Contacts of the helix formed by residues 130 - 143 (chain A) in PDB entry 1M0E
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 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A ALA 4.0 18.2 - - - -
126A SER* 3.5 7.6 + - - +
127A HIS 3.1 9.1 + - - -
129A ASN* 1.3 72.3 - - - +
131A ASN* 1.3 57.0 + - - +
132A THR 3.3 2.7 - - - -
133A LEU* 3.3 6.0 + - - +
134A GLU* 2.9 29.9 + - - +
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Residues in contact with ASN 131 (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 ASP* 2.9 39.6 + - - +
129A ASN* 3.0 16.5 + - - +
130A GLY* 1.3 76.9 - - - +
132A THR* 1.3 54.0 + - - +
134A GLU* 3.5 17.7 - - - +
135A VAL* 2.7 44.2 + - + +
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Residues in contact with THR 132 (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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84A PHE* 3.4 30.7 - - + -
93A PHE* 3.5 27.2 + - + -
124A PHE* 3.7 21.3 - - + +
127A HIS* 2.7 38.5 + - - -
128A ASP* 3.6 6.2 + - - +
130A GLY 3.3 0.4 - - - -
131A ASN* 1.3 76.2 - - - +
133A LEU* 1.3 63.2 + - - +
135A VAL* 3.2 5.4 + - - +
136A VAL* 3.1 23.1 + - - +
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Residues in contact with LEU 133 (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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124A PHE* 4.2 22.3 + - + +
125A ALA* 3.7 38.6 - - + +
130A GLY* 3.3 7.7 + - - +
132A THR* 1.3 81.7 - - - +
134A GLU* 1.3 63.2 + - - +
136A VAL* 3.1 5.2 + - + +
137A LYS* 2.9 21.5 + - + +
147A PHE* 3.7 30.5 - - + -
149A ALA* 4.7 4.9 - - + -
166A ILE* 4.0 20.9 - - + -
168A MET* 4.4 0.7 - - - -
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Residues in contact with GLU 134 (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 GLY 2.9 18.4 + - - +
131A ASN* 3.2 21.4 + - - +
133A LEU* 1.3 74.3 - - - +
135A VAL* 1.3 59.0 + - + +
137A LYS* 3.1 13.6 + - + +
138A ASN* 2.8 57.2 + - - +
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Residues in contact with VAL 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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93A PHE* 3.8 30.7 - - + -
101A PHE* 5.2 0.7 - - + -
102A PHE* 4.2 16.2 - - + -
131A ASN* 2.7 31.9 + - + +
132A THR 3.3 7.2 - - - +
134A GLU* 1.3 74.4 - - + +
136A VAL* 1.3 57.0 + - + +
138A ASN* 3.9 6.1 - - - +
139A THR* 2.6 46.1 + - - +
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Residues in contact with VAL 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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79A PHE* 5.2 0.2 - - + -
93A PHE* 4.8 5.2 - - + -
101A PHE* 3.7 45.1 - - + -
118A MET* 4.2 4.5 - - + -
124A PHE* 3.5 26.2 - - + -
132A THR 3.1 12.6 + - - +
133A LEU* 3.4 8.3 - - - +
135A VAL* 1.3 75.3 - - - +
137A LYS* 1.3 58.6 + - - +
139A THR* 3.2 1.9 + - - -
140A MET* 2.8 30.5 + - + +
147A PHE* 3.5 26.9 - - + -
168A MET* 4.1 11.0 - - - -
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Residues in contact with LYS 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* 2.9 13.8 + - + +
134A GLU* 3.4 16.8 - - + +
136A VAL* 1.3 75.7 - - - +
138A ASN* 1.3 65.9 + - - +
140A MET* 3.1 4.3 + - - +
141A ASN* 2.8 57.4 + - - +
147A PHE* 3.7 41.0 + - + +
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Residues in contact with ASN 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 GLU* 2.8 51.0 + - - +
135A VAL* 3.9 5.1 - - - +
137A LYS* 1.3 77.0 + - - +
139A THR* 1.3 66.1 + - - +
141A ASN* 3.8 13.0 + - - +
142A GLU* 2.9 27.0 + - - +
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Residues in contact with THR 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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101A PHE* 3.6 29.0 - - + -
102A PHE* 4.9 6.2 - - + -
105A ALA* 3.9 17.9 - - + -
109A ARG* 4.7 9.4 - - - +
135A VAL* 2.6 30.4 + - - +
136A VAL 3.5 4.3 - - - -
138A ASN* 1.3 78.3 - - - +
140A MET* 1.3 66.6 + - + +
142A GLU* 3.3 7.2 + - - +
143A LEU* 3.2 24.7 + - + +
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Residues in contact with MET 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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101A PHE* 3.4 31.0 - - + -
104A ILE* 5.3 0.9 - - + -
105A ALA* 4.6 7.0 - - + +
108A VAL* 5.1 6.3 - - + -
116A VAL* 4.6 14.1 - - + -
118A MET* 4.3 9.6 - - + -
136A VAL* 2.8 19.4 + - + +
137A LYS 3.6 4.0 - - - +
139A THR* 1.3 76.1 - - + +
141A ASN* 1.3 62.3 + - - +
143A LEU* 3.1 38.7 + - + +
145A TYR* 3.2 28.2 + - + +
147A PHE* 3.9 20.0 - - + -
170A CYS* 3.8 31.2 - - - -
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Residues in contact with ASN 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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137A LYS* 2.8 52.8 + - - +
138A ASN* 3.8 10.8 + - - +
140A MET* 1.3 75.7 - - - +
142A GLU* 1.3 56.6 + - - +
144A ASP* 2.8 23.4 + - - +
145A TYR 2.9 21.0 + - - +
146A SER* 4.4 0.9 - - - -
147A PHE* 4.0 14.4 + - - +
173A ASN* 4.7 2.5 + - - +
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Residues in contact with GLU 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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109A ARG* 4.0 21.0 + - - -
138A ASN 2.9 18.4 + - - +
139A THR* 3.3 6.7 + - - +
141A ASN* 1.3 75.0 - - - +
143A LEU* 1.3 59.9 + - - +
144A ASP* 3.0 4.9 + - - +
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Residues in contact with LEU 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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105A ALA* 3.9 12.3 - - + +
108A VAL* 3.9 13.2 - - + -
109A ARG* 3.4 57.4 - - + +
112A LYS* 2.8 32.0 + - - +
139A THR* 3.2 19.8 + - + +
140A MET* 3.1 39.6 + - + +
142A GLU* 1.3 77.5 - - - +
144A ASP* 1.3 62.9 + - - +
145A TYR* 3.3 18.8 - - + -
172A ARG* 5.7 0.2 - - - +
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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