Contacts of the helix formed by residues 117 - 132 (chain H) in PDB entry 3MIW
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 117 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112F MET* 4.0 16.8 + - - +
115F LYS* 3.9 28.0 - - + -
116F LEU* 3.8 31.5 - - + +
119F ARG* 4.6 6.3 - - + -
113H ILE* 2.9 20.0 + - - +
114H ASP 3.8 5.6 + - - -
115H LYS 3.4 0.2 - - - -
116H LEU* 1.3 75.3 - - - +
118H THR* 1.3 60.5 + - - +
119H ARG 3.2 0.9 - - - -
120H GLU* 3.5 8.3 - - + -
121H ILE* 3.1 31.2 + - + +
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Residues in contact with THR 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114H ASP* 2.9 18.7 + - - -
115H LYS* 3.5 13.3 - - - -
116H LEU 3.2 0.2 - - - -
117H THR* 1.3 81.5 - - - +
119H ARG* 1.3 65.1 + - - +
121H ILE* 3.5 9.0 + - + +
122H GLU* 2.9 41.6 + - + +
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Residues in contact with ARG 119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115H LYS* 3.2 19.0 + - - +
116H LEU* 3.4 10.0 + - - +
118H THR* 1.3 82.7 - - - +
120H GLU* 1.3 62.2 + - - +
122H GLU* 2.9 37.0 + - - +
123H GLN* 3.2 29.8 + - - +
117J THR* 4.7 10.4 - - + +
120J GLU* 3.9 25.4 - - + -
121J ILE* 5.1 14.9 - - - +
124J ILE* 3.7 9.5 - - + +
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Residues in contact with GLU 120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F LEU* 3.1 31.6 - - + +
119F ARG* 4.2 17.3 - - + +
120F GLU* 2.6 26.0 - - - +
123F GLN* 3.1 19.6 + - - +
116H LEU* 3.3 8.7 + - + +
117H THR* 3.5 12.1 - - + +
118H THR 3.2 0.2 - - - -
119H ARG* 1.3 79.8 - - - +
121H ILE* 1.3 57.9 + - - +
122H GLU 3.3 0.2 - - - -
123H GLN* 3.3 7.3 + - - +
124H ILE* 3.3 24.6 + - - +
120J GLU* 2.8 38.5 - - - +
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Residues in contact with ILE 121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115F LYS* 5.3 5.4 - - + -
119F ARG* 3.8 42.6 - - + +
117H THR* 3.1 22.4 + - + +
118H THR* 4.0 7.4 - - + +
119H ARG 3.4 0.2 - - - -
120H GLU* 1.3 76.3 - - - +
122H GLU* 1.3 62.2 + - - +
124H ILE* 2.8 29.4 - - + +
125H GLU* 3.1 20.9 - - + +
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Residues in contact with GLU 122 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118H THR* 2.9 29.4 + - + +
119H ARG* 2.9 42.6 + - - +
120H GLU 3.3 0.4 - - - -
121H ILE* 1.3 75.1 - - - +
123H GLN* 1.3 65.8 + - - +
125H GLU* 3.0 7.4 + - - +
126H LEU* 2.9 26.0 + - + +
124J ILE* 3.1 30.9 - - + +
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Residues in contact with GLN 123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A GLN* 5.2 0.4 + - - +
123F GLN* 2.9 34.2 + - - +
119H ARG 3.2 14.1 + - - +
120H GLU* 3.3 18.7 - - - +
122H GLU* 1.3 77.7 - - - +
124H ILE* 1.3 55.4 + - - +
126H LEU* 3.2 3.2 + - - +
127H LEU* 2.9 33.8 + - - +
120J GLU* 3.3 15.3 + - - +
123J GLN* 2.6 54.3 + - - +
124J ILE* 3.1 17.0 - - + +
127J LEU* 3.9 17.1 - - + +
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Residues in contact with ILE 124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119F ARG* 4.7 7.9 - - + +
122F GLU* 3.6 50.9 - - + +
123F GLN* 3.6 14.1 - - + +
126F LEU* 3.3 36.9 - - + +
120H GLU 3.3 8.0 + - - +
121H ILE* 2.8 44.2 - - + +
123H GLN* 1.3 78.7 - - - +
