Contacts of the helix formed by residues 113 - 133 (chain A) in PDB entry 3L32
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 ARG 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A GLY 3.8 1.0 + - - -
112A GLU* 1.3 85.1 + - - +
114A PHE* 1.4 69.7 - - - +
115A LEU* 3.7 36.6 - - - +
116A LYS* 3.1 24.1 + - + +
117A ILE* 3.3 11.2 + - - +
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Residues in contact with PHE 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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104A ILE* 3.7 24.7 - - + -
108A MET* 3.9 28.0 - - + +
112A GLU 3.5 2.8 + - - -
113A ARG* 1.4 73.5 - - - +
115A LEU* 1.3 61.2 + - + +
117A ILE* 3.0 12.4 + - + +
118A TRP* 2.7 62.5 + + + +
101B GLY* 3.7 21.3 - - - -
104B ILE* 3.7 22.4 - - + -
105B VAL* 3.4 22.2 - - + -
108B MET* 3.7 20.2 - - + -
114B PHE* 3.8 12.3 - + - -
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Residues in contact with LEU 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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113A ARG* 3.2 32.8 - - + +
114A PHE* 1.3 84.1 - - + +
116A LYS* 1.3 57.5 + - - +
118A TRP* 3.7 9.5 - - + +
119A SER* 3.0 28.6 + - - -
98B ASP 5.5 0.7 - - - +
101B GLY* 3.7 34.3 - - - +
102B VAL* 4.1 16.4 - - + +
105B VAL* 3.8 20.6 - - + -
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Residues in contact with LYS 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 GLU* 3.3 40.2 - - + +
113A ARG* 3.1 26.3 + - + +
115A LEU* 1.3 75.8 - - - +
117A ILE* 1.4 64.9 + - + +
119A SER* 2.8 22.9 + - - +
120A GLN* 3.2 41.7 + - + +
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Residues in contact with ILE 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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103A GLN 5.6 0.2 - - - -
104A ILE* 4.2 28.0 - - + -
107A GLN* 3.6 28.9 - - + +
108A MET* 3.6 44.9 - - + +
112A GLU* 3.9 19.7 - - + +
113A ARG 3.3 13.4 + - - +
114A PHE* 3.0 8.2 + - - +
116A LYS* 1.4 76.1 - - + +
118A TRP* 1.3 60.7 - - - +
120A GLN* 3.1 16.7 + - - +
121A THR* 2.9 32.1 + - + +
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Residues in contact with TRP 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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100A VAL* 5.4 0.2 - - + -
104A ILE* 3.8 10.3 - - + -
114A PHE* 2.7 40.0 + + + +
115A LEU* 3.7 13.2 - - + +
116A LYS 3.2 0.2 - - - -
117A ILE* 1.3 78.7 - - - +
119A SER* 1.3 65.8 + - - +
120A GLN 3.2 0.2 + - - -
121A THR* 3.2 17.5 + - - -
122A VAL* 2.9 46.8 + - + +
125A ILE* 4.2 14.6 - - + -
97B LEU* 2.9 36.6 + - + -
98B ASP* 4.8 6.3 - - - -
100B VAL* 3.9 21.5 - - + -
101B GLY* 3.3 22.1 - - - -
104B ILE* 4.3 2.7 - - + -
118B TRP* 3.5 39.7 - + - -
125B ILE* 4.5 2.5 - - + -
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Residues in contact with SER 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 LEU 3.0 15.6 + - - -
116A LYS* 2.8 23.6 + - - +
118A TRP* 1.3 78.7 - - - +
120A GLN* 1.3 63.0 + - - +
122A VAL* 3.7 18.3 - - - +
123A GLU* 3.9 10.0 + - - +
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Residues in contact with GLN 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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107A GLN* 6.0 2.3 - - - +
116A LYS* 3.4 43.2 - - + +
117A ILE* 3.1 14.0 + - - +
119A SER* 1.3 79.0 + - - +
121A THR* 1.3 66.4 + - + +
123A GLU* 3.2 24.9 + - - +
124A GLU* 3.9 4.7 + - - +
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Residues in contact with THR 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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100A VAL* 4.2 16.8 - - + +
103A GLN* 4.4 12.8 - - + +
104A ILE* 3.9 21.6 - - + +
117A ILE* 2.9 26.9 + - + +
118A TRP* 3.2 30.4 + - - -
120A GLN* 1.3 70.9 - - + +
122A VAL* 1.3 66.4 + - - +
123A GLU 3.0 1.8 - - - -
124A GLU* 2.8 34.3 + - - +
125A ILE* 3.2 14.9 + - - +
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Residues in contact with VAL 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 TRP* 2.9 53.4 + - + +
119A SER* 3.7 10.8 - - - +
120A GLN 3.3 0.2 - - - -
121A THR* 1.3 75.3 + - - +
123A GLU* 1.3 60.6 + - + +
125A ILE* 3.0 10.5 + - - +
126A VAL* 2.8 36.3 + - + +
94B GLN* 3.9 23.8 - - - +
97B LEU* 3.8 29.6 - - + +
98B ASP* 4.9 4.9 - - - +
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Residues in contact with GLU 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 SER 4.0 10.1 - - - +
120A GLN* 3.4 16.2 - - - +
