Contacts of the helix formed by residues 142 - 153 (chain X) 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 ASP 142 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56X GLU 5.6 0.7 - - - -
132X VAL* 5.9 1.2 - - - +
141X HIS* 1.3 79.1 - - - +
143X THR* 1.3 57.5 + - - +
144X GLU* 3.7 10.5 - - + +
145X GLY* 3.3 18.5 - - - +
146X ILE* 2.6 31.2 + - - +
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Residues in contact with THR 143 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56X GLU* 2.8 40.8 + - + +
57X PRO 3.9 1.3 - - - -
58X SER* 3.8 28.0 - - - +
141X HIS 4.0 0.4 + - - -
142X ASP* 1.3 75.1 + - - +
144X GLU* 1.3 61.3 + - - +
146X ILE* 4.2 0.4 - - - +
147X ASP* 2.8 35.5 + - - +
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Residues in contact with GLU 144 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142X ASP* 3.0 11.4 - - + +
143X THR* 1.3 81.1 - - - +
145X GLY* 1.3 56.1 + - - +
147X ASP* 3.8 5.7 - - - +
148X ASP* 2.7 47.8 + - - +
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Residues in contact with GLY 145 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137X GLN* 5.0 2.3 + - - -
141X HIS* 4.1 12.2 + - - -
142X ASP* 2.8 21.5 + - - +
144X GLU* 1.3 79.5 - - - +
146X ILE* 1.3 62.9 + - - -
148X ASP* 3.3 18.1 + - - +
149X LEU* 3.4 12.3 + - - +
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Residues in contact with ILE 146 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3X ALA* 4.2 7.6 - - + +
5X VAL* 5.4 2.0 - - + -
53X ALA 4.5 3.8 - - - +
54X PHE* 3.6 23.8 - - - +
55X GLY* 3.5 32.5 - - - +
56X GLU 4.6 0.2 - - - +
57X PRO* 3.7 16.6 - - + -
141X HIS* 3.7 13.3 - - + +
142X ASP 2.6 16.7 + - - +
143X THR 4.2 0.7 - - - +
145X GLY* 1.3 67.9 - - - -
147X ASP* 1.3 72.2 - - - +
149X LEU* 3.1 14.2 + - + +
150X LEU* 2.8 58.7 + - + +
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Residues in contact with ASP 147 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57X PRO* 3.3 8.7 - - - +
58X SER* 2.3 46.7 + - - -
61X THR* 2.6 23.5 + - - +
143X THR* 2.8 24.5 + - - +
144X GLU* 3.8 7.3 - - - +
146X ILE* 1.3 81.5 - - - +
148X ASP* 1.3 54.8 + - - +
150X LEU* 3.8 0.2 - - - +
151X GLU* 2.7 46.5 + - - +
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Residues in contact with ASP 148 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144X GLU* 2.7 32.4 + - - +
145X GLY* 3.6 8.3 - - - +
146X ILE 3.2 0.8 - - - -
147X ASP* 1.3 77.4 - - - +
149X LEU* 1.3 59.2 + - - +
151X GLU* 3.7 8.4 - - - +
152X ALA* 2.9 31.6 + - - +
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Residues in contact with LEU 149 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5X VAL* 4.9 3.6 - - + -
7X LEU* 4.3 5.8 - - + -
53X ALA* 3.6 31.4 - - + -
121X PRO* 4.4 7.6 - - + -
125X HIS* 4.2 15.9 - - + -
137X GLN* 4.0 35.0 - - + +
141X HIS* 4.4 2.5 - - + -
145X GLY 3.4 7.6 + - - +
146X ILE* 3.1 16.2 + - + +
148X ASP* 1.3 78.6 - - - +
150X LEU* 1.3 64.0 + - + +
152X ALA* 3.1 6.1 + - + +
153X MET* 3.0 58.1 + - + +
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Residues in contact with LEU 150 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3X ALA* 4.0 11.2 - - + -
5X VAL* 4.0 17.3 - - + -
32X CYS* 4.3 9.2 - - - -
57X PRO* 3.8 18.4 - - + -
61X THR* 3.7 17.9 - - + -
62X LEU* 5.8 2.5 - - + +
65X VAL* 3.7 22.3 - - + +
118X LEU* 3.8 26.0 - - + +
146X ILE* 2.8 46.9 + - + +
149X LEU* 1.3 74.7 - - + +
151X GLU* 1.3 62.2 + - - +
153X MET* 3.4 7.6 + - + +
154X ARG* 3.2 19.2 + - - -
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Residues in contact with GLU 151 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60X GLU* 5.8 0.9 - - - +
61X THR* 2.6 38.5 + - + +
64X THR* 5.2 15.0 + - + +
65X VAL* 5.4 0.7 - - + -
147X ASP* 2.7 27.8 + - - +
148X ASP* 3.8 7.7 - - - +
150X LEU* 1.3 75.8 - - - +
152X ALA* 1.3 58.2 + - - +
154X ARG* 3.0 43.1 + - + +
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Residues in contact with ALA 152 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121X PRO* 4.2 9.6 - - + -
122X ARG* 2.7 69.0 + - - +
124X GLY 5.9 0.4 - - - +
148X ASP 2.9 17.9 + - - +
149X LEU* 3.1 6.0 + - + +
151X GLU* 1.3 76.2 - - - +
153X MET* 1.3 52.7 + - - +
154X ARG* 3.3 3.8 - - - +
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Residues in contact with MET 153 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5X VAL* 3.6 29.4 - - + -
7X LEU* 4.6 4.5 - - + -
30X ASN* 4.3 12.8 - - - +
118X LEU* 3.5 29.2 - - + +
119X HIS 3.0 40.1 + - - +
121X PRO* 3.5 32.1 - - + -
122X ARG* 3.6 3.8 - - - +
149X LEU* 3.0 44.7 + - + +
150X LEU* 3.5 5.8 - - - +
151X GLU 3.1 0.4 - - - -
152X ALA* 1.3 76.8 - - - +
154X ARG* 1.3 64.8 + - - +
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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