Contacts of the helix formed by residues 109 - 130 (chain A) in PDB entry 1R42
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 109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A LEU* 1.3 73.5 - - - +
110A GLU* 1.3 55.3 + - - +
111A ASP* 3.1 6.1 + - - +
112A LYS* 2.5 55.3 + - - +
113A SER 3.1 6.5 + - - -
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Residues in contact with GLU 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A LEU 3.6 4.0 + - - -
109A SER* 1.3 69.1 - - - +
111A ASP* 1.3 62.9 + - - +
113A SER* 4.1 9.8 - - - -
114A LYS* 2.9 36.8 + - + +
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Residues in contact with ASP 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A SER* 2.8 8.5 + - - +
110A GLU* 1.3 80.8 - - - +
112A LYS* 1.3 62.4 + - + +
114A LYS* 3.9 5.8 - - - +
115A ARG* 3.2 21.8 + - - +
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Residues in contact with LYS 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A LEU* 3.9 21.3 - - + -
109A SER* 2.5 36.5 + - - +
111A ASP* 1.3 70.8 - - + +
113A SER* 1.3 53.6 + - - +
114A LYS 3.1 1.6 - - - -
115A ARG* 3.0 6.8 + - + +
116A LEU* 2.8 36.4 + - - +
186A LEU* 4.0 23.3 - - + +
189A GLU* 2.6 33.5 + - - +
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Residues in contact with SER 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A SER* 3.2 29.0 + - - -
106A SER* 4.8 1.7 - - - -
108A LEU* 3.3 23.8 + - - +
109A SER 3.1 2.1 + - - -
110A GLU* 3.9 15.4 - - - -
112A LYS* 1.3 77.7 - - - +
114A LYS* 1.3 57.6 + - - +
116A LEU* 3.5 3.8 + - - +
117A ASN* 3.0 41.0 + - - -
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Residues in contact with LYS 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A GLU* 2.9 27.9 + - + +
111A ASP* 3.9 7.9 - - - +
113A SER* 1.3 78.2 - - - +
115A ARG* 1.3 63.2 + - - +
117A ASN* 3.3 8.9 + - - +
118A THR* 3.0 40.3 + - - +
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Residues in contact with ARG 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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111A ASP 3.2 15.7 + - - +
112A LYS* 3.0 7.5 + - + +
114A LYS* 1.3 79.9 - - - +
116A LEU* 1.3 59.2 + - - +
118A THR* 3.1 27.7 + - - +
119A ILE* 2.8 40.8 + - + +
179A LEU* 4.6 10.9 - - - +
182A GLU* 2.7 44.7 + - - +
186A LEU* 4.1 10.8 - - + -
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Residues in contact with LEU 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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105A SER* 4.1 21.3 - - - +
108A LEU* 4.1 17.0 - - + -
112A LYS 2.8 19.8 + - - +
113A SER* 3.8 6.1 - - - +
115A ARG* 1.3 72.6 - - - +
117A ASN* 1.3 60.8 + - - +
119A ILE* 3.2 5.7 + - + +
120A LEU* 2.9 47.2 + - + +
183A TYR* 4.4 13.2 - - + +
186A LEU* 4.1 28.7 - - + +
187A LYS* 3.9 35.0 - - + +
190A MET* 5.5 1.6 - - + -
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Residues in contact with ASN 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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105A SER* 5.8 2.6 + - - -
113A SER* 3.0 28.3 + - - +
114A LYS* 3.7 7.4 - - - +
116A LEU* 1.3 76.6 - - - +
118A THR* 1.3 61.0 + - - +
120A LEU* 3.3 17.7 + - - +
121A ASN* 2.9 43.0 + - - +
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Residues in contact with THR 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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114A LYS* 3.0 34.7 + - - +
115A ARG* 3.4 30.3 - - - +
117A ASN* 1.3 76.1 - - - +
119A ILE* 1.3 55.1 + - - +
121A ASN* 3.2 8.0 + - - +
122A THR* 2.6 45.3 + - - +
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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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115A ARG* 2.8 33.5 + - - +
116A LEU* 3.2 8.5 + - + +
118A THR* 1.3 77.4 - - + +
120A LEU* 1.3 62.8 + - - +
122A THR* 3.8 6.1 - - - -
123A MET* 3.0 38.4 + - + +
179A LEU* 3.6 33.2 - - + +
182A GLU* 3.3 48.9 - - + +
183A TYR* 4.0 10.5 - - + +
186A LEU* 4.1 12.1 - - + -
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Residues in contact with LEU 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 LEU* 2.9 38.8 + - + +
117A ASN* 3.7 16.4 - - - +
119A ILE* 1.3 76.1 - - - +
121A ASN* 1.3 66.3 + - - +
123A MET* 3.9 9.8 - - + +
