Contacts of the helix formed by residues 141 - 155 (chain E) in PDB entry 2I2X
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 ASP 141 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137E GLN* 4.9 7.2 + - - +
140E GLY* 1.3 71.0 - - - -
142E LYS* 1.3 75.1 + - - +
143E TYR 3.0 5.6 - - - -
144E SER* 2.9 26.7 + - - -
145E VAL* 4.3 5.4 + - - +
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Residues in contact with LYS 142 (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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93E ASN* 4.7 5.8 - - - +
129E ILE* 3.3 35.3 - - + +
130E ARG* 4.4 8.7 - - + -
131E GLU 3.5 27.4 + - - +
132E ASN* 4.7 3.2 - - - +
137E GLN* 3.8 26.5 - - - +
140E GLY 3.3 0.9 - - - -
141E ASP* 1.3 95.1 - - + +
143E TYR* 1.3 51.6 + - - +
144E SER 3.5 0.4 - - - -
145E VAL* 3.2 14.2 + - + +
146E PHE* 2.8 35.3 + - - +
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Residues in contact with TYR 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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130E ARG* 3.7 22.7 - - - +
137E GLN 5.5 0.2 + - - -
138E LEU 3.1 27.4 - - - +
139E ARG* 4.4 5.2 - - - -
140E GLY* 3.5 18.6 + - - +
141E ASP 3.0 1.0 - - - -
142E LYS* 1.3 73.3 - - - +
144E SER* 1.3 69.5 + - - +
146E PHE* 2.9 20.3 + + - +
147E LEU* 2.9 35.7 + - + +
198E LEU* 3.4 29.0 - - + +
199E ILE* 3.7 17.9 - - + -
202E ASP* 2.7 31.3 + - - +
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Residues in contact with SER 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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141E ASP* 2.9 18.7 + - - -
143E TYR* 1.3 80.3 - - - +
145E VAL* 1.3 57.2 + - - +
147E LEU* 3.2 8.6 + - - +
148E GLU* 2.9 43.8 + - - +
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Residues in contact with VAL 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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92E SER 3.7 19.5 - - - +
93E ASN* 3.7 17.3 - - - +
95E PRO* 3.8 11.1 - - + +
129E ILE* 3.8 10.8 - - + -
141E ASP 4.7 7.6 - - - +
142E LYS* 3.2 14.3 + - + +
143E TYR 3.1 0.8 - - - -
144E SER* 1.3 73.7 + - - +
146E PHE* 1.3 61.0 + - - +
148E GLU* 3.1 19.3 + - - +
149E ALA* 2.9 28.2 + - - +
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Residues in contact with PHE 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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126E ILE* 3.7 6.3 - - + -
127E GLY 3.6 25.1 - - - -
128E ASP* 3.7 13.2 - - - -
129E ILE* 4.1 17.7 - - + -
130E ARG* 4.0 31.2 - - + -
142E LYS 2.8 14.0 + - - +
143E TYR* 3.2 18.4 - + - +
145E VAL* 1.3 76.1 - - - +
147E LEU* 1.3 67.0 + - + +
149E ALA* 3.5 12.2 - - - +
150E PHE* 3.2 52.9 - + - -
163E VAL* 3.8 19.1 - - + -
199E ILE* 4.5 18.4 - - + -
203E ILE* 4.7 2.9 - - + -
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Residues in contact with LEU 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 TYR* 2.9 41.8 + - + +
144E SER* 3.6 9.6 - - - +
146E PHE* 1.3 84.1 - - + +
148E GLU* 1.3 64.6 + - - +
149E ALA 3.2 0.4 - - - -
150E PHE* 3.7 4.6 + - + +
151E GLU* 3.2 29.4 + - - +
199E ILE* 5.1 0.9 - - - +
202E ASP* 3.8 27.6 - - + +
203E ILE* 4.8 7.4 - - + +
206E ILE* 3.6 29.0 - - + +
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Residues in contact with GLU 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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95E PRO* 3.7 19.0 - - + +
144E SER* 2.9 33.1 + - - +
145E VAL* 3.1 27.0 + - - +
