 75.5 - - - +
147A ILE* 1.3 65.2 + - - +
149A ARG* 3.0 21.2 + - + +
150A VAL* 3.0 26.6 + - + -
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Residues in contact with ILE 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A MET* 4.8 1.3 - - + -
136A PHE* 3.9 19.1 - - + -
139A LEU* 3.4 23.1 + - + +
140A ASN* 2.9 41.7 - - - +
144A PRO 2.9 13.8 + - - +
146A MET* 1.3 79.4 - - - +
148A THR* 1.3 61.4 + - - +
149A ARG 3.1 0.3 + - - -
150A VAL* 3.1 15.2 + - + -
151A GLN* 2.8 28.7 + - + +
288A GLY 5.1 0.9 - - - +
291A GLY* 3.5 26.5 - - - +
292A GLY 4.3 0.4 - - - +
295A LEU* 4.0 17.9 - - + -
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Residues in contact with THR 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 3.7 25.3 - - + +
14A PRO* 3.1 31.9 + - - +
15A VAL* 5.8 0.4 - - - -
18A MET* 3.7 22.0 - - + -
144A PRO 2.8 25.1 - - - +
145A LYS* 3.9 4.2 + - - -
147A ILE* 1.3 77.5 - - + +
149A ARG* 1.3 56.9 + - - +
151A GLN* 3.2 10.1 - - - +
152A ALA* 2.8 30.1 + - - +
295A LEU* 4.9 4.7 - - + -
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Residues in contact with ARG 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 6.2 0.8 - - - +
14A PRO* 5.4 12.0 - - + +
145A LYS* 3.1 52.7 + - - +
146A MET* 3.0 21.8 + - - +
148A THR* 1.3 78.6 + - - +
150A VAL* 1.3 64.0 + - - +
151A GLN 3.3 0.2 + - - -
152A ALA* 3.5 6.3 + - - +
153A VAL* 3.4 24.1 + - + +
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Residues in contact with VAL 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A PHE* 4.1 15.0 - - + -
139A LEU* 3.3 26.9 - - + -
146A MET* 3.0 26.7 + - + +
147A ILE* 3.4 10.5 - - + +
149A ARG* 1.3 73.7 - - - +
151A GLN* 1.3 60.7 + - - +
153A VAL* 3.2 10.5 + - - +
154A ALA* 3.1 23.7 + - - +
287A LEU* 3.5 30.2 - - + +
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Residues in contact with GLN 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A MET* 4.1 24.5 - - + +
21A GLY* 4.0 7.5 + - - -
22A ASN* 3.8 8.9 + - - +
147A ILE 2.8 17.7 + - - +
148A THR* 3.2 11.0 - - - +
150A VAL* 1.3 73.6 - - - +
152A ALA* 1.3 69.2 + - - +
153A VAL 3.2 0.2 + - - -
154A ALA* 3.3 1.0 + - - +
155A THR* 3.0 57.6 + - + +
288A GLY* 2.4 43.0 - - - +
289A SER* 3.4 5.6 - - - +
292A GLY* 3.0 25.1 + - - +
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Residues in contact with ALA 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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14A PRO* 4.5 13.0 - - + +
17A LEU* 3.7 37.4 - - + +
148A THR 2.8 21.0 + - - +
149A ARG* 3.8 7.4 - - - +
151A GLN* 1.3 72.3 - - - +
153A VAL* 1.3 67.2 + - + +
155A THR* 3.6 2.4 + - - -
156A VAL* 3.1 22.0 + - - +
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Residues in contact with VAL 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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149A ARG 3.4 15.5 - - - +
150A VAL* 3.2 9.4 + - - +
151A GLN 3.1 0.8 - - - -
152A ALA* 1.3 77.7 - - + +
154A ALA* 1.3 65.8 + - - +
156A VAL* 3.0 20.5 + - + +
157A LEU* 3.0 28.4 + - + +
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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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150A VAL 3.1 4.7 + - - +
151A GLN 3.3 0.2 + - - -
153A VAL* 1.3 79.3 - - + +
155A THR* 1.3 63.6 + - - +
157A LEU* 3.0 28.9 + - + +
158A ALA* 3.1 9.5 + - - +
284A ALA* 3.0 27.4 - - - +
287A LEU* 3.8 20.4 - - + -
288A GLY* 3.4 23.6 - - - +
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Residues in contact with THR 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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17A LEU* 3.5 27.6 + - - +
21A GLY* 3.8 23.3 - - - +
24A MET* 6.1 3.6 - - + -
151A GLN* 3.0 42.8 + - - +
152A ALA* 3.6 2.1 + - - -
154A ALA* 1.3 75.3 - - - +
156A VAL* 1.3 64.8 + - - +
158A ALA* 3.0 10.5 + - - +
159A LEU* 3.0 26.6 + - - +
284A ALA 4.8 0.7 - - - -
285A GLY* 4.3 13.9 - - - +
288A GLY* 4.4 1.1 - - - -
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Residues in contact with VAL 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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17A LEU* 4.3 20.4 - - + -
152A ALA 3.1 14.4 + - - +
153A VAL* 3.0 14.1 + - + +
155A THR* 1.3 76.6 + - - +
157A LEU* 1.3 67.2 + - + +
159A LEU* 3.2 27.3 + - + +
160A ILE* 3.4 10.7 + - + +
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Residues in contact with LEU 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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153A VAL* 3.0 22.7 + - + +