124A SER* 2.9 25.6 + - - -
183A TYR* 3.8 24.2 - - + -
187A LYS* 4.5 4.5 - - - +
507A SER 4.7 3.1 - - - +
508A ASN 5.5 0.7 - - - -
509A ASP* 3.8 36.3 - - + +
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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 ASN* 2.9 32.6 + - - +
118A THR* 3.7 6.0 - - - +
120A LEU* 1.3 77.7 - - - +
122A THR* 1.3 56.8 + - - +
124A SER* 3.4 6.6 + - - -
125A THR* 2.9 38.4 + - + +
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Residues in contact with THR 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A THR* 2.6 33.5 + - - +
119A ILE* 3.8 5.6 - - - -
121A ASN* 1.3 74.2 - - - +
123A MET* 1.3 65.1 + - - +
125A THR* 3.0 10.1 + - - +
126A ILE* 3.0 35.4 + - + +
179A LEU* 3.8 26.2 - - + -
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Residues in contact with MET 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 ILE* 3.0 25.9 + - + +
120A LEU* 3.9 9.9 - - + +
122A THR* 1.3 76.4 - - - +
124A SER* 1.3 62.6 + - - +
126A ILE* 3.6 4.0 + - - +
127A TYR* 3.1 23.7 + - - +
176A LEU* 3.9 22.2 - - + +
179A LEU* 3.7 21.8 - - + -
180A TYR* 3.8 37.7 - - + -
183A TYR* 3.6 37.5 - - + -
506A VAL 5.1 0.2 - - - +
507A SER* 3.6 32.2 - - - +
509A ASP* 5.7 0.4 - - + -
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Residues in contact with SER 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 LEU 2.9 18.6 + - - -
121A ASN* 3.5 9.4 - - - -
123A MET* 1.3 78.5 - - - +
125A THR* 1.3 62.5 + - - +
127A TYR* 3.4 5.4 + - - +
128A SER* 3.1 23.6 + - - -
507A SER 4.3 1.8 + - - -
508A ASN* 2.9 31.8 + - - +
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Residues in contact with THR 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 19.5 + - + +
122A THR* 3.0 14.1 + - - +
124A SER* 1.3 75.5 - - - +
126A ILE* 1.3 64.5 + - - +
127A TYR 3.0 2.0 - - - -
128A SER* 3.1 6.7 + - - +
129A THR* 2.7 43.3 + - - +
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Residues in contact with ILE 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 THR* 3.0 29.2 + - + +
123A MET 3.6 2.2 - - - +
125A THR* 1.3 79.4 + - - +
127A TYR* 1.3 62.0 + - - +
129A THR* 4.0 7.6 - - - -
130A GLY* 2.8 28.1 + - - +
172A VAL* 3.5 34.6 - - + +
175A GLN* 4.3 24.7 - - + +
176A LEU* 3.1 43.1 - - + -
179A LEU* 4.9 4.0 - - + -
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Residues in contact with TYR 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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123A MET 3.1 14.5 + - - +
124A SER 3.5 5.2 - - - +
125A THR 3.0 0.6 - - - -
126A ILE* 1.3 88.1 - - + +
128A SER* 1.3 68.0 + - - +
129A THR 3.6 0.3 + - - -
130A GLY 4.3 0.3 + - - +
144A LEU* 3.2 32.9 - - + +
168A TRP* 3.6 31.9 - + - -
176A LEU* 5.2 2.7 - - + -
271A TRP* 3.5 11.4 - - - -
501A ALA 4.3 5.6 - - - -
502A SER* 3.5 17.0 - - - -
503A LEU 3.6 0.9 - - - -
504A PHE* 3.0 53.0 + + + +
507A SER* 3.4 20.6 - - - +
508A ASN* 3.9 12.8 - - - +
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Residues in contact with SER 128 (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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124A SER* 3.1 13.8 + - - -
125A THR* 3.1 9.8 + - - +
127A TYR* 1.3 86.3 - - - +
129A THR* 1.3 61.4 + - - +
130A GLY 5.2 0.7 - - - -
143A LEU* 4.8 14.1 - - - +
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Residues in contact with THR 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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125A THR* 2.7 34.5 + - - +
126A ILE* 4.0 4.9 - - - -
128A SER* 1.3 82.9 - - - +
130A GLY* 1.3 68.1 + - - +
131A LYS* 3.7 15.9 + - - +
143A LEU* 5.0 5.2 - - - +
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Residues in contact with GLY 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 ILE* 2.8 22.5 + - - -
127A TYR 4.3 1.3 + - - +
128A SER 3.8 0.7 - - - -
129A THR* 1.3 82.2 + - - +
131A LYS* 1.3 59.6 + - - +
143A LEU* 3.8 15.9 - - - +
144A LEU 4.2 1.2 + - - -
168A TRP* 3.8 9.8 - - - -
172A VAL* 3.9 18.2 - - - -
175A GLN* 5.6 3.4 - - - -
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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
------------------------------------------------------------
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