Contacts of the helix formed by residues 119 - 130 (chain A) in PDB entry 1MPU
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 ASN 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A LYS* 1.3 80.0 - - - +
120A TRP* 1.3 58.4 + - - +
121A TYR* 2.9 17.8 + - - +
122A GLU* 2.6 58.7 + - - +
123A SER* 2.9 24.1 + - - -
154A TRP* 3.5 1.1 - - - -
203A CYS 3.3 12.8 - - - +
204A SER* 3.3 21.6 + - - +
205A THR 3.9 2.2 - - - -
206A PRO* 3.7 12.1 - - + +
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Residues in contact with TRP 120 (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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119A ASN* 1.3 71.9 - - - +
121A TYR* 1.3 83.9 + + - +
123A SER* 3.2 4.4 - - - -
124A GLN* 2.9 42.7 + - + -
134A LEU* 3.6 19.7 - - + +
154A TRP* 3.3 46.5 - + + +
155A MET 3.1 20.6 + - - -
156A GLY* 4.6 0.4 - - - -
157A LEU 4.4 0.6 + - - -
158A VAL* 3.4 30.0 - - + +
169A GLU* 3.9 26.2 - - + -
189A CYS* 3.4 23.8 - - + +
190A ALA 4.8 0.2 - - - -
203A CYS* 2.9 19.2 + - + +
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Residues in contact with TYR 121 (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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119A ASN* 2.9 14.8 + - + +
120A TRP* 1.3 95.9 - + - +
122A GLU* 1.3 67.1 + - + +
123A SER 2.9 2.4 + - - -
124A GLN* 3.0 13.0 + - - +
125A ALA* 3.1 12.2 + - - +
189A CYS* 5.6 0.4 - - - -
203A CYS* 3.8 38.1 - - + +
204A SER* 4.5 9.9 - - - -
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Residues in contact with GLU 122 (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* 3.7 27.6 - - + +
119A ASN* 2.6 48.5 + - - +
121A TYR* 1.3 72.7 - - + +
123A SER* 1.3 61.4 + - - +
125A ALA* 3.3 9.5 + - - +
126A SER* 3.2 24.5 + - - -
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Residues in contact with SER 123 (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* 4.5 1.6 - - - -
119A ASN 2.9 20.1 + - - -
120A TRP* 3.2 12.1 - - - -
121A TYR 2.9 0.2 - - - -
122A GLU* 1.3 78.3 - - - +
124A GLN* 1.3 61.6 + - - +
125A ALA 3.2 0.5 + - - -
126A SER* 3.3 16.8 + - - -
127A CYS* 3.5 14.9 + - - -
134A LEU* 3.1 10.6 - - - +
154A TRP* 3.7 9.5 - - - -
209A TYR* 3.0 42.6 - - - +
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Residues in contact with GLN 124 (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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120A TRP* 2.9 34.4 + - + +
121A TYR 3.0 4.5 + - - +
123A SER* 1.3 76.1 - - - +
125A ALA* 1.3 61.2 + - - +
127A CYS* 3.7 0.8 + - - +
128A MET* 3.1 43.8 + - - +
133A SER* 3.2 23.6 - - - +
134A LEU* 2.9 45.4 - - + +
169A GLU* 3.3 16.7 - - + +
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Residues in contact with ALA 125 (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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121A TYR 3.1 10.5 + - - +
122A GLU* 3.3 15.5 - - - +
123A SER 3.1 0.4 - - - -
124A GLN* 1.3 76.4 - - - +
126A SER* 1.3 60.3 + - - +
128A MET* 3.2 9.5 + - - +
129A SER* 2.8 31.6 + - - -
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Residues in contact with SER 126 (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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114A PHE* 5.5 0.2 - - - -
118A LYS* 2.9 18.6 + - - -
122A GLU 3.2 10.3 + - - -
123A SER 3.3 6.7 + - - -
125A ALA* 1.3 76.5 - - - +
127A CYS* 1.3 65.7 + - - +
129A SER* 2.8 24.6 + - - -
130A GLN* 3.1 21.9 + - - +
209A TYR* 2.8 33.0 + - - -
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Residues in contact with CYS 127 (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 SER 3.5 12.3 + - - -
124A GLN 3.8 5.6 - - - +
125A ALA 3.3 0.4 - - - -
126A SER* 1.3 78.8 - - - +
128A MET* 1.3 60.9 + - - +
130A GLN* 3.0 13.7 + - - +
131A ASN 3.2 0.9 + - - -
132A ALA* 2.9 22.6 + - - +
133A SER* 3.5 31.2 - - - +
134A LEU* 3.7 16.8 - - - +
209A TYR* 4.2 0.4 - - - -
211A CYS* 2.0 55.8 - - + -
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Residues in contact with MET 128 (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 GLN* 3.1 42.2 + - - +
125A ALA* 3.7 6.5 - - - +
127A CYS* 1.3 70.7 - - - +
129A SER* 1.3 56.0 + - - +
130A GLN 2.9 4.9 - - - -
131A ASN* 2.6 25.9 + - - +
132A ALA 3.2 18.2 - - - +
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Residues in contact with SER 129 (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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125A ALA 2.8 13.9 + - - -
126A SER* 3.0 18.2 - - - -
128A MET* 1.3 76.3 - - - +
130A GLN* 1.3 65.6 + - - +
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Residues in contact with GLN 130 (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 PRO* 4.9 8.0 - - + +
103A TRP* 4.5 22.2 + - + +
114A PHE* 3.3 39.4 - - - -
126A SER* 3.1 19.8 + - - +
127A CYS* 3.0 8.8 + - - +
128A MET 2.9 0.6 - - - -
129A SER* 1.3 90.9 + - - +
131A ASN* 1.3 68.9 + - - +
132A ALA* 4.5 1.7 - - - +
211A CYS* 5.4 0.2 - - - -
213A GLN* 4.0 6.2 + - - -
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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