Contacts of the helix formed by residues 119 - 131 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115D ILE* 3.5 24.5 + - + +
117D GLY 3.2 0.4 - - - -
118D VAL* 1.3 95.7 - - + +
120D SER* 1.3 70.4 + - - +
121D MET 3.5 1.1 - - - -
122D ASN* 3.2 4.2 + - - +
123D LEU* 3.1 38.8 + - + +
143D TRP* 3.7 22.0 - - + -
146D ILE* 3.8 36.1 - - + -
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Residues in contact with SER 120 (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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116D ILE* 3.2 18.4 + - - +
119D ILE* 1.3 81.4 - - - +
121D MET* 1.3 64.1 + - - +
124D PHE* 2.9 27.9 + - - +
143D TRP* 3.0 15.3 + - - +
146D ILE* 4.5 2.8 - - - +
147D ASP* 2.9 36.1 + - - +
533D TYR* 3.0 26.2 - - - -
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Residues in contact with MET 121 (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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77D LEU* 3.6 22.4 - - + -
78D ALA* 3.5 30.1 - - + +
81D THR* 3.5 17.9 - - - +
116D ILE* 3.3 15.2 + - + +
117D GLY* 3.5 25.8 - - - +
119D ILE 3.5 0.4 - - - -
120D SER* 1.3 75.3 - - - +
122D ASN* 1.3 63.5 + - - +
124D PHE* 3.5 0.9 - - - +
125D THR* 2.8 30.9 + - - -
530D TRP* 3.1 30.8 - - + -
533D TYR* 3.5 30.7 - - + +
536D SER* 6.4 0.2 - - - -
537D THR* 4.0 4.7 - - - +
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Residues in contact with ASN 122 (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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75D GLY* 5.6 1.6 - - - -
78D ALA* 3.0 29.2 - - - +
82D ILE* 5.8 2.2 - - - +
117D GLY 3.5 4.2 + - - -
118D VAL* 2.5 35.4 + - - +
119D ILE 3.7 3.1 - - - +
120D SER 3.1 0.8 - - - -
121D MET* 1.3 73.2 - - - +
123D LEU* 1.3 68.3 + - + +
124D PHE 3.0 1.3 - - - -
125D THR* 2.8 26.0 + - - -
126D THR* 2.9 13.0 + - - -
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Residues in contact with LEU 123 (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 VAL 5.0 1.6 - - - +
119D ILE* 3.1 26.8 + - + +
122D ASN* 1.3 79.3 - - + +
124D PHE* 1.3 57.2 + - - +
126D THR* 3.4 6.9 + - - +
127D TYR* 2.9 30.3 + - - +
133D TRP* 4.4 15.2 - - + -
135D LEU* 5.3 12.3 - - + -
139D ALA 5.7 0.4 - - - +
143D TRP* 3.3 45.1 - - + +
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Residues in contact with PHE 124 (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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120D SER 2.9 20.5 + - - +
121D MET 3.5 5.2 - - - +
123D LEU* 1.3 77.1 - - - +
125D THR* 1.3 63.0 + - - +
127D TYR* 3.1 7.0 + - - +
128D ILE* 2.9 32.8 + - + +
143D TRP* 3.5 23.6 - - + -
529D TYR* 5.6 3.4 - - + -
530D TRP* 4.8 5.6 - - + -
533D TYR* 4.1 13.7 - - + +
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Residues in contact with THR 125 (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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71D ALA* 4.4 18.3 - - + +
74D THR* 3.0 25.4 + - + +
75D GLY* 5.3 1.3 - - - +
121D MET 2.8 19.4 + - - -
122D ASN* 2.8 20.4 + - - -
124D PHE* 1.3 72.0 - - - +
126D THR* 1.3 54.4 + - - +
128D ILE* 3.5 9.2 + - - +
129D ILE* 2.9 25.4 + - + +
530D TRP* 2.9 22.1 - - - -
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Residues in contact with THR 126 (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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122D ASN 2.9 9.9 + - - -
123D LEU* 3.7 10.1 - - - -
125D THR* 1.3 75.3 - - - +
127D TYR* 1.3 66.4 + - - +
128D ILE 3.1 1.3 - - - -
129D ILE* 2.8 19.7 + - - +
130D MET* 2.9 25.0 + - - +
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Residues in contact with TYR 127 (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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123D LEU 2.9 18.3 + - - +
124D PHE* 3.1 9.4 + - - +
126D THR* 1.3 75.2 - - - +
128D ILE* 1.3 70.4 + - + +
130D MET* 6.1 0.2 - - - -
131D ASN* 3.4 17.6 + - - -
132D ARG* 3.5 17.2 + - - +
133D TRP* 3.2 46.4 - + + -
143D TRP* 5.6 7.2 - + + -
218D GLY 4.9 1.7 + - - -
219D GLU* 3.9 12.0 - - - +
220D CYS* 3.6 43.0 + - + -
526D ASN* 4.9 11.0 - - - -
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Residues in contact with ILE 128 (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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124D PHE* 2.9 23.1 + - + +
125D THR* 3.5 9.0 - - - +
127D TYR* 1.3 82.2 - - + +
129D ILE* 1.3 69.4 + - - +
131D ASN* 3.0 23.1 + - - +
526D ASN* 4.4 29.2 - - + +
530D TRP* 3.7 29.4 - - + +
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Residues in contact with ILE 129 (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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71D ALA* 5.8 7.4 - - + -
125D THR* 2.9 16.3 + - + +
126D THR* 2.8 18.1 + - - +
128D ILE* 1.3 77.0 - - - +
130D MET* 1.3 66.2 + - + +
131D ASN* 3.0 11.6 + - - +
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Residues in contact with MET 130 (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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126D THR* 2.9 22.9 + - - +
127D TYR* 6.1 0.2 - - - -
129D ILE* 1.3 75.9 - - + +
131D ASN* 1.3 64.9 + - - +
132D ARG* 2.9 80.7 + - + +
134D ALA* 3.4 24.9 - - + -
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Residues in contact with ASN 131 (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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127D TYR* 3.4 10.6 + - - -
128D ILE* 3.0 23.0 + - - +
129D ILE 3.0 13.5 + - - +
130D MET* 1.3 77.6 - - - +
132D ARG* 1.3 56.4 - - - +
218D GLY 4.1 5.0 - - - +
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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