154A ALA* 3.0 29.3 + - + +
156A VAL* 1.3 79.6 - - + +
158A ALA* 1.3 56.5 + - - +
160A ILE* 3.3 32.8 - - + +
161A PRO* 3.4 0.2 - - - +
280A PHE* 4.1 29.6 - - + -
281A CYS* 3.2 24.9 - - - -
284A ALA* 4.2 10.5 - - + -
287A LEU* 6.0 3.8 - - + -
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Residues in contact with ALA 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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24A MET* 6.3 2.7 - - + -
154A ALA 3.1 5.0 + - - +
155A THR* 3.0 9.6 + - - +
157A LEU* 1.3 76.7 - - - +
159A LEU* 1.3 62.6 + - - +
160A ILE 3.2 1.3 - - - -
161A PRO* 3.2 14.5 - - - +
162A ILE* 3.7 15.4 + - - +
281A CYS 3.0 25.4 - - - +
282A ALA* 5.3 0.2 - - - -
285A GLY* 3.9 23.6 - - - +
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Residues in contact with LEU 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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17A LEU* 5.8 7.6 - - + -
20A SER* 6.0 0.7 - - - +
24A MET* 3.6 34.3 - - + -
155A THR* 3.0 17.9 + - - +
156A VAL* 3.2 22.0 + - + +
158A ALA* 1.3 78.8 - - - +
160A ILE* 1.3 71.2 + - - +
162A ILE* 4.6 1.3 - - + +
163A VAL* 2.9 43.8 + - + +
164A GLY 3.6 0.7 + - - -
234A ILE* 5.1 10.3 - - + -
238A CYS* 4.6 4.7 - - - -
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Residues in contact with ILE 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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156A VAL* 3.4 8.4 + - + +
157A LEU* 3.3 33.7 - - + +
159A LEU* 1.3 81.3 - - - +
161A PRO* 1.3 71.4 - - + +
163A VAL 3.8 0.3 - - - -
164A GLY* 2.8 23.2 + - - -
277A ILE* 4.9 10.3 - - + -
281A CYS* 4.1 13.7 - - - -
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Residues in contact with PRO 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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29A PHE* 6.2 1.8 - - + -
157A LEU 3.4 4.7 - - - +
158A ALA* 3.2 19.3 - - - +
160A ILE* 1.3 97.5 - - + +
162A ILE* 1.3 56.4 + - + +
164A GLY* 2.5 29.0 + - - -
165A ILE* 2.9 13.1 + - - +
277A ILE* 6.1 0.2 - - + -
278A VAL* 3.4 31.2 - - + +
281A CYS* 3.4 25.8 - - + +
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Residues in contact with ILE 162 (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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24A MET* 3.8 24.0 - - + -
28A VAL* 3.3 39.5 - - + -
158A ALA 3.7 12.3 + - - +
159A LEU* 3.4 2.3 + - - +
161A PRO* 1.3 80.9 - - + +
163A VAL* 1.3 67.4 + - + +
165A ILE* 3.0 22.4 + - - +
166A ALA* 3.0 12.2 + - + +
238A CYS* 3.9 33.7 - - + +
242A SER* 4.1 15.4 - - - +
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Residues in contact with VAL 163 (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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159A LEU* 2.9 41.7 + - + +
160A ILE 3.8 1.1 - - - -
162A ILE* 1.3 73.2 - - + +
164A GLY* 1.3 62.8 + - - +
166A ALA* 3.6 24.2 + - + -
167A VAL* 4.0 18.2 + - + +
168A PHE* 4.9 2.3 - - - -
237A VAL* 6.3 2.5 - - + -
238A CYS* 4.1 20.9 - - - -
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Residues in contact with GLY 164 (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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160A ILE 2.8 15.6 + - - -
161A PRO* 2.5 18.9 + - - -
163A VAL* 1.3 73.3 - - - +
165A ILE* 1.3 53.2 + - - -
168A PHE* 2.6 47.8 + - - +
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Residues in contact with ILE 165 (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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161A PRO 2.9 12.8 + - - +
162A ILE* 3.0 8.3 + - - +
164A GLY* 1.3 75.4 - - - +
166A ALA* 1.3 58.2 + - - +
167A VAL 2.9 9.1 + - - -
169A GLY* 2.8 35.8 + - - +
170A TRP 3.0 5.0 + - - -
241A LEU 4.0 13.1 - - - +
242A SER* 4.9 7.0 - - - +
245A ALA* 3.8 30.3 - - + -
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Residues in contact with ALA 166 (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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162A ILE* 3.0 10.1 + - + +
163A VAL* 3.6 32.8 - - + -
164A GLY 3.5 1.0 - - - -
165A ILE* 1.3 75.2 - - - +
167A VAL* 1.3 63.9 + - + +
170A TRP* 4.1 9.8 - - - +
237A VAL* 5.9 0.7 - - + -
238A CYS* 5.9 2.7 - - - +
241A LEU* 3.7 49.1 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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