147E LEU* 1.3 74.2 - - - +
149E ALA* 1.3 56.4 + - - +
151E GLU* 4.2 15.3 - - - +
152E GLN* 2.8 42.5 + - + +
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Residues in contact with ALA 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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87E HIS* 4.9 1.8 - - + -
92E SER* 4.2 20.2 - - - +
95E PRO* 4.0 13.2 - - + +
126E ILE* 3.7 26.5 - - + -
129E ILE* 6.4 0.2 - - + -
145E VAL 2.9 12.1 + - - +
146E PHE* 3.5 13.0 - - - +
147E LEU 3.2 0.2 - - - -
148E GLU* 1.3 74.6 - - - +
150E PHE* 1.3 66.9 + - - +
152E GLN* 3.9 0.5 - - - +
153E CYS* 3.1 30.7 + - - -
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Residues in contact with PHE 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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126E ILE* 3.8 23.7 - - + +
146E PHE* 3.2 54.0 + + - -
147E LEU* 3.9 8.5 - - + +
148E GLU 3.6 0.2 - - - -
149E ALA* 1.3 77.5 - - - +
151E GLU* 1.3 58.7 + - - +
153E CYS* 4.0 1.6 - - - +
154E ALA* 3.0 30.5 + - - +
161E LEU* 3.9 24.0 - - + +
162E SER* 3.4 38.4 - - - -
163E VAL* 3.6 16.6 - - + -
200E TRP* 5.4 0.2 - + - -
203E ILE* 3.7 31.9 - - + -
206E ILE* 4.2 17.5 - - + -
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Residues in contact with GLU 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 LEU* 3.2 21.1 + - - +
148E GLU* 4.0 15.9 - - + +
150E PHE* 1.3 77.1 - - - +
152E GLN* 1.3 65.6 + - + +
154E ALA* 3.7 2.7 - - - +
155E GLU* 2.9 47.1 + - - +
206E ILE* 3.7 26.1 - - + +
209E LYS* 2.9 36.9 + - - +
210E THR* 4.4 4.0 - - + +
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Residues in contact with GLN 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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95E PRO* 4.3 18.6 - - + +
96E SER* 4.0 17.6 - - - +
99E ALA* 3.6 22.4 - - + +
148E GLU* 2.8 29.6 + - + +
149E ALA 3.9 1.8 - - - +
151E GLU* 1.3 72.6 - - + +
153E CYS* 1.3 66.5 + - - +
155E GLU* 3.0 24.9 + - - +
156E ASN* 3.0 28.3 + - - +
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Residues in contact with CYS 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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87E HIS* 3.4 37.5 - - - -
95E PRO 4.8 2.0 - - - -
98E GLY* 4.1 0.2 - - - -
99E ALA* 3.8 24.8 - - - +
102E ALA* 4.3 1.5 - - + +
124E HIS* 3.6 21.1 - - + -
126E ILE* 4.2 5.6 - - + -
149E ALA 3.1 20.7 + - - +
150E PHE 4.0 2.2 - - - +
152E GLN* 1.3 74.4 - - - +
154E ALA* 1.3 58.6 + - - +
156E ASN* 2.9 18.0 + - - +
157E GLY 3.2 1.4 + - - -
158E ALA* 3.2 26.2 + - + -
161E LEU* 5.2 1.1 - - + -
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Residues in contact with ALA 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 PHE 3.0 21.7 + - - +
151E GLU* 3.7 4.0 - - - +
153E CYS* 1.3 75.7 - - - +
155E GLU* 1.3 59.0 + - - +
156E ASN 3.2 1.8 + - - -
157E GLY 4.7 1.4 + - - -
158E ALA* 4.0 13.0 - - - +
161E LEU* 3.9 13.2 - - + +
206E ILE* 5.0 0.7 - - + -
210E THR* 3.6 29.9 - - + +
212E THR* 3.6 25.8 - - + +
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Residues in contact with GLU 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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151E GLU* 2.9 39.9 + - - +
152E GLN* 3.0 22.5 + - - +
154E ALA* 1.3 75.2 - - - +
156E ASN* 1.3 68.7 + - - +
157E GLY 4.0 0.2 - - - -
209E LYS* 5.0 4.5 - - - -
210E THR* 4.1 17.6 - - + +
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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