Contacts of the helix formed by residues 109 - 122 (chain A) in PDB entry 1MMM
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 VAL 109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A LEU* 3.8 29.8 - - + -
99A LYS* 4.4 11.7 - - + -
102A ILE* 4.1 10.8 - - + -
103A GLU* 4.1 26.8 + - + +
108A SER* 1.3 73.4 - - - +
110A ASP* 1.3 59.4 + - - +
112A PHE* 3.1 6.7 + - + +
113A LYS* 2.9 56.6 + - + +
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Residues in contact with ASP 110 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A SER* 3.1 10.3 + - - +
109A VAL* 1.3 77.4 - - - +
111A ASN* 1.3 66.8 + - - +
113A LYS* 3.9 9.4 - - - +
114A ALA* 3.0 25.7 + - - +
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Residues in contact with ASN 111 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A PHE* 2.9 31.5 + - + +
107A GLY* 3.9 8.5 - - - -
108A SER* 3.2 19.1 + - - +
110A ASP* 1.3 78.4 - - - +
112A PHE* 1.3 63.0 + - - +
114A ALA* 3.8 5.0 - - - +
115A GLU* 3.0 27.6 + - - +
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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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94A LEU* 5.7 0.2 - - + -
102A ILE* 3.5 31.4 - - + -
106A PHE* 3.6 34.7 - + + +
108A SER 3.1 5.7 + - - +
109A VAL* 3.1 13.0 + - + +
111A ASN* 1.3 78.5 - - - +
113A LYS* 1.3 75.1 + - + +
115A GLU* 3.1 4.0 + - - +
116A PHE* 2.8 31.6 + + + +
131A LEU* 3.8 26.0 - - + -
140A VAL* 4.0 12.1 - - + -
164A MET* 3.7 24.5 - - + -
189A TRP* 3.8 22.4 - + - -
194A TRP* 3.8 22.4 - + - -
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Residues in contact with LYS 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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94A LEU* 5.7 0.9 - - - -
109A VAL* 2.9 41.4 + - + +
110A ASP* 4.0 10.5 - - - +
112A PHE* 1.3 82.4 - - + +
114A ALA* 1.3 57.2 + - - +
116A PHE* 3.2 0.5 + - - +
117A GLU* 2.8 40.5 + - - +
189A TRP* 3.7 57.5 + - + +
194A TRP* 4.9 12.0 - - - +
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Residues in contact with ALA 114 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A ASP 3.0 17.8 + - - +
111A ASN* 3.8 5.6 - - - +
113A LYS* 1.3 75.2 - - - +
115A GLU* 1.3 61.7 + - - +
117A GLU* 3.5 12.9 + - - +
118A LYS* 3.1 24.4 + - - +
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Residues in contact with GLU 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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106A PHE* 3.5 28.5 - - - -
111A ASN* 3.0 19.1 + - - +
112A PHE* 3.5 4.3 - - - +
114A ALA* 1.3 75.6 - - - +
116A PHE* 1.3 64.8 + - - +
118A LYS* 3.4 9.0 + - + +
119A ALA* 3.1 23.4 + - - +
139A ALA* 5.5 0.2 - - - -
140A VAL* 3.5 29.3 + - + +
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Residues in contact with PHE 116 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A PHE* 2.8 29.2 + + + +
113A LYS 3.6 3.8 - - - +
115A GLU* 1.3 77.0 - - - +
117A GLU* 1.3 59.1 + - - +
119A ALA* 3.2 2.6 + - - +
120A ALA* 2.9 32.3 + - + +
129A ALA* 3.7 24.0 - - + +
130A TRP* 3.7 33.4 - - - -
131A LEU 4.0 0.2 - - - -
140A VAL* 3.8 16.5 - - + +
164A MET* 3.8 22.0 - - - -
166A LEU* 3.9 21.1 - - + -
185A ILE* 5.3 2.2 - - + -
188A PHE* 3.6 23.8 - + - -
189A TRP* 3.5 27.4 - + + -
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Residues in contact with GLU 117 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A LYS* 2.8 28.7 + - - +
114A ALA* 3.8 13.0 + - - +
116A PHE* 1.3 76.3 - - - +
118A LYS* 1.3 56.4 + - - +
120A ALA* 3.3 2.1 + - - +
121A ALA* 2.8 31.9 + - - +
185A ILE* 4.0 24.1 - - + +
186A LYS* 2.9 38.6 + - - +
189A TRP* 3.0 33.9 + - + +
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Residues in contact with LYS 118 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A ALA 3.1 17.9 + - - +
115A GLU* 3.7 9.4 - - + +
117A GLU* 1.3 76.5 - - - +
119A ALA* 1.3 54.1 + - - +
121A ALA* 3.9 4.0 - - - +
122A SER* 2.7 50.2 + - - +
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Residues in contact with ALA 119 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A GLU 3.1 7.8 + - - +
116A PHE 3.2 4.7 + - - +
118A LYS* 1.3 77.1 - - - +
120A ALA* 1.3 62.9 + - - +
122A SER* 3.6 6.2 + - - -
123A ARG* 3.3 23.9 + - - +
129A ALA* 4.4 9.0 - - + -
140A VAL* 3.5 31.6 - - + +
141A VAL* 5.0 2.5 - - - +
142A SER* 4.3 17.2 + - - +
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Residues in contact with ALA 120 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A PHE* 2.9 18.7 + - + +
117A GLU* 3.5 3.8 - - - +
119A ALA* 1.3 79.6 - - - +
121A ALA* 1.3 57.0 + - - +
123A ARG* 3.9 4.1 + - - +
129A ALA* 3.7 21.5 - - + +
166A LEU* 4.4 5.4 - - + -
168A VAL* 3.7 13.7 - - + +
181A ARG* 2.9 26.0 + - - -
185A ILE* 3.4 28.7 - - + -
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Residues in contact with ALA 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 GLU 2.8 21.4 + - - +
118A LYS* 3.9 4.3 - - - +
120A ALA* 1.3 75.4 - - - +
122A SER* 1.3 61.0 + - - +
123A ARG 3.5 1.2 + - - +
181A ARG* 3.5 16.3 + - - +
182A PRO* 5.2 11.9 - - + -
185A ILE* 3.6 13.0 - - + +
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Residues in contact with SER 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* 2.7 39.2 + - - +
119A ALA* 3.6 7.8 + - - -
121A ALA* 1.3 72.4 - - - +
123A ARG* 1.3 61.0 + - - +
124A PHE* 2.8 14.6 + - - +
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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