Contacts of the helix formed by residues 111 - 125 (chain A) in PDB entry 1MA1
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 SER 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A ILE* 3.8 6.4 - - - +
106A GLU* 3.9 9.6 + - - +
109A PHE* 3.2 10.2 + - - +
110A GLY* 1.3 79.9 - - - +
112A PHE* 1.3 63.0 + - - +
113A GLU* 3.3 16.5 + - - +
114A ARG* 2.9 24.8 + - - +
115A PHE* 3.2 16.6 + - - +
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Residues in contact with PHE 112 (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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95A GLY 4.2 7.4 - - - -
96A GLU* 3.8 45.1 - - + +
97A PRO* 3.4 31.9 - - + -
105A ILE* 3.9 13.5 - - + +
106A GLU* 5.2 3.4 - - - +
111A SER* 1.3 71.6 - - - +
113A GLU* 1.3 72.5 + - - +
115A PHE* 3.2 19.2 + + - +
116A ARG* 2.7 60.5 + - + +
188A TRP* 4.6 5.4 - + - -
193A TRP* 3.8 22.2 - + - -
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Residues in contact with GLU 113 (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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96A GLU* 4.6 10.3 - - - +
111A SER* 3.3 15.4 + - - +
112A PHE* 1.3 87.1 + - - +
114A ARG* 1.3 64.3 + - - +
116A ARG* 3.2 11.7 + - - +
117A LYS* 2.9 25.4 + - - +
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Residues in contact with ARG 114 (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 PHE* 2.9 30.3 - - + +
111A SER* 2.9 16.5 + - - +
113A GLU* 1.3 76.7 - - - +
115A PHE* 1.3 64.6 + - - +
117A LYS* 3.1 31.5 + - - +
118A GLU* 2.8 58.6 + - - +
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Residues in contact with PHE 115 (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 ILE* 3.6 30.3 - - + -
109A PHE* 3.7 36.2 - + + +
111A SER 3.2 3.4 + - - +
112A PHE* 3.2 22.3 + + - +
114A ARG* 1.3 78.4 - - - +
116A ARG* 1.3 67.4 + - - +
117A LYS 3.0 0.3 + - - -
118A GLU* 3.2 1.6 + - - +
119A PHE* 2.8 57.4 + + + +
134A LEU* 4.0 28.9 - - + -
145A ILE* 4.2 2.7 - - + -
163A LEU* 4.1 13.2 - - + -
188A TRP* 3.9 13.5 - + - -
193A TRP* 3.8 23.8 - + - -
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Residues in contact with ARG 116 (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 PHE* 2.7 45.3 + - + +
113A GLU* 3.4 10.5 - - - +
115A PHE* 1.3 80.3 - - - +
117A LYS* 1.3 54.5 + - - +
120A SER* 2.7 40.1 + - - -
185A GLU* 2.8 39.2 + - - -
188A TRP* 3.4 58.0 - - + +
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Residues in contact with LYS 117 (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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113A GLU 2.9 17.4 + - - +
114A ARG* 3.4 30.2 - - - +
116A ARG* 1.3 77.3 - - - +
118A GLU* 1.3 61.9 + - + +
120A SER* 3.2 6.7 + - - -
121A GLN* 2.9 55.0 + - + +
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Residues in contact with GLU 118 (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 PHE* 3.5 27.7 - - + -
114A ARG* 2.8 55.1 + - - +
115A PHE* 3.8 3.8 - - - +
117A LYS* 1.3 77.9 - - + +
119A PHE* 1.3 57.0 + - - +
121A GLN* 3.1 15.0 + - - +
122A ALA* 2.9 28.6 + - - +
145A ILE* 4.2 11.3 - - + +
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Residues in contact with PHE 119 (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 PHE* 2.8 34.8 + + + +
116A ARG 3.9 3.6 - - - +
118A GLU* 1.3 73.0 - - - +
120A SER* 1.3 57.3 + - - +
122A ALA* 3.3 6.2 + - - +
123A ALA* 3.1 23.6 + - - +
132A ALA* 3.3 26.0 - - + +
133A VAL 3.8 9.2 - - - -
134A LEU* 3.6 29.4 - - + -
145A ILE* 3.8 23.9 - - + +
163A LEU* 3.9 23.3 - - + -
164A VAL 4.7 0.2 - - - -
165A LEU* 3.8 28.9 - - + -
187A PHE* 4.5 2.5 - + - -
188A TRP* 3.5 28.5 - + + -
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Residues in contact with SER 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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116A ARG* 2.7 26.5 + - - +
117A LYS* 3.2 8.7 + - - -
119A PHE* 1.3 75.3 - - - +
121A GLN* 1.3 59.3 + - - +
123A ALA* 3.2 2.3 + - - +
124A ILE* 2.8 42.4 + - - +
184A VAL* 3.7 17.1 - - - +
185A GLU* 5.6 0.5 + - - -
188A TRP* 3.1 24.7 + - - -
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Residues in contact with GLN 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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117A LYS* 2.9 45.8 + - + +
118A GLU* 3.5 14.0 - - - +
120A SER* 1.3 73.0 - - - +
122A ALA* 1.3 56.7 + - - +
124A ILE* 4.4 6.7 - - + +
125A SER* 2.6 44.2 + - - -
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Residues in contact with ALA 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 GLU 2.9 13.4 + - - +
119A PHE 3.4 10.1 - - - +
120A SER 3.2 0.2 - - - -
121A GLN* 1.3 77.3 - - - +
123A ALA* 1.3 60.5 + - - +
125A SER* 4.2 0.7 - - - -
126A ALA* 3.8 2.3 + - - +
131A TRP 4.8 0.7 - - - +
132A ALA* 4.0 9.5 - - + +
145A ILE* 3.9 25.1 - - + -
147A GLN* 2.9 42.6 + - + +
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Residues in contact with ALA 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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119A PHE 3.1 11.5 + - - +
120A SER 3.6 6.7 - - - +
121A GLN 3.2 0.2 - - - -
122A ALA* 1.3 75.8 - - - +
124A ILE* 1.3 65.3 + - - +
125A SER 3.3 0.3 + - - -
126A ALA 3.5 4.3 + - - -
132A ALA* 3.9 11.2 - - + +
165A LEU* 3.7 31.2 - - + -
167A VAL* 3.5 26.0 - - + +
180A ARG* 3.2 14.4 + - - -
184A VAL* 3.8 12.1 - - + -
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Residues in contact with ILE 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 SER* 2.8 37.8 + - - +
121A GLN* 4.2 4.7 - - - +
123A ALA* 1.3 72.7 - - - +
125A SER* 1.3 60.4 + - - +
180A ARG* 2.8 30.3 + - + +
181A PRO* 3.8 43.7 - - + +
184A VAL* 4.0 22.0 - - + -
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Residues in contact with SER 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 GLN* 2.6 27.1 + - - +
122A ALA* 4.2 0.3 - - - -
124A ILE* 1.3 77.9 - - - +
126A ALA* 1.3 65.4 + - - +
127A GLU* 3.3 11.6 + - - +
147A GLN* 3.1 16.0 + - - +
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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