Contacts of the helix formed by residues 119 - 131 (chain A) in PDB entry 4DAJ
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 ILE 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A ILE* 3.3 34.1 + - + +
117A GLY 3.4 1.2 - - - -
118A VAL* 1.3 95.7 - - + +
120A SER* 1.3 71.7 + - - +
121A MET 3.5 0.7 - - - -
122A ASN* 3.3 2.4 + - - +
123A LEU* 3.1 40.0 + - + +
143A TRP* 4.2 16.8 - - + -
146A ILE* 4.6 28.7 - - + -
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Residues in contact with SER 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ILE 5.2 0.2 + - - -
116A ILE* 3.1 22.9 + - - +
119A ILE* 1.3 77.4 - - - +
121A MET* 1.3 69.0 + - - +
124A PHE* 2.9 26.5 + - - +
143A TRP* 3.2 14.6 + - - +
146A ILE* 5.2 1.9 - - - +
147A ASP* 2.9 46.3 + - - +
533A TYR* 3.5 11.9 - - - -
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Residues in contact with MET 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A LEU* 3.8 10.1 - - + -
78A ALA* 3.6 41.3 - - + +
81A THR* 3.5 25.4 - - - +
116A ILE* 3.3 14.0 + - + +
117A GLY* 3.6 15.0 - - - +
119A ILE 3.5 0.4 - - - -
120A SER* 1.3 75.2 - - - +
122A ASN* 1.3 54.6 + - - +
124A PHE* 3.3 0.3 - - - +
125A THR* 2.8 36.6 + - - -
530A TRP* 3.1 26.1 - - + -
533A TYR* 3.9 41.3 - - + +
534A ILE* 5.2 2.0 - - + +
536A SER* 5.8 0.9 - - - -
537A THR* 4.0 5.8 - - - +
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Residues in contact with ASN 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ALA* 3.4 27.1 - - - +
82A ILE* 5.8 3.0 - - - +
117A GLY 3.4 4.0 + - - +
118A VAL* 2.8 34.8 + - - +
119A ILE 3.7 4.5 - - - +
120A SER 3.1 1.0 - - - -
121A MET* 1.3 73.6 - - - +
123A LEU* 1.3 62.6 + - + +
124A PHE 2.9 3.8 - - - -
125A THR* 2.7 29.1 + - - -
126A THR* 2.9 15.2 + - - -
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Residues in contact with LEU 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A VAL 5.3 0.9 - - - +
119A ILE* 3.1 29.4 + - + +
122A ASN* 1.3 80.8 - - + +
124A PHE* 1.3 56.0 + - - +
126A THR* 3.4 13.3 - - - +
127A TYR* 2.9 28.2 + - - +
133A TRP* 4.6 13.2 - - + -
135A LEU* 5.3 13.5 - - + -
139A ALA* 5.5 3.1 - - + +
143A TRP* 3.8 38.1 - - + +
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Residues in contact with PHE 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A SER 2.9 21.3 + - - +
121A MET 3.3 3.6 - - - +
123A LEU* 1.3 75.7 - - - +
125A THR* 1.3 65.5 + - - +
126A THR 3.2 0.2 + - - -
127A TYR* 3.2 12.2 + + - +
128A ILE* 2.9 46.1 + - + +
143A TRP* 3.9 24.3 - + + -
526A ASN* 3.6 21.1 - - - -
529A TYR* 3.5 35.7 - + + -
530A TRP* 3.3 51.4 - + - -
533A TYR* 3.5 13.5 - + + -
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Residues in contact with THR 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ALA* 4.5 11.0 - - + +
72A PHE* 6.0 0.7 - - - -
74A THR* 3.1 29.9 + - + +
75A GLY* 4.6 6.3 + - - +
78A ALA* 5.9 0.5 - - - +
121A MET 2.8 21.1 + - - -
122A ASN* 2.7 16.1 + - - -
124A PHE* 1.3 71.8 - - - +
126A THR* 1.3 56.7 + - - +
128A ILE* 3.5 4.9 + - - +
129A ILE* 2.9 32.3 + - + +
530A TRP* 3.1 14.2 - - - -
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Residues in contact with THR 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ASN 2.9 12.8 + - - -
123A LEU* 3.4 17.4 - - - +
125A THR* 1.3 74.4 - - - +
127A TYR* 1.3 67.7 + - - +
129A ILE* 3.1 6.9 + - - +
130A MET* 2.9 45.5 + - + +
134A ALA* 6.0 1.3 - - + -
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Residues in contact with TYR 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A LEU 2.9 14.4 + - - +
124A PHE* 3.2 15.2 + + + +
126A THR* 1.3 79.8 - - - +
128A ILE* 1.3 73.2 + - + +
131A ASN* 3.1 22.4 + - - -
132A ARG* 3.7 15.8 + - - +
133A TRP* 3.3 46.9 - + + +
143A TRP* 5.7 4.3 - + + -
218A GLY 4.0 7.2 - - - -
219A GLU* 3.8 19.3 + - + +
220A CYS* 3.7 37.4 + - + -
522A LYS* 6.1 1.0 - - - +
526A ASN* 5.4 6.5 - - - -
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Residues in contact with ILE 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A THR* 5.9 0.7 - - + -
124A PHE* 2.9 44.9 + - + +
125A THR* 3.8 4.0 - - - +
127A TYR* 1.3 83.1 - - + +
129A ILE* 1.3 66.1 + - - +
131A ASN* 3.2 18.0 + - - +
526A ASN* 4.4 22.0 - - + +
530A TRP* 3.3 33.9 - - + +
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Residues in contact with ILE 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ALA* 5.7 9.6 - - + -
125A THR* 2.9 22.1 + - + +
126A THR* 3.5 6.3 - - - +
128A ILE* 1.3 78.6 - - - +
130A MET* 1.3 59.7 + - + +
131A ASN* 3.0 20.4 + - - -
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Residues in contact with MET 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A THR* 2.9 34.5 + - + +
129A ILE* 1.3 77.1 - - + +
131A ASN* 1.3 68.2 + - - +
132A ARG* 2.8 60.0 + - + +
134A ALA* 3.6 24.0 - - + -
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Residues in contact with ASN 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A TYR* 3.1 16.6 + - - -
128A ILE* 3.2 9.3 + - - +
129A ILE 3.0 23.4 + - - -
130A MET* 1.3 76.7 + - - +
132A ARG* 1.3 57.1 + - - +
218A GLY 4.7 1.4 - - - +
219A GLU* 5.2 7.4 - - - +
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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