Contacts of the helix formed by residues 137 - 149 (chain A) in PDB entry 1X1R
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 THR 137 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A TYR* 4.8 0.3 + - - -
134A ARG* 3.7 5.9 + - - +
135A LYS 5.2 3.4 - - - +
136A VAL* 1.3 78.6 - - - +
138A ARG* 1.3 65.9 + - - +
139A ASP* 3.5 8.4 + - - +
140A GLN* 3.0 37.9 + - - +
141A GLY* 3.1 18.0 + - - -
152A TYR* 4.5 0.9 + - - -
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Residues in contact with ARG 138 (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 ARG* 3.4 16.1 - - - +
137A THR* 1.3 73.1 - - - +
139A ASP* 1.3 79.6 + - - +
141A GLY* 3.1 3.6 + - - -
142A LYS* 2.9 68.2 + - - +
152A TYR* 3.8 11.7 + - + -
154A GLU* 3.3 26.9 - - - +
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Residues in contact with ASP 139 (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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137A THR* 3.2 8.1 + - - +
138A ARG* 1.3 102.5 + - - +
140A GLN* 1.3 58.0 + - + +
142A LYS* 4.0 3.7 - - - +
143A GLU* 2.9 32.7 + - - +
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Residues in contact with GLN 140 (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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97A LYS* 4.6 11.8 + - - +
100A PHE* 3.6 19.1 - - + -
135A LYS 3.9 5.2 - - - +
136A VAL* 3.5 18.5 - - + +
137A THR* 3.0 43.7 + - - +
139A ASP* 1.3 77.3 - - + +
141A GLY* 1.3 61.8 + - - +
143A GLU* 4.0 4.4 - - - +
144A MET* 3.1 23.4 + - - +
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Residues in contact with GLY 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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92A TYR* 3.3 25.5 + - - -
100A PHE* 4.1 6.7 - - - -
123A LEU* 3.5 8.5 - - - +
137A THR 3.1 10.9 + - - -
138A ARG 3.1 1.5 + - - -
140A GLN* 1.3 77.0 - - - +
142A LYS* 1.3 61.6 + - - +
144A MET* 3.3 4.7 + - - +
145A ALA 3.0 18.5 + - - -
152A TYR* 3.5 14.8 - - - -
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Residues in contact with LYS 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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138A ARG* 2.9 55.5 + - - +
139A ASP* 3.4 3.6 + - - +
141A GLY* 1.3 75.0 - - - +
143A GLU* 1.3 58.4 + - - +
145A ALA* 3.3 2.5 + - + +
146A THR* 2.9 44.1 + - - +
150A ILE 5.5 3.2 + - - -
151A PRO* 5.6 1.6 - - - +
152A TYR* 3.9 36.3 + - + +
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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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139A ASP 2.9 18.5 + - - +
140A GLN* 4.0 5.1 - - - +
142A LYS* 1.3 73.3 - - - +
144A MET* 1.3 61.4 + - - +
146A THR* 3.2 8.4 + - - -
147A LYS* 2.9 31.4 + - + +
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Residues in contact with MET 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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100A PHE* 3.5 52.3 - - + +
101A GLU* 5.0 2.7 - - - +
103A VAL* 3.5 31.2 - - + -
104A ASP* 4.9 2.7 - - + +
123A LEU* 3.7 12.8 - - + -
140A GLN 3.1 14.7 + - - +
141A GLY 3.5 7.4 - - - +
143A GLU* 1.3 77.6 - - - +
145A ALA* 1.3 62.8 + - - +
147A LYS* 3.2 11.5 + - + +
148A TYR* 3.1 46.5 + - + +
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Residues in contact with ALA 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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123A LEU* 3.8 11.9 - - + +
141A GLY 3.0 9.5 + - - +
142A LYS* 3.6 8.1 - - + +
144A MET* 1.3 77.7 - - - +
146A THR* 1.3 58.3 + - - +
148A TYR* 3.2 2.0 + - - -
149A ASN 2.8 24.1 + - - -
150A ILE* 3.0 37.7 + - + +
151A PRO 4.1 3.8 - - - +
152A TYR* 3.6 28.3 - - + -
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Residues in contact with THR 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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142A LYS* 2.9 35.2 + - - +
143A GLU* 3.5 9.6 - - - -
145A ALA* 1.3 76.3 - - - +
147A LYS* 1.3 63.5 + - - +
149A ASN* 3.0 17.1 + - - +
150A ILE 5.1 0.4 - - - -
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Residues in contact with LYS 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 GLU* 2.9 16.7 + - + +
144A MET* 3.2 13.2 + - + +
146A THR* 1.3 78.3 - - - +
148A TYR* 1.3 82.4 + - + +
149A ASN* 3.4 1.6 + - - +
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Residues in contact with TYR 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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103A VAL* 3.9 18.2 - - + -
104A ASP* 2.7 43.6 + - - +
107A HIS* 3.5 50.1 + + + +
118A SER* 6.0 1.6 - - - -
123A LEU* 5.4 0.2 - - + -
144A MET* 3.1 44.2 + - + +
145A ALA* 3.9 3.4 - - - +
147A LYS* 1.3 95.5 + - + +
149A ASN* 1.3 69.3 + - - +
150A ILE* 3.5 28.1 + - + +
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Residues in contact with ASN 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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145A ALA 2.8 8.8 + - - -
146A THR* 3.0 13.7 + - - +
147A LYS 4.8 1.3 - - - +
148A TYR* 1.3 82.5 - - - +
150A ILE* 1.3 58.8 + - - +
151A PRO* 4.9 0.3 - - - +
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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