121A THR 3.0 0.8 - - - -
122A VAL* 1.3 80.4 - - - +
124A GLU* 1.3 60.6 + - + +
126A VAL* 4.1 11.3 - - - +
127A SER* 3.0 30.3 + - - +
94B GLN* 5.3 4.1 - - - +
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Residues in contact with GLU 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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96A TYR* 2.9 33.1 + - + +
100A VAL* 3.5 14.4 - - + +
103A GLN* 2.6 42.8 + - - +
120A GLN 4.7 2.8 - - - +
121A THR* 2.8 23.6 + - - +
123A GLU* 1.3 78.9 - - + +
125A ILE* 1.3 59.3 + - - +
127A SER* 3.4 4.5 + - - -
128A TYR* 3.0 20.4 + - - +
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Residues in contact with ILE 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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93A PHE* 4.3 17.3 - - + -
96A TYR* 4.4 5.8 - - + -
97A LEU* 3.8 25.1 - - + -
100A VAL* 4.6 18.6 - - + -
118A TRP* 4.2 25.6 - - + -
121A THR 3.7 12.1 - - - +
122A VAL* 3.0 10.0 + - - +
124A GLU* 1.3 75.4 - - - +
126A VAL* 1.4 66.3 + - - +
128A TYR* 3.2 3.0 + - - +
129A VAL* 3.0 23.6 + - - +
93B PHE* 3.9 24.5 - - + -
97B LEU* 3.9 13.7 - - + -
118B TRP* 4.7 0.9 - - + -
125B ILE* 4.4 9.6 - - + -
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Residues in contact with VAL 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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122A VAL* 2.8 27.3 + - + +
123A GLU* 4.1 12.1 - - - +
125A ILE* 1.4 74.7 - - - +
127A SER* 1.3 62.7 + - - +
129A VAL* 3.3 3.3 + - - +
130A THR* 3.0 34.0 + - - +
90B ASN 5.7 9.0 - - - +
93B PHE* 4.2 17.9 - - + -
94B GLN* 4.2 16.6 - - + +
97B LEU* 3.9 18.8 - - + -
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Residues in contact with SER 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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96A TYR* 5.3 1.1 - - - -
123A GLU* 3.0 21.6 + - - +
124A GLU* 3.8 5.8 - - - -
126A VAL* 1.3 76.9 - - - +
128A TYR* 1.3 66.1 + - - +
130A THR* 3.3 8.4 + - - -
131A VAL* 3.1 28.9 + - - +
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Residues in contact with TYR 128 (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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90A ASN* 4.3 2.1 + - - -
92A LEU* 3.2 26.4 - - + +
93A PHE* 3.2 57.0 + + + +
96A TYR* 3.5 49.8 + + + -
124A GLU 3.0 18.3 + - - +
125A ILE* 3.5 5.4 - - - +
127A SER* 1.3 77.7 - - - +
129A VAL* 1.3 67.2 + - + +
131A VAL* 3.1 3.4 + - - -
132A ASN* 2.9 60.6 + - + +
133A PHE* 4.0 6.7 - + - -
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Residues in contact with VAL 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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93A PHE* 3.8 23.3 - - + -
125A ILE 3.0 16.5 + - - +
126A VAL 3.9 2.2 - - - +
128A TYR* 1.3 74.4 - - - +
130A THR* 1.3 56.5 + - - +
133A PHE* 2.9 50.4 + - + +
93B PHE* 3.6 28.9 - - + -
129B VAL* 4.0 11.2 - - + -
133B PHE* 4.0 34.1 - - + -
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Residues in contact with THR 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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126A VAL* 3.0 22.8 + - - +
127A SER* 3.4 13.8 - - - -
129A VAL* 1.3 77.5 - - - +
131A VAL* 1.3 64.0 + - + +
133A PHE 4.0 8.6 - - - +
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Residues in contact with VAL 131 (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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127A SER* 3.1 17.1 + - - +
128A TYR* 3.1 3.6 + - - +
130A THR* 1.3 81.0 - - + +
132A ASN* 1.3 81.8 + - - +
133A PHE 3.7 1.4 - - - +
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Residues in contact with ASN 132 (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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92A LEU* 4.4 11.4 - - - +
128A TYR* 2.9 68.9 + - + +
131A VAL* 1.3 96.6 - - - +
133A PHE* 1.3 71.1 + - + +
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Residues in contact with PHE 133 (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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90A ASN* 3.5 27.4 - - - -
93A PHE* 4.4 8.1 - + - -
128A TYR* 4.0 23.1 - + - -
129A VAL* 2.9 32.3 + - + +
130A THR* 4.0 9.5 - - - +
131A VAL 4.8 1.4 - - - +
132A ASN* 1.3 87.3 - - + +
129B VAL* 3.7 36.1 - - + -
130B THR* 5.1 8.3 - - - -
133B PHE* 3.9 37.0 - - + -
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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