125H GLU* 1.3 72.4 + - - +
127H LEU* 4.1 2.0 - - - -
128H LYS* 3.6 6.1 + - + +
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Residues in contact with GLU 125 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121H ILE* 3.1 23.9 - - + +
122H GLU* 3.0 8.4 + - - +
123H GLN 3.0 0.8 - - - -
124H ILE* 1.3 91.2 - - - +
126H LEU* 1.3 53.9 + - - +
127H LEU 3.0 1.3 - - - -
128H LYS* 2.6 32.3 + - - +
129H ARG* 2.7 29.9 + - - +
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Residues in contact with LEU 126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122H GLU* 2.9 15.4 + - + +
123H GLN 3.8 4.3 - - - +
125H GLU* 1.3 75.0 - - - +
127H LEU* 1.3 57.3 + - - +
129H ARG* 3.7 15.6 - - - +
130H ILE* 2.8 37.5 + - - +
124J ILE* 3.4 42.0 - - + +
127J LEU* 3.7 17.7 - - + +
128J LYS* 3.4 29.6 - - + +
131J HIS* 4.2 17.4 - - + +
132J ASP* 5.7 0.4 - - - +
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Residues in contact with LEU 127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D GLN* 5.4 0.2 - - - +
127D LEU* 6.3 0.7 - - + -
123F GLN* 3.6 41.3 - - + +
126F LEU* 3.0 33.6 - - + +
127F LEU* 4.4 17.0 - - + -
130F ILE* 3.7 21.6 - - + +
123H GLN 2.9 16.8 + - - +
126H LEU* 1.3 76.5 - - - +
128H LYS* 1.3 53.3 + - - +
130H ILE* 3.9 4.9 - - + +
131H HIS* 2.7 36.7 + - - +
127J LEU* 3.6 29.6 - - + -
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Residues in contact with LYS 128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126F LEU* 3.3 28.9 - - + +
129F ARG* 5.1 12.1 - - - +
124H ILE* 3.7 8.3 - - + +
125H GLU* 2.6 24.3 + - - +
127H LEU* 1.3 74.8 - - - +
129H ARG* 1.3 55.0 + - + +
131H HIS* 4.2 8.5 - - - +
132H ASP* 2.7 66.8 + - - +
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Residues in contact with ARG 129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125H GLU* 2.7 35.3 + - + +
126H LEU* 3.8 13.5 - - - +
128H LYS* 1.3 72.5 - - + +
130H ILE* 1.3 60.5 + - - +
132H ASP* 4.0 8.2 - - - +
133H ASN* 3.7 15.1 + - - +
131J HIS* 3.6 40.2 + - + +
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Residues in contact with ILE 130 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F ILE* 5.0 12.3 - - + -
126H LEU 2.8 23.9 + - - +
127H LEU* 3.9 4.3 - - + +
129H ARG* 1.3 74.1 - - - +
131H HIS* 1.3 73.2 + - - +
133H ASN* 2.8 23.6 + - - +
127J LEU* 3.1 42.2 - - + +
130J ILE* 3.8 14.1 - - + -
131J HIS* 3.1 33.7 - - + +
134J LEU* 3.7 22.5 - - + +
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Residues in contact with HIS 131 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126F LEU* 3.9 13.7 - - + -
129F ARG* 3.9 17.0 - - + +
130F ILE* 3.6 46.2 - - + +
133F ASN* 3.6 22.6 + - - -
127H LEU 2.7 25.5 + - - +
128H LYS* 3.7 10.7 - - + +
130H ILE* 1.3 74.1 - - - +
132H ASP* 1.3 71.3 + - - +
133H ASN 2.6 20.6 + - - -
134H LEU* 3.4 13.8 + - - +
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Residues in contact with ASP 132 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35H EDO 4.0 5.0 + - - -
128H LYS* 2.7 51.3 + - - +
129H ARG* 4.0 8.8 + - - +
131H HIS* 1.3 88.8 + - - +
133H ASN* 1.3 51.4 + - - +
134H LEU* 2.8 18.7 + - - -
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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