Contacts of the helix formed by residues 116 - 125 (chain A) in PDB entry 1MUK
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 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A LEU 2.9 23.0 + - - -
103A LEU 4.7 1.1 - - - -
104A GLU* 3.3 24.6 + - - +
114A ARG 3.2 1.2 + - - -
115A LEU* 1.3 72.9 - - - +
117A GLU* 1.3 62.7 + - - +
118A ALA* 3.2 11.1 + - - +
119A ILE* 3.2 34.3 + - - +
120A GLU* 3.1 23.8 + - - +
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Residues in contact with GLU 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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104A GLU* 2.9 24.9 + - - +
115A LEU 3.3 4.2 + - - +
116A SER* 1.3 71.4 - - - +
118A ALA* 1.3 62.6 + - - +
120A GLU* 3.5 6.8 + - + +
121A ASN* 3.0 48.7 + - - +
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Residues in contact with ALA 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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104A GLU* 3.4 6.9 + - - +
116A SER* 3.1 8.9 + - - +
117A GLU* 1.3 80.4 - - - +
119A ILE* 1.3 57.8 + - - +
121A ASN* 3.4 6.1 + - - +
122A ARG* 2.9 51.3 + - - +
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Residues in contact with ILE 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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101A GLU 5.0 1.8 - - - +
102A LEU* 3.9 34.3 - - + +
115A LEU* 4.7 6.1 - - + -
116A SER* 3.1 29.9 + - - +
118A ALA* 1.3 77.0 - - - +
120A GLU* 1.3 57.3 + - - +
122A ARG* 3.4 23.3 + - - +
123A ALA* 2.9 24.4 + - - +
130A ALA* 3.3 16.8 - - + +
133A ALA* 3.8 25.1 - - + -
134A THR* 3.8 10.8 - - - +
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Residues in contact with GLU 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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115A LEU* 3.3 34.0 - - + +
116A SER 3.1 14.8 + - - +
117A GLU* 3.9 8.1 - - + +
118A ALA 3.3 0.2 - - - -
119A ILE* 1.3 76.1 - - - +
121A ASN* 1.3 55.0 + - - +
123A ALA* 3.2 3.3 + - - +
124A LYS* 2.8 56.4 + - - +
134A THR* 3.6 10.9 - - + +
138A ARG* 3.0 35.9 + - - +
669A PRO* 6.0 0.2 - - - +
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Residues in contact with ASN 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* 3.0 40.3 + - - +
118A ALA* 3.9 5.0 - - - +
120A GLU* 1.3 71.9 - - - +
122A ARG* 1.3 66.3 + - - +
123A ALA 3.0 1.6 - - - -
124A LYS* 3.4 31.2 - - - +
125A ASP* 2.9 30.7 + - - +
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Residues in contact with ARG 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 ALA* 2.9 40.5 + - - +
119A ILE* 3.6 25.9 - - - +
121A ASN* 1.3 78.1 - - - +
123A ALA* 1.3 57.9 + - - +
125A ASP* 2.7 27.4 - - - +
127A ASP* 3.0 37.2 + - + +
129A GLN* 5.7 4.9 - - - +
130A ALA* 3.8 13.0 - - + +
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Residues in contact with ALA 123 (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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119A ILE 2.9 17.3 + - - +
120A GLU 3.4 4.5 - - - +
121A ASN 3.0 0.2 - - - -
122A ARG* 1.3 77.7 - - - +
124A LYS* 1.3 59.7 + - - +
125A ASP 3.2 0.4 - - - -
126A GLY* 2.9 20.1 + - - -
127A ASP 4.2 2.2 - - - -
130A ALA* 3.5 5.6 - - - +
131A ARG* 3.6 36.2 - - + +
134A THR* 3.4 20.2 - - + +
669A PRO* 4.5 11.6 - - + +
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Residues in contact with LYS 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 GLU* 2.8 38.3 + - - +
121A ASN* 3.1 34.5 + - - +
123A ALA* 1.3 77.1 - - + +
125A ASP* 1.3 57.5 + - - +
126A GLY 3.2 2.9 + - - -
138A ARG* 3.6 25.5 - - - +
669A PRO* 5.5 6.5 - - + -
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Residues in contact with ASP 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 ASN* 2.9 21.7 + - - +
122A ARG* 2.7 28.3 - - - +
123A ALA 3.2 0.2 - - - -
124A LYS* 1.3 75.8 - - - +
126A GLY* 1.3 57.2 + - - +
127A ASP* 3.8 4.9 + - - +
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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