Contacts of the helix formed by residues 149 - 160 (chain E) in PDB entry 1NJI
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 LYS 149 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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327A A 2.5 37.8 + - - -
328A U 2.8 27.0 + - - +
148E VAL* 1.3 90.9 + - + +
150E THR* 1.3 65.4 + - - +
151E GLN* 4.2 5.4 - - + +
152E GLU* 3.3 38.2 + - + +
153E VAL* 3.6 14.4 + - - +
203E ALA* 3.7 2.7 - - - +
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Residues in contact with THR 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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327A A 3.2 51.5 + - + +
328A U 2.8 19.7 + - - -
329A A 4.1 3.1 + - - -
148E VAL 3.9 0.4 + - - -
149E LYS* 1.3 70.2 - - - +
151E GLN* 1.3 68.4 + - - +
153E VAL* 2.8 16.8 + - - +
154E VAL* 3.1 8.4 + - + +
203E ALA 3.1 21.5 + - - +
206E ASN* 4.7 1.7 - - - +
207E LEU* 3.4 34.5 - - + +
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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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326A G 2.8 35.7 + - - -
327A A 3.2 59.4 + - + +
149E LYS* 4.8 5.4 - - + -
150E THR* 1.3 77.2 - - - +
152E GLU* 1.3 58.7 + - + +
154E VAL* 2.9 31.8 + - - +
155E SER* 3.1 10.7 + - - -
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Residues in contact with GLU 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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147E LEU* 4.3 26.2 - - + +
148E VAL* 4.5 5.4 + - - +
149E LYS* 3.3 37.5 + - + +
150E THR 3.1 1.0 - - - -
151E GLN* 1.3 80.3 - - + +
153E VAL* 1.3 60.2 + - - +
155E SER* 3.5 7.7 + - - +
156E LEU* 3.3 21.1 + - - +
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Residues in contact with VAL 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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144E PHE* 3.8 23.1 - - + -
147E LEU* 3.7 22.9 - - + -
149E LYS 3.6 14.8 - - - +
150E THR 2.8 7.6 + - - +
152E GLU* 1.3 74.7 - - - +
154E VAL* 1.3 61.8 + - - +
156E LEU* 3.8 4.8 - - + +
157E LEU* 2.9 40.0 + - + +
194E PHE* 4.1 3.8 - - + -
203E ALA* 3.7 26.7 - - + +
204E ALA* 4.0 7.9 - - + +
207E LEU* 4.0 12.1 - - + -
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Residues in contact with VAL 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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327A A 3.9 15.5 - - - +
150E THR 3.4 14.1 - - - +
151E GLN* 2.9 20.3 + - - +
153E VAL* 1.3 76.7 - - - +
155E SER* 1.3 70.4 + - - +
157E LEU* 2.8 10.4 + - - +
158E GLU* 2.8 41.5 + - - +
163E HIS* 3.6 24.2 - - + -
207E LEU* 3.9 22.2 - - + -
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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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151E GLN 3.1 8.9 + - - -
152E GLU* 3.8 10.6 - - - -
154E VAL* 1.3 78.4 - - - +
156E LEU* 1.3 57.4 + - - +
158E GLU* 3.0 18.5 + - - +
159E ALA* 2.8 31.4 + - - +
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Residues in contact with LEU 156 (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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6E TYR* 5.9 0.2 - - + -
7E ASP 3.9 20.0 - - - +
8E LEU* 3.9 35.0 - - + +
9E ASP 4.6 0.4 - - - -
10E GLY* 4.1 7.0 - - - +
140E VAL* 4.6 8.7 - - + -
144E PHE* 3.9 33.0 - - + -
147E LEU* 4.5 4.9 - - + -
152E GLU 3.3 14.5 + - - +
153E VAL* 3.8 6.1 - - + +
154E VAL 3.2 0.4 - - - -
155E SER* 1.3 78.5 - - - +
157E LEU* 1.3 60.1 + - + +
159E ALA* 3.2 5.4 + - - +
160E LEU* 2.9 55.7 + - + +
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Residues in contact with LEU 157 (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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153E VAL* 2.9 24.0 + - + +
154E VAL* 2.8 10.5 + - - +
156E LEU* 1.3 76.9 - - + +
158E GLU* 1.3 63.1 + - - +
160E LEU* 3.1 13.8 + - + +
161E ASP 3.1 4.0 + - - -
162E VAL* 3.0 34.7 + - + -
163E HIS* 3.9 15.3 - - + +
166E ILE* 3.5 31.0 - - + -
192E ILE* 4.1 15.5 - - + -
194E PHE* 3.8 24.9 - - + -
207E LEU* 3.6 14.8 - - + -
234E VAL* 5.2 5.8 - - + -
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Residues in contact with GLU 158 (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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154E VAL* 2.8 29.5 + - - +
155E SER* 3.5 24.1 + - - +
157E LEU* 1.3 76.8 - - - +
159E ALA* 1.3 61.6 + - - +
161E ASP* 3.2 18.7 + - - +
163E HIS* 3.7 31.9 + - + +
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Residues in contact with ALA 159 (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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9E ASP 3.6 24.0 - - - +
10E GLY* 4.3 9.7 - - - +
155E SER 2.8 13.5 + - - +
156E LEU* 3.4 13.2 - - - +
158E GLU* 1.3 77.3 - - - +
160E LEU* 1.3 61.5 + - - +
161E ASP* 3.2 10.4 + - - +
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Residues in contact with LEU 160 (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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6E TYR* 3.5 46.2 - - + -
10E GLY* 4.1 8.7 - - - +
133E ARG* 4.4 14.6 + - - +
138E VAL* 4.0 23.3 - - + -
140E VAL* 4.5 9.9 - - + -
156E LEU* 2.9 43.2 + - + +
157E LEU* 3.1 15.9 + - + +
159E ALA* 1.3 79.1 - - - +
161E ASP* 1.3 73.3 + - - +
162E VAL* 3.2 17.6 + - + +
234E VAL* 6.1 1.6 - - + -
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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