Contacts of the helix formed by residues 134 - 143 (chain A) in PDB entry 4ROE
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 134 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A LEU* 4.7 1.1 - - - -
132A PRO 3.6 0.6 + - - +
133A LEU* 1.3 79.0 - - - +
135A MET* 1.3 58.5 + - - +
136A GLY* 3.8 2.7 + - - -
137A ALA* 3.1 27.4 + - + +
138A ILE* 3.1 28.9 + - - +
167A LEU* 4.2 11.2 - - + -
172A LEU* 4.0 36.1 - - + -
222A PRO* 5.4 2.5 - - + -
223A LEU* 5.3 8.7 - - + -
286B GLU* 3.4 15.0 - - - +
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Residues in contact with MET 135 (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* 3.7 20.9 - - + -
127A ARG* 3.5 24.9 - - - +
134A THR* 1.3 68.9 - - - +
136A GLY* 1.3 60.2 + - - +
138A ILE* 3.1 12.3 - - - +
139A CYS* 3.0 31.0 + - - -
146A LEU* 4.1 13.9 - - + -
149A PHE* 3.8 14.4 - - + -
150A SER* 5.4 0.2 - - - -
153A TYR* 3.9 28.0 - - + -
284B GLU* 3.8 11.2 - - + +
286B GLU* 2.9 25.1 + - + +
287B LEU* 3.6 38.4 - - + -
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Residues in contact with GLY 136 (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 THR* 3.3 4.1 + - - -
135A MET* 1.3 80.9 - - - +
137A ALA* 1.4 51.3 + - - +
139A CYS* 3.5 6.9 + - - +
140A THR* 2.8 37.3 + - - -
146A LEU* 4.4 10.9 - - - +
286B GLU* 4.4 1.2 + - - -
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Residues in contact with ALA 137 (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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133A LEU* 4.4 10.8 - - + -
134A THR* 3.1 28.7 + - + +
136A GLY* 1.4 75.8 - - - +
138A ILE* 1.4 60.5 + - - +
140A THR* 3.3 8.6 + - - -
141A LEU* 3.2 26.8 + - + +
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Residues in contact with ILE 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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79A LEU* 3.6 31.9 - - + -
83A LEU* 3.8 13.0 - - + -
119A GLY* 4.2 14.4 - - - +
122A VAL* 4.5 1.6 - - + -
123A LEU* 4.9 5.8 - - + -
133A LEU* 3.7 30.2 - - + +
134A THR 3.1 16.6 + - - +
135A MET* 3.1 24.2 - - - +
137A ALA* 1.4 73.8 - - - +
139A CYS* 1.4 55.3 + - - +
141A LEU* 3.4 6.8 + - + +
142A LEU* 3.0 41.0 + - + +
149A PHE* 3.6 27.1 - - + -
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Residues in contact with CYS 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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135A MET 3.0 20.2 + - - +
136A GLY* 3.8 7.2 - - - +
138A ILE* 1.4 72.8 - - - +
140A THR* 1.4 59.6 + - - +
142A LEU* 5.4 0.4 - - - -
143A TYR* 3.0 8.0 + - - -
144A ALA* 2.9 48.0 + - - +
145A ASP 4.3 0.7 - - - -
146A LEU* 3.7 26.7 - - + +
149A PHE* 3.5 39.9 - - - -
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Residues in contact with THR 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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136A GLY 2.8 22.3 + - - -
137A ALA* 3.3 9.2 + - - -
139A CYS* 1.4 72.6 - - - +
141A LEU* 1.3 64.4 + - + +
143A TYR* 3.4 26.8 + - + +
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Residues in contact with LEU 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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79A LEU* 4.6 15.0 - - + -
82A VAL* 4.3 20.4 - - + -
83A LEU* 3.5 36.8 - - + -
133A LEU* 5.1 1.1 - - + -
137A ALA* 3.2 16.8 + - + +
138A ILE* 3.4 13.2 + - - +
140A THR* 1.3 77.1 - - + +
142A LEU* 1.3 60.5 + - - +
143A TYR* 3.6 15.6 - - - -
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Residues in contact with LEU 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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79A LEU* 3.8 31.0 - - + -
115A GLU 4.5 11.7 - - - +
116A VAL* 5.0 3.8 - - - -
118A VAL* 5.2 4.5 - - + -
119A GLY* 3.7 32.1 - - - +
138A ILE* 3.0 26.1 + - + +
141A LEU* 1.3 78.1 - - - +
143A TYR* 1.4 70.8 + - - +
144A ALA* 3.4 19.8 + - + +
149A PHE* 5.0 4.5 - - + -
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Residues in contact with TYR 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 CYS 3.0 7.2 + - - -
140A THR* 3.4 13.4 + - + +
141A LEU* 3.3 18.4 - - - -
142A LEU* 1.4 79.4 - - - +
144A ALA* 1.3 59.4 + - - +
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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