Contacts of the helix formed by residues 140 - 151 (chain A) in PDB entry 1RL3
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 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A LEU* 1.3 74.8 - - - +
141A ASP* 1.3 59.3 - - - +
142A ASN* 2.6 23.9 + - - +
143A GLU* 2.5 58.9 + - - +
144A ARG* 2.6 36.7 + - - +
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Residues in contact with ASP 141 (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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140A ASP* 1.3 76.8 - - - +
142A ASN* 1.3 71.1 + - - +
144A ARG* 3.3 9.8 + - - +
145A SER* 3.1 19.9 + - - -
520B TYR* 5.7 0.5 - - - -
521B LYS* 6.1 0.2 - - - -
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Residues in contact with ASN 142 (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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140A ASP* 2.6 19.5 + - - +
141A ASP* 1.3 80.9 - - - +
143A GLU* 1.3 60.5 + - + +
145A SER* 3.1 21.7 + - - -
146A ASP* 3.4 12.5 + - - +
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Residues in contact with GLU 143 (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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138A HIS 4.1 3.8 - - - +
139A LEU* 3.7 18.4 - - + +
140A ASP* 2.5 49.1 + - - +
142A ASN* 1.3 72.6 - - + +
144A ARG* 1.3 61.9 + - - +
146A ASP* 3.1 21.1 + - - +
147A ILE* 3.2 16.6 + - - +
231A ARG 4.9 3.3 - - - +
232A ILE* 4.2 29.7 - - + +
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Residues in contact with ARG 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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127A ALA 5.5 0.4 + - - -
130A ILE* 4.1 23.5 - - + +
131A GLU* 4.8 13.3 - - - +
136A PHE* 5.2 8.5 + - - +
139A LEU* 4.3 22.1 + - + +
140A ASP 2.6 22.2 + - - +
141A ASP* 3.4 8.7 - - - +
143A GLU* 1.3 73.9 - - - +
145A SER* 1.3 62.4 + - - +
147A ILE* 3.4 3.0 + - + +
148A PHE* 3.2 59.2 + - + -
520B TYR* 4.2 11.7 + - - -
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Residues in contact with SER 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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141A ASP 3.1 11.5 + - - -
142A ASN* 3.2 13.0 - - - -
144A ARG* 1.3 76.5 - - - +
146A ASP* 1.3 59.7 + - - +
148A PHE* 3.5 2.8 + - - +
149A ASP* 2.9 38.0 + - - +
520B TYR* 3.4 30.8 - - - -
521B LYS* 4.0 16.8 - - - +
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Residues in contact with ASP 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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112A VAL* 2.9 42.7 - - - +
142A ASN* 3.4 13.3 + - - +
143A GLU* 3.1 9.7 + - - +
145A SER* 1.3 76.1 + - - +
147A ILE* 1.3 56.7 + - - +
149A ASP* 2.9 6.7 + - - +
150A ALA* 2.3 42.8 + - + +
231A ARG* 4.3 7.4 + - - +
232A ILE* 3.3 23.2 - - + +
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Residues in contact with ILE 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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130A ILE* 3.6 20.9 - - + -
136A PHE* 3.7 15.3 - - + -
139A LEU* 3.8 19.7 - - + -
143A GLU 3.2 3.7 + - - +
144A ARG* 3.9 5.6 - - - +
146A ASP* 1.3 78.1 - - - +
148A PHE* 1.3 56.2 + - - +
150A ALA* 4.2 2.5 - - - -
151A MET* 2.6 55.2 + - + +
224A ILE* 3.6 22.0 - - + -
228A SER 4.8 0.2 - - - +
232A ILE* 3.6 39.7 - - + -
233A LEU* 4.0 15.3 - - + -
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Residues in contact with PHE 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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118A LYS* 3.0 23.5 - - - -
123A MET* 4.4 8.3 - - + -
126A LEU* 3.4 25.7 - - + +
127A ALA* 3.4 47.8 - - + -
130A ILE* 3.9 21.8 - - + -
144A ARG* 3.2 55.6 + - + -
145A SER 3.6 5.6 - - - +
147A ILE* 1.3 79.4 - - - +
149A ASP* 1.3 63.5 + - - +
151A MET 3.6 1.2 + - - -
520B TYR* 3.5 44.6 - + + -
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Residues in contact with ASP 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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115A VAL* 4.3 21.5 - - + +
116A ILE* 3.4 23.6 + - - +
118A LYS* 3.7 7.6 + - - +
145A SER* 2.9 22.2 + - - +
146A ASP* 3.4 8.2 - - - +
148A PHE* 1.3 80.7 - - - +
150A ALA* 1.3 62.2 + - - +
151A MET 3.4 6.2 + - - +
519B ASP* 3.5 23.6 - - - +
520B TYR* 3.2 33.7 + - - +
521B LYS* 4.8 0.9 + - - +
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Residues in contact with ALA 150 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A ARG 5.8 1.1 - - - -
114A LYS* 4.2 16.8 - - + +
115A VAL 5.0 0.2 - - - +
116A ILE* 4.3 5.6 - - - +
146A ASP* 2.3 37.8 + - + +
147A ILE 3.9 1.3 - - - +
149A ASP* 1.3 65.2 - - - +
151A MET* 1.3 62.2 + - - +
152A PHE* 4.1 11.4 - - - -
224A ILE* 4.0 10.5 - - + +
225A ASP* 4.0 12.1 - - - +
228A SER* 3.5 32.3 - - - +
231A ARG* 5.8 0.4 - - - +
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Residues in contact with MET 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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116A ILE* 4.1 2.1 - - - +
118A LYS* 3.1 25.5 - - - -
126A LEU* 3.4 40.6 - - + -
129A ALA* 6.2 0.4 - - + -
130A ILE* 3.5 26.5 - - + +
136A PHE* 3.7 19.5 - - + -
147A ILE* 2.6 37.5 + - + +
149A ASP 3.3 2.1 - - - +
150A ALA* 1.3 77.5 - - - +
152A PHE* 1.3 60.4 + - - +
172A PHE* 6.2 0.2 - - - -
174A VAL* 5.1 7.0 - - + -
222A TRP* 4.1 22.2 - - + -
223A GLY 3.6 11.9 - - - +
224A ILE* 4.0 19.7 - - + -
233A LEU* 6.1 1.1 - - - -
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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