Contacts of the helix formed by residues 142 - 155 (chain E) in PDB entry 2GRA
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 GLN 142 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116E ARG* 3.3 25.3 - - - +
137E THR* 4.6 3.0 + - - -
140E HIS 2.8 14.4 + - - +
141E ALA* 1.3 76.6 - - - +
143E VAL* 1.3 55.8 + - - +
144E GLU* 2.8 29.9 + - + +
145E ASP* 2.6 33.2 + - - +
146E GLY* 3.4 7.6 + - - -
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Residues in contact with VAL 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E ALA 3.8 0.6 + - - -
142E GLN* 1.3 72.1 - - - +
144E GLU* 1.3 69.1 + - + +
146E GLY* 4.1 6.5 + - - +
147E ARG* 4.2 12.7 + - - +
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Residues in contact with GLU 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E GLN* 2.8 17.4 - - + +
143E VAL* 1.3 92.6 - - + +
145E ASP* 1.3 66.8 + - - +
146E GLY 3.2 2.2 + - - -
147E ARG* 3.5 30.3 + - - +
148E LEU* 3.4 17.0 + - - +
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Residues in contact with ASP 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E ILE* 3.1 40.0 - - + +
116E ARG* 3.3 18.6 + - - -
118E ILE* 5.3 5.2 - - + -
141E ALA* 3.6 7.7 - - + -
142E GLN* 2.6 43.7 + - - +
144E GLU* 1.3 76.2 - - - +
146E GLY* 1.3 67.4 + - - +
148E LEU* 3.0 10.4 + - - +
149E MET* 2.7 25.7 + - - +
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Residues in contact with GLY 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118E ILE* 5.6 2.4 - - - +
135E TYR* 4.0 19.1 + - - -
137E THR* 5.2 8.8 + - - -
142E GLN 3.4 7.6 + - - -
143E VAL* 4.1 4.9 + - - -
144E GLU 3.2 0.8 - - - -
145E ASP* 1.3 80.1 - - - +
147E ARG* 1.3 63.8 + - - +
149E MET* 2.9 6.1 + - - +
150E GLU* 2.8 24.9 + - - +
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Residues in contact with ARG 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143E VAL* 4.2 10.6 + - - +
144E GLU* 3.5 31.6 + - - +
146E GLY* 1.3 72.6 - - - +
148E LEU* 1.3 57.1 + - - +
150E GLU* 3.9 8.0 - - - +
151E GLN* 2.9 42.9 + - + +
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Residues in contact with LEU 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-1E ARG 6.0 4.0 - - - +
1E MET* 4.0 32.1 - - + -
65E VAL* 4.5 12.1 - - + -
91E ILE* 5.6 8.5 - - + -
144E GLU 3.4 8.7 + - - +
145E ASP* 3.0 12.6 + - - +
147E ARG* 1.3 76.7 - - - +
149E MET* 1.3 68.2 + - - +
151E GLN* 4.4 13.5 - - + +
152E LEU* 2.8 31.1 + - + +
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Residues in contact with MET 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E ILE* 6.2 2.2 - - + -
93E VAL* 3.6 32.8 - - + -
118E ILE* 3.9 16.8 - - + -
120E CYS* 3.5 35.2 - - + -
133E THR* 6.5 0.4 - - - -
135E TYR* 3.6 36.6 - - + -
145E ASP 2.7 15.7 + - - +
146E GLY* 3.4 10.5 - - - +
148E LEU* 1.3 74.9 - - - +
150E GLU* 1.3 67.1 + - - +
152E LEU* 3.0 18.6 - - - +
153E LEU* 3.1 39.9 - - + +
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Residues in contact with GLU 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E TYR* 3.2 26.5 + - - +
146E GLY 2.8 11.0 + - - +
147E ARG* 3.9 7.3 - - - +
149E MET* 1.3 72.2 - - - +
151E GLN* 1.3 55.7 + - + +
152E LEU 2.5 18.2 + - - -
153E LEU 2.9 2.3 + - - -
154E SER* 2.8 40.6 + - - +
159E CYS* 3.4 30.6 - - - +
160E THR* 3.6 11.8 + - - +
161E GLU* 4.4 1.0 + - - +
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Residues in contact with GLN 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147E ARG* 2.9 34.6 + - + +
148E LEU* 3.8 14.5 - - + +
150E GLU* 1.3 73.3 - - - +
152E LEU* 1.3 51.7 + - - +
154E SER* 4.0 7.1 - - - -
155E SER* 2.7 32.1 + - - -
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Residues in contact with LEU 152 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E MET* 4.0 30.1 - - + -
3E VAL* 5.2 2.5 - - + -
19E PHE* 3.4 36.7 - - + -
24E VAL* 4.3 15.5 - - + -
25E LEU* 5.5 1.3 - - + -
65E VAL* 4.6 11.7 - - + -
67E PHE* 3.8 23.3 - - + -
93E VAL* 6.0 0.2 - - + -
148E LEU* 2.8 17.8 + - + +
149E MET* 3.0 15.3 - - - +
150E GLU 2.5 6.3 + - - -
151E GLN* 1.3 72.6 - - - +
153E LEU* 1.3 73.4 + - + +
155E SER* 2.9 26.3 - - - -
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Residues in contact with LEU 153 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E LEU* 3.9 23.1 - - + -
19E PHE* 3.8 16.2 - - + -
67E PHE* 4.3 12.8 - - + -
120E CYS* 4.6 2.2 - - - -
122E THR* 4.0 22.4 - - + -
126E VAL* 6.3 0.4 - - + -
133E THR* 3.9 19.1 + - + +
149E MET* 3.1 43.7 - - + +
150E GLU 2.9 4.0 + - - -
152E LEU* 1.3 85.9 - - + +
154E SER* 1.3 57.2 + - - +
155E SER 2.9 2.0 - - - -
156E VAL* 2.6 38.5 + - + +
157E GLY 3.7 1.9 - - - +
159E CYS* 4.2 7.2 - - - +
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Residues in contact with SER 154 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150E GLU* 2.8 40.1 + - - +
151E GLN* 4.0 7.0 - - - -
153E LEU* 1.3 76.5 - - - +
155E SER* 1.3 51.3 - - - +
156E VAL 2.9 1.7 + - - -
157E GLY 2.8 11.1 - - - +
159E CYS* 3.3 20.8 + - - +
5300E NAP 2.1 37.2 + - - -
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Residues in contact with SER 155 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E ALA* 3.8 10.5 - - - +
24E VAL* 4.1 27.5 - - - +
129E ARG* 4.4 5.4 + - - +
151E GLN 2.7 21.7 + - - -
152E LEU* 2.9 14.2 + - - -
154E SER* 1.3 78.3 - - - +
156E VAL* 1.3 62.1 - - - +
5300E NAP 3.8 12.3 + - - -
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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