Contacts of the helix formed by residues 145 - 156 (chain D) in PDB entry 5E6J
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 ALA 145 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96D PHE* 3.7 18.2 - - + -
103D THR* 4.3 3.4 - - + -
118D LEU* 3.8 16.8 - - + -
136D ALA 4.9 0.9 - - - -
139D ARG* 4.0 1.6 - - - +
140D ALA* 3.5 39.4 - - + +
144D ASP* 1.3 78.3 - - - +
146D ALA* 1.3 63.6 + - - +
147D ASN* 3.2 3.8 - - - +
148D PHE* 3.8 5.4 - - + +
149D CYS* 3.2 26.9 + - - -
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Residues in contact with ALA 146 (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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88D LEU* 4.7 3.5 - - + +
91D THR* 2.9 35.2 + - - +
92D LYS* 4.1 16.4 - - + +
96D PHE* 3.6 24.2 - - + -
144D ASP* 2.7 23.6 + - - +
145D ALA* 1.3 73.9 - - - +
147D ASN* 1.3 66.9 + - - +
150D ALA* 3.8 3.6 + - - +
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Residues in contact with ASN 147 (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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84D TYR* 3.3 24.3 + - - +
88D LEU* 3.3 19.1 - - - +
136D ALA* 4.5 11.4 - - + -
139D ARG* 3.2 43.7 + - + +
144D ASP* 4.3 2.2 + - - -
145D ALA* 3.2 0.8 - - - +
146D ALA* 1.3 84.3 - - - +
148D PHE* 1.3 59.7 + - - +
149D CYS 3.2 2.2 - - - -
150D ALA* 3.0 8.5 + - - +
151D LEU* 2.8 31.4 + - - +
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Residues in contact with PHE 148 (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* 4.6 16.6 - - + -
121D LEU* 3.8 26.9 - - + -
128D PHE* 4.4 9.4 - + - -
133D LEU* 3.7 34.5 - - + -
136D ALA* 3.6 27.0 + - + +
137D TYR* 3.5 35.2 - + + -
140D ALA* 4.1 15.5 - - + -
145D ALA* 3.4 8.4 + - - +
147D ASN* 1.3 79.5 - - - +
149D CYS* 1.3 58.2 + - - +
151D LEU* 3.1 5.4 + - - +
152D ILE* 2.8 55.6 + - + +
173D LEU* 4.4 3.1 - - + -
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Residues in contact with CYS 149 (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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91D THR* 4.3 3.8 - - + -
94D TRP* 4.1 18.8 - - + -
96D PHE* 3.7 11.7 - - - -
105D ILE* 3.4 32.5 - - - -
114D LEU* 4.7 9.0 - - + +
118D LEU* 4.2 11.4 - - - -
145D ALA 3.2 18.7 + - - +
146D ALA 4.3 4.0 - - - +
147D ASN 3.2 0.4 - - - -
148D PHE* 1.3 79.8 - - - +
150D ALA* 1.3 57.0 + - - +
152D ILE* 3.2 12.7 + - - +
153D LEU* 2.9 34.5 + - - +
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Residues in contact with ALA 150 (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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84D TYR* 3.6 19.8 - - + +
87D ALA* 3.9 13.1 - - + +
88D LEU* 3.7 29.8 - - + +
91D THR* 3.7 11.8 + - - +
146D ALA 3.8 3.4 + - - +
147D ASN 3.0 9.4 + - - +
149D CYS* 1.3 77.5 - - - +
151D LEU* 1.3 57.6 + - - +
153D LEU* 3.3 5.3 + - - +
154D ALA* 2.8 29.6 + - - +
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Residues in contact with LEU 151 (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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73D TYR* 4.4 9.6 - - + -
80D PHE* 4.3 9.4 - - + -
84D TYR* 3.3 36.8 - - + +
132D ALA* 3.5 23.8 - - + +
133D LEU* 4.1 11.9 - - + +
136D ALA* 3.4 32.3 - - + -
147D ASN 2.8 13.8 + - - +
148D PHE* 3.3 7.2 - - - +
150D ALA* 1.3 73.8 - - - +
152D ILE* 1.3 60.4 + - - +
154D ALA* 3.0 3.3 + - - +
155D TYR* 2.8 55.6 + - + -
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Residues in contact with ILE 152 (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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114D LEU* 3.5 23.1 - - + +
117D VAL* 3.8 23.3 - - + -
118D LEU* 5.3 2.2 - - + +
133D LEU* 5.2 1.8 - - + +
148D PHE* 2.8 51.9 + - + +
149D CYS* 3.4 14.1 - - - +
151D LEU* 1.3 72.8 - - - +
153D LEU* 1.3 64.4 + - - +
155D TYR 3.3 0.7 + - - -
156D SER* 2.8 31.0 + - - +
169D THR* 3.2 33.0 - - + -
173D LEU* 3.8 23.3 - - + -
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Residues in contact with LEU 153 (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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87D ALA* 4.1 17.5 - - + -
91D THR* 4.1 23.6 - - + -
94D TRP* 4.5 1.8 - - + -
113D TYR* 3.6 24.5 - - - +
114D LEU* 3.8 22.0 - - + -
149D CYS 2.9 17.6 + - - +
150D ALA* 3.5 7.4 - - - +
152D ILE* 1.3 75.0 - - - +
154D ALA* 1.3 61.2 + - - +
156D SER* 3.4 3.5 + - - -
157D ASN* 3.1 3.5 + - - -
158D LYS* 3.0 53.8 + - + +
159D THR 3.9 9.2 - - - +
160D VAL* 4.1 17.9 - - - +
161D GLY 5.7 0.2 - - - +
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Residues in contact with ALA 154 (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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80D PHE* 3.4 31.6 - - + +
83D ARG* 3.0 34.0 + - + +
84D TYR* 4.2 21.3 - - + +
87D ALA* 5.5 0.4 - - - +
150D ALA 2.8 20.2 + - - +
151D LEU* 3.4 4.5 - - - +
153D LEU* 1.3 74.2 - - - +
155D TYR* 1.3 61.8 + - - +
156D SER 3.1 1.6 + - - -
157D ASN* 3.1 8.3 + - - -
158D LYS 5.0 0.2 - - - -
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Residues in contact with TYR 155 (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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73D TYR* 3.0 41.4 + - - +
75D THR* 4.9 5.2 - - + -
80D PHE* 3.4 28.5 - + - -
130D ALA* 4.0 8.8 - - - +
132D ALA* 4.4 2.9 - - - +
133D LEU* 3.7 34.2 - - + +
151D LEU* 2.8 41.5 + - + +
152D ILE* 4.0 4.3 - - - +
154D ALA* 1.3 73.2 - - - +
156D SER* 1.3 59.9 + - - +
157D ASN* 3.4 8.3 + - - +
172D HIS* 4.0 17.2 - - - +
173D LEU* 4.7 10.1 - - + -
176D HIS* 3.2 38.8 - + + -
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Residues in contact with SER 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152D ILE* 2.8 18.6 + - - +
153D LEU* 4.0 2.2 - - - -
154D ALA 3.1 0.4 - - - -
155D TYR* 1.3 79.0 - - - +
157D ASN* 1.3 71.7 + - - +
158D LYS* 3.1 27.3 + - - +
169D THR* 3.8 23.1 - - - +
172D HIS* 3.5 35.0 + - - +
173D LEU* 4.3 2.4 - - - +
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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