Contacts of the helix formed by residues 148 - 159 (chain B) in PDB entry 3AEV
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 148 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144B ILE* 3.0 28.7 - - - -
145B GLY 2.7 12.6 + - - -
147B LYS* 1.3 72.8 - - - +
149B ARG* 1.3 65.2 + - - +
151B ARG* 3.4 5.3 + - - +
152B GLN* 3.0 25.1 + - - +
5C C 3.6 14.3 + - - -
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Residues in contact with ARG 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B ILE 3.5 0.4 + - - -
146B ARG* 3.1 15.9 + - + +
147B LYS* 3.1 3.3 - - + -
148B GLY* 1.3 77.6 - - - +
150B THR* 1.3 57.8 + - - +
152B GLN* 2.7 44.3 + - - +
153B ILE* 2.9 53.9 + - + +
198B TYR* 4.7 4.9 - - - +
1C G 2.8 55.8 + - + +
3C A 4.6 8.3 - - + -
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Residues in contact with THR 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B ARG 3.6 10.3 - - - +
143B ILE 3.1 20.4 - - - +
144B ILE 3.0 7.9 + - - -
145B GLY* 3.2 4.0 - - - -
149B ARG* 1.3 74.4 - - - +
151B ARG* 1.3 64.6 + - - +
153B ILE* 3.1 2.6 + - - +
154B ILE* 2.8 40.4 + - + +
188B LEU* 3.8 9.4 - - + -
194B HIS* 3.2 22.3 + - + -
197B VAL* 5.9 1.1 - - + -
198B TYR* 3.2 25.2 + - + +
3C A 3.2 9.2 - - - -
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Residues in contact with ARG 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B ARG* 3.5 17.2 - - - +
143B ILE* 3.2 10.6 + - + +
144B ILE* 3.0 14.6 + - - +
148B GLY* 3.8 9.6 + - - +
150B THR* 1.3 76.9 - - - +
152B GLN* 1.3 61.1 + - - +
154B ILE* 3.3 7.9 + - - +
155B GLU* 2.9 58.2 + - - +
162B VAL* 3.2 40.1 + - + -
163B SER* 5.3 0.2 - - - +
164B VAL* 4.8 13.0 - - + +
5C C 2.5 44.8 + - - +
6C A 3.6 29.4 + - - -
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Residues in contact with GLN 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B GLY 3.0 18.0 + - - +
149B ARG* 2.7 50.4 + - - +
151B ARG* 1.3 77.2 - - - +
153B ILE* 1.3 63.1 + - - +
155B GLU* 3.3 11.4 + - - +
156B GLU* 2.9 37.6 + - + +
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Residues in contact with ILE 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B ARG* 2.9 58.6 + - + +
150B THR 3.8 2.5 - - - +
152B GLN* 1.3 78.6 - - - +
154B ILE* 1.3 66.9 + - - +
156B GLU* 3.3 3.7 + - - -
157B MET* 2.9 40.4 + - + +
198B TYR* 3.6 48.2 - - + -
201B LEU* 4.4 4.5 - - + -
1C G 5.7 0.7 - - - +
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Residues in contact with ILE 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B ILE* 4.5 8.5 - - + +
150B THR* 2.8 39.5 + - + +
151B ARG* 3.7 5.8 - - - +
153B ILE* 1.3 76.9 - - + +
155B GLU* 1.3 61.4 + - - +
158B SER* 2.9 32.9 + - - +
162B VAL* 4.5 10.3 - - + -
181B ALA* 3.8 35.7 - - + +
184B ALA* 4.4 9.2 - - + -
185B ILE* 4.4 15.7 - - + -
188B LEU* 3.9 17.5 - - + -
197B VAL* 5.1 1.1 - - + -
198B TYR* 5.8 0.4 - - + -
201B LEU* 4.1 22.8 - - + +
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Residues in contact with GLU 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B ARG* 2.7 31.3 + - - -
151B ARG* 2.9 37.3 + - - +
152B GLN* 3.7 9.5 - - - +
153B ILE 3.2 0.2 - - - -
154B ILE* 1.3 76.6 - - - +
156B GLU* 1.3 56.8 + - - +
158B SER* 3.9 0.7 - - - -
159B GLY* 2.8 32.2 + - - -
160B ALA 3.3 22.4 + - - +
161B SER* 4.2 1.6 - - - -
162B VAL* 2.9 30.5 + - + +
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Residues in contact with GLU 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B GLN* 2.9 29.4 + - + +
153B ILE* 3.8 4.5 - - - +
155B GLU* 1.3 77.4 - - - +
157B MET* 1.3 83.4 + - + +
159B GLY* 4.0 5.0 + - - -
205B LYS* 5.3 4.0 + - - +
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Residues in contact with MET 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B ILE* 2.9 36.4 + - + +
154B ILE 4.1 0.2 - - - +
156B GLU* 1.3 97.8 - - + +
158B SER* 1.3 62.6 + - - +
180B ILE* 4.7 8.0 - - - +
201B LEU* 3.7 42.4 - - + +
202B GLU* 4.2 20.6 - - - +
205B LYS* 3.7 52.1 + - + +
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Residues in contact with SER 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B ILE* 2.9 22.3 + - - -
155B GLU* 3.5 0.5 + - - -
157B MET* 1.3 78.3 - - - +
159B GLY* 1.3 57.7 + - - +
160B ALA* 2.8 24.4 + - - +
177B GLN* 3.3 36.7 - - - +
180B ILE* 3.8 30.7 - - - +
181B ALA* 3.8 13.1 - - - +
201B LEU* 5.5 0.2 - - - -
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Residues in contact with GLY 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B ARG* 2.7 26.9 + - - -
155B GLU 2.8 12.0 + - - -
156B GLU 4.0 4.1 + - - -
157B MET 3.4 2.4 - - - -
158B SER* 1.3 77.2 - - - +
160B ALA* 1.3 52.0 + - - +
177B GLN* 3.6 22.4 + - - +
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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