Contacts of the helix formed by residues 143 - 152 (chain A) in PDB entry 5LS6
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 143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A ASP* 2.8 27.8 + - - -
142A ASP* 1.3 69.6 - - - +
144A THR* 1.3 61.4 + - - +
145A PHE 3.2 0.4 - - - -
146A ILE* 3.1 25.7 + - - +
147A GLU* 3.5 8.8 + - - +
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Residues in contact with THR 144 (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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142A ASP* 3.3 27.6 - - + +
143A GLY* 1.3 76.3 - - - +
145A PHE* 1.3 65.6 + - + +
147A GLU* 3.1 15.0 + - - +
148A GLU* 2.9 32.3 + - - +
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Residues in contact with PHE 145 (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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134A MET* 3.8 25.8 - - + -
142A ASP 2.8 20.4 + - - +
144A THR* 1.3 74.9 - - + +
146A ILE* 1.3 70.2 + - + +
148A GLU* 3.4 23.8 - - - +
149A LEU* 2.8 60.3 + - + +
656A LYS* 3.6 33.0 - - - -
657A VAL* 4.5 5.6 - - + -
659A ASP* 6.0 0.7 - - + -
660A LYS* 3.6 43.3 - - + -
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Residues in contact with ILE 146 (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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131A ILE* 4.6 17.7 - - + -
132A PRO* 5.1 4.3 - - + +
134A MET* 3.8 19.1 - - + -
135A GLY* 6.5 0.4 - - - -
140A ASP* 6.2 2.9 - - - -
142A ASP 5.3 0.4 - - - +
143A GLY* 3.1 18.7 + - - +
145A PHE* 1.3 96.9 - - + +
147A GLU* 1.3 59.6 + - - +
149A LEU* 4.0 8.7 - - + +
150A ILE* 3.1 43.7 + - + +
4Q ALA* 4.8 13.5 - - + -
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Residues in contact with GLU 147 (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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143A GLY 3.5 5.8 + - - +
144A THR* 3.1 16.6 + - - +
146A ILE* 1.3 78.1 - - - +
148A GLU* 1.3 58.4 + - - +
150A ILE* 3.0 23.8 + - + +
151A LYS* 3.1 36.3 + - + +
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Residues in contact with GLU 148 (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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144A THR* 2.9 21.1 + - - +
145A PHE* 3.4 31.8 + - + +
147A GLU* 1.3 75.7 - - - +
149A LEU* 1.3 66.3 + - - +
151A LYS* 3.5 16.6 + - + +
152A ASN* 2.9 24.8 + - - -
656A LYS* 3.7 23.2 + - - +
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Residues in contact with LEU 149 (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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128A LEU* 4.4 13.0 - - + -
131A ILE* 5.2 4.0 - - + -
132A PRO* 3.7 30.1 - - + -
145A PHE* 2.8 44.8 + - + +
146A ILE* 4.0 10.1 - - + +
148A GLU* 1.3 79.1 - - - +
150A ILE* 1.3 62.0 + - + +
152A ASN* 3.7 6.9 + - + +
153A TYR* 3.4 32.9 - - + -
653A ARG 4.6 2.2 - - - +
656A LYS* 4.3 14.6 - - + +
657A VAL* 3.9 32.5 - - + +
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Residues in contact with ILE 150 (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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128A LEU* 5.0 6.1 - - + -
131A ILE* 5.3 13.9 - - + -
146A ILE* 3.1 30.7 - - + +
147A GLU* 3.0 11.7 + - + +
149A LEU* 1.3 78.8 - - + +
151A LYS* 1.3 55.8 + - - +
152A ASN 3.3 0.2 - - - -
153A TYR* 3.1 13.8 + - - +
155A GLY* 2.8 53.1 + - - +
157A VAL* 4.1 23.6 - - + -
2Q LEU 5.6 6.1 - - - +
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Residues in contact with LYS 151 (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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147A GLU* 3.1 35.0 + - + +
148A GLU* 3.7 14.6 - - - +
149A LEU 3.4 0.6 - - - -
150A ILE* 1.3 71.2 - - - +
152A ASN* 1.3 60.2 + - - +
153A TYR 3.1 2.0 - - - -
154A ASP* 3.0 23.7 + - - +
155A GLY* 4.2 5.8 - - - +
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Residues in contact with ASN 152 (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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148A GLU 2.9 25.5 + - - -
149A LEU* 3.8 9.6 + - + +
150A ILE 3.3 0.6 - - - -
151A LYS* 1.3 75.6 - - - +
153A TYR* 1.3 65.5 + - + +
154A ASP* 3.4 4.9 + - - +
652A ASP* 4.0 16.6 - - - +
653A ARG* 3.9 26.3 + - + +
656A LYS* 3.1 34.5 - - - +
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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