Contacts of the helix formed by residues 142 - 153 (chain B) in PDB entry 3A4T
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ILE* 3.8 20.9 - - + +
141B ALA* 1.4 69.2 - - - +
143B MET* 1.3 60.3 + - - +
144B ARG* 2.6 59.2 + - - +
145B LYS* 2.9 22.3 + - + +
146B TYR* 2.8 28.3 + - - +
501B SFG 3.0 13.1 + - - -
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Residues in contact with MET 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B LEU* 4.2 4.9 - - + -
90B MET* 3.4 45.3 - - + +
114B VAL* 4.0 26.5 - - + -
141B ALA 3.6 2.0 + - - -
142B ASP* 1.3 73.3 + - - +
144B ARG* 1.3 55.9 + - - +
146B TYR* 4.1 7.0 - - + -
147B LYS* 3.0 40.2 + - + +
150B LEU* 3.9 17.9 - - + -
193B LEU* 4.1 8.3 - - + -
196B ILE* 4.3 5.2 - - + -
200B LEU* 3.9 28.5 - - + -
501B SFG 3.2 28.7 + - + +
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Residues in contact with ARG 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ILE* 4.1 7.7 - - - +
142B ASP* 2.6 38.2 + - - +
143B MET* 1.3 74.7 - - - +
145B LYS* 1.3 56.8 + - + +
147B LYS* 3.8 18.1 - - - -
148B ASP* 4.1 4.0 - - - +
189B ARG* 3.3 34.6 - - - +
192B GLU* 3.4 39.6 + - - +
193B LEU* 4.5 8.3 - - + -
196B ILE* 3.8 17.9 - - + -
501B SFG 4.4 4.3 - - - +
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Residues in contact with LYS 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B ALA* 5.8 4.5 - - + -
142B ASP* 2.9 23.5 + - + +
144B ARG* 1.3 78.1 - - + +
146B TYR* 1.3 69.9 + - + +
147B LYS 3.3 1.3 - - - -
148B ASP* 3.2 29.0 + - - +
149B TYR* 3.9 2.6 + - - +
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Residues in contact with TYR 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B LEU* 5.4 0.2 - - + -
112B VAL* 4.1 7.8 - - + +
114B VAL* 3.9 28.5 - - + -
139B ILE* 3.0 41.2 - - + +
141B ALA* 4.0 15.7 - - + -
142B ASP 2.8 15.4 + - - +
143B MET* 3.9 10.8 - - + +
145B LYS* 1.3 79.2 - - - +
147B LYS* 1.3 60.7 + - - +
149B TYR* 3.1 32.5 + + + +
150B LEU* 3.1 54.2 + - + +
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Residues in contact with LYS 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B MET* 3.0 23.8 + - + +
144B ARG 3.8 14.8 - - - +
146B TYR* 1.3 72.6 - - - +
148B ASP* 1.3 80.6 + - - +
150B LEU* 3.7 9.8 - - - +
151B LEU* 2.7 51.0 + - + +
196B ILE* 3.6 46.6 - - + +
199B ASP* 4.9 6.6 + - + +
200B LEU* 4.0 13.7 - - + -
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Residues in contact with ASP 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B ARG 4.1 3.1 - - - +
145B LYS* 3.2 23.9 + - - +
147B LYS* 1.3 101.4 + - - +
149B TYR* 1.3 63.3 + - - +
151B LEU* 4.1 5.3 - - - +
152B LYS* 3.0 31.3 + - - +
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Residues in contact with TYR 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B LYS 3.9 1.6 + - - +
146B TYR* 3.1 41.1 + + + +
148B ASP* 1.3 79.5 - - - +
150B LEU* 1.3 72.9 + - + +
152B LYS* 4.2 20.4 - - - +
153B ASN* 2.8 55.0 + - - +
155B ILE* 4.1 25.3 - - + +
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Residues in contact with LEU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B LEU* 4.7 2.7 - - + -
112B VAL* 5.9 0.9 - - + -
143B MET* 3.9 7.9 - - + -
146B TYR* 3.1 54.1 + - + +
147B LYS* 3.1 3.5 + - - +
149B TYR* 1.3 87.3 - - + +
151B LEU* 1.3 58.7 + - - +
153B ASN 3.3 1.2 + - - -
154B GLU 3.0 21.7 + - - -
155B ILE* 3.1 42.3 + - + +
157B PHE* 4.3 16.2 - - + -
200B LEU* 3.6 38.4 - - + -
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Residues in contact with LEU 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B LYS* 2.7 46.0 + - + +
148B ASP* 4.1 4.5 - - - +
150B LEU* 1.3 70.0 - - - +
152B LYS* 1.3 61.8 + - - +
154B GLU* 3.0 23.5 + - - +
156B PHE* 3.9 15.9 - - + -
199B ASP* 3.5 44.4 - - + +
200B LEU* 3.8 15.5 - - + -
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Residues in contact with LYS 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B ASP 3.0 17.6 + - - +
149B TYR* 4.2 21.7 - - - +
151B LEU* 1.3 76.3 - - - +
153B ASN* 1.3 84.1 + - - +
154B GLU* 3.6 8.1 + - - +
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Residues in contact with ASN 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B TYR* 2.8 57.8 + - - +
152B LYS* 1.3 95.0 - - - +
154B GLU* 1.3 68.5 + - - +
155B ILE* 3.2 24.5 + - + +
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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