Contacts of the helix formed by residues 133 - 143 (chain D) in PDB entry 3NJ4
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 GLY 133 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130D ASP* 3.2 17.6 + - - -
131D ASP 3.6 1.8 - - - -
132D GLY* 1.3 79.1 - - - +
134D ASP* 1.3 64.1 + - - +
136D THR* 3.2 8.2 + - - -
137D ASN* 3.1 34.7 + - - -
155D GLU* 3.6 8.4 + - - -
160D GLY* 4.4 6.3 - - - -
163D ASN* 4.7 7.9 - - - -
164D LEU* 6.5 1.1 - - - -
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Residues in contact with ASP 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D CYS* 4.7 4.9 - - - -
79D CYS* 5.6 2.2 - - + -
110D TYR* 2.6 41.6 + - - +
114D ILE* 4.6 11.9 - - + +
130D ASP* 3.5 1.6 + - - +
131D ASP 5.8 0.4 - - - +
132D GLY* 3.4 1.9 - - - -
133D GLY* 1.3 77.8 - - - +
135D LEU* 1.3 61.1 + - - +
137D ASN* 3.7 9.9 + - - +
138D LEU* 3.3 21.8 + - - +
301D HIS* 5.7 1.3 - - - -
302D PHE* 3.5 31.4 - - - -
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Residues in contact with LEU 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D ALA* 3.0 35.4 - - + +
52D GLY 4.2 0.4 - - - -
53D CYS* 4.0 21.4 - - + +
114D ILE* 4.1 21.3 - - + -
117D THR* 5.3 2.0 - - - +
118D LEU* 4.5 11.9 - - + -
125D LEU* 4.5 2.5 - - + -
128D ILE* 4.0 18.2 - - + -
129D LEU 4.2 1.8 - - - +
130D ASP* 3.0 17.0 + - - +
134D ASP* 1.3 76.4 - - - +
136D THR* 1.3 67.9 + - - +
138D LEU* 2.9 17.4 + - + +
139D ILE* 3.1 38.8 + - + +
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Residues in contact with THR 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D ILE* 4.0 13.9 - - + -
130D ASP* 2.9 28.6 + - + +
133D GLY* 3.2 14.2 + - - +
135D LEU* 1.3 73.0 - - - +
137D ASN* 1.3 66.2 + - - +
139D ILE* 3.3 1.9 + - - +
140D HIS* 2.9 42.9 + - - +
153D ILE* 3.8 35.7 - - + -
155D GLU* 5.1 1.3 - - - +
163D ASN* 4.3 4.9 + - - -
164D LEU* 4.8 11.1 - - + +
167D MET* 4.6 5.6 - - - -
173D LEU* 6.3 0.4 - - - -
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Residues in contact with ASN 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D GLY 5.5 0.8 + - - -
133D GLY 3.1 22.4 + - - +
134D ASP* 3.9 9.7 + - - +
136D THR* 1.3 81.7 + - - +
138D LEU* 1.3 52.1 + - - +
140D HIS* 4.6 4.3 - - - +
141D THR* 2.7 47.2 + - + +
163D ASN* 2.9 32.2 + - - +
167D MET* 3.4 15.6 - - - +
302D PHE* 6.2 1.2 - - - -
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Residues in contact with LEU 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D LEU* 4.5 27.1 - - + -
114D ILE* 4.2 23.6 - - + -
115D GLU* 4.0 25.6 - - + +
118D LEU* 4.3 10.3 - - + -
134D ASP 3.3 11.0 + - - +
135D LEU* 2.9 11.2 + - + +
137D ASN* 1.3 80.9 - - - +
139D ILE* 1.3 55.3 + - + +
141D THR* 4.0 2.9 - - - +
142D LYS* 2.7 52.2 + - + +
143D TYR* 3.3 21.8 + - + -
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Residues in contact with ILE 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D LEU* 4.1 13.2 - - + -
125D LEU* 3.4 30.7 - - + -
128D ILE* 3.5 12.1 - - + -
135D LEU* 3.1 34.2 + - + +
136D THR* 3.9 6.1 - - - +
138D LEU* 1.3 79.2 - - + +
140D HIS* 1.3 60.4 + - - +
143D TYR* 2.8 46.5 + - + +
144D PRO 2.9 4.0 - - - -
146D LEU* 4.1 8.7 - - + -
147D LEU* 3.1 20.9 - - + +
150D ILE* 3.6 17.9 - - + -
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Residues in contact with HIS 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D ILE* 6.1 1.1 - - + +
136D THR* 2.9 29.9 + - - +
137D ASN 4.2 2.0 - - - +
139D ILE* 1.3 81.0 - - + +
141D THR* 1.3 61.2 - - + +
144D PRO* 4.5 10.0 - - - +
147D LEU* 3.8 28.7 - - + +
150D ILE* 6.3 0.9 - - + -
153D ILE* 4.7 5.8 - - + -
167D MET* 4.2 22.0 - - + -
172D ILE* 3.2 30.1 - - + +
173D LEU* 3.7 11.8 - - + +
174D LYS 3.1 22.3 + - - -
175D VAL* 3.4 27.8 - - + -
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Residues in contact with THR 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D ASN* 2.7 28.9 + - + +
138D LEU* 3.7 3.6 + - - +
140D HIS* 1.3 86.9 - - + +
142D LYS* 1.3 79.9 + - - +
144D PRO* 4.5 4.8 - - - +
167D MET* 5.4 5.2 - - + -
172D ILE* 6.3 2.0 - - + -
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Residues in contact with LYS 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D LEU* 2.7 29.8 + - + +
141D THR* 1.3 91.4 + - - +
143D TYR* 1.3 77.4 + - + +
144D PRO* 3.3 9.8 - - - +
145D GLN* 3.9 5.5 - - - +
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Residues in contact with TYR 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D GLU* 2.9 29.1 + - - +
118D LEU* 3.5 27.7 - - + +
119D TYR* 3.8 27.1 - + - -
138D LEU* 3.6 29.4 - - + -
139D ILE* 2.8 19.6 + - + +
142D LYS* 1.3 95.4 - - + +
144D PRO* 1.3 66.5 - - - +
145D GLN* 3.1 15.7 - - - +
146D LEU* 2.9 35.9 + - + +
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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