Contacts of the helix formed by residues 145 - 155 (chain E) in PDB entry 2P1N
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 145 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144E SER* 1.3 73.1 + - - +
146E ASP* 1.3 67.8 + - - +
147E GLY 3.2 0.2 - - - -
148E LEU* 4.0 11.2 - - + -
149E ALA* 3.0 17.8 + - - +
168E VAL* 4.0 6.3 - - + +
169E ASP 3.1 2.0 + - - -
170E ASP* 3.7 27.1 - - - +
171E VAL* 3.2 18.3 + - - +
172E SER* 3.1 39.9 + - - +
175E TRP* 3.5 24.2 - - + +
194E LEU* 4.7 4.5 - - + -
196E SER* 4.0 1.1 - - - +
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Residues in contact with ASP 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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119E ASP* 3.2 16.6 - - + +
123E GLU* 5.0 6.7 - - - +
144E SER* 2.9 8.9 + - - +
145E THR* 1.3 85.2 + - - +
147E GLY* 1.3 59.2 + - - +
149E ALA* 3.1 24.5 - - - +
150E ALA* 3.2 8.1 + - - +
171E VAL* 4.8 15.7 - - - +
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Residues in contact with GLY 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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119E ASP* 3.1 22.0 + - - -
122E LEU* 3.9 23.7 - - - +
123E GLU* 5.4 1.6 - - - -
144E SER 2.9 8.6 + - - -
146E ASP* 1.3 73.0 - - - +
148E LEU* 1.3 66.2 + - - +
150E ALA* 2.9 17.3 + - - +
151E ILE* 3.1 15.3 + - - +
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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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122E LEU* 4.4 7.4 - - + +
135E LEU* 5.6 0.4 - - + -
137E LEU* 5.1 2.2 - - + -
143E PHE* 4.0 15.9 - - + -
144E SER 3.5 8.4 + - - +
145E THR* 4.1 13.2 - - - +
146E ASP 3.5 0.4 - - - -
147E GLY* 1.3 74.8 - - - +
149E ALA* 1.3 64.3 + - - +
150E ALA 2.8 1.0 + - - -
151E ILE* 3.1 9.3 + - + +
152E ALA* 2.9 22.7 + - - +
161E LEU* 4.7 13.1 - - + +
163E LEU* 3.9 39.0 - - + -
168E VAL* 4.8 4.3 - - + -
175E TRP* 3.7 44.8 - - + +
194E LEU* 4.5 9.9 - - + -
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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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145E THR 3.0 15.8 + - - +
146E ASP* 3.1 18.4 + - - +
148E LEU* 1.3 74.4 - - - +
150E ALA* 1.3 58.7 + - - +
152E ALA 3.4 1.0 + - - -
153E ALA* 3.2 19.1 + - - +
175E TRP* 3.6 22.9 - - + +
178E HIS* 3.6 32.3 + - + +
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Residues in contact with ALA 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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123E GLU* 4.0 36.3 - - + +
126E ALA* 4.2 4.7 - - + -
146E ASP 3.2 7.1 + - - +
147E GLY* 2.9 11.9 + - - +
148E LEU 2.8 1.4 + - - -
149E ALA* 1.3 76.0 - - - +
151E ILE* 1.3 66.0 + - - +
153E ALA* 3.2 13.0 + - - -
154E THR* 3.3 21.5 + - - +
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Residues in contact with ILE 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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122E LEU* 3.5 39.0 - - + +
125E ILE* 4.3 12.1 - - + -
126E ALA* 4.0 11.2 - - + -
132E PHE* 5.0 1.6 - - + -
135E LEU* 4.3 15.0 - - + -
147E GLY 3.1 11.8 + - - +
148E LEU* 3.5 12.1 - - + +
150E ALA* 1.3 76.0 - - - +
152E ALA* 1.3 62.8 + - - +
155E CYS* 3.1 41.1 + - - +
158E LEU* 4.4 22.4 - - + -
161E LEU* 4.7 17.5 - - + -
179E PHE* 5.2 0.4 - - + -
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Residues in contact with ALA 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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148E LEU 2.9 17.8 + - - +
149E ALA 3.4 3.3 + - - +
151E ILE* 1.3 74.4 - - - +
153E ALA* 1.3 60.2 + - - +
154E THR 3.5 0.2 - - - -
155E CYS 4.7 3.6 + - - +
161E LEU* 5.9 0.9 - - + +
175E TRP* 4.5 10.8 - - + +
178E HIS* 3.4 3.8 - - + +
179E PHE* 3.3 74.6 - - + +
180E PRO* 3.7 4.7 - - - +
183E TYR* 5.7 0.3 - - - -
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Residues in contact with ALA 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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149E ALA 3.2 13.8 + - - +
150E ALA* 3.2 5.9 + - - +
152E ALA* 1.3 79.1 - - - +
154E THR* 1.3 68.3 + - - +
155E CYS 5.3 0.7 - - - -
156E ARG* 5.8 1.7 - - - +
178E HIS* 3.6 26.2 - - + +
180E PRO* 4.4 12.7 - - - +
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Residues in contact with THR 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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126E ALA* 3.5 35.0 - - + +
127E LYS* 4.3 8.1 - - + +
130E LYS* 5.7 2.4 - - - +
150E ALA* 3.3 15.9 + - - +
153E ALA* 1.3 86.5 - - - +
155E CYS* 1.3 60.3 + - - +
156E ARG* 2.9 13.8 + - - +
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Residues in contact with CYS 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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126E ALA* 4.3 15.3 - - - -
129E PHE 5.4 2.0 - - - -
130E LYS 5.7 2.7 - - - -
132E PHE* 4.0 31.6 - - + +
151E ILE* 3.1 41.0 + - + +
152E ALA 5.1 3.0 - - - +
153E ALA 3.8 1.7 - - - -
154E THR* 1.3 72.5 - - - +
156E ARG* 1.3 64.5 + - - +
157E ASN 3.2 3.4 + - - +
158E LEU* 3.6 31.2 + - + +
179E PHE* 5.5 1.3 - - + -
183E TYR* 3.8 9.4 - - - -
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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