Contacts of the helix formed by residues 98 - 121 (chain A) in PDB entry 3PEJ
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 98 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A LEU* 3.9 34.8 - - + -
95A GLN* 2.9 32.5 + - + +
96A LYS 3.1 0.4 + - - -
97A GLU* 1.3 71.8 - - - +
99A PHE* 1.3 65.6 + - - +
100A LEU 3.1 2.9 - - - -
101A ARG* 3.1 51.9 + - - +
102A GLU* 3.4 13.4 + - + +
187A ILE* 5.9 1.6 - - + -
196A SER* 5.6 2.0 - - - -
199A LEU* 4.7 4.9 - - + -
267A TYR* 3.7 17.9 - - - +
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Residues in contact with PHE 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A LYS 3.3 23.5 + - - +
97A GLU* 4.0 8.1 - - - -
98A VAL* 1.3 79.2 - - - +
100A LEU* 1.4 79.8 + - + +
102A GLU* 3.4 3.6 + - - +
103A LEU* 3.1 39.0 + - + +
144A LEU* 3.7 26.5 - - + -
146A ILE* 4.8 0.2 - - + -
196A SER* 3.4 42.5 + - - +
197A ALA* 4.1 2.5 - - - +
199A LEU* 4.8 0.4 - - + -
200A VAL* 3.7 17.7 - - + -
245A LEU* 3.6 31.4 - - + -
254A LEU* 3.7 32.8 - - + -
260A LEU* 6.3 0.2 - - + -
263A LEU* 5.3 0.2 - - + -
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Residues in contact with LEU 100 (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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97A GLU 3.9 5.8 - - - +
98A VAL 3.1 0.6 - - - -
99A PHE* 1.4 105.5 - - + +
101A ARG* 1.3 58.3 + - - +
103A LEU* 3.4 2.1 + - + +
104A ILE* 3.0 50.4 + - + +
135A ILE* 4.7 8.7 - - + -
144A LEU* 4.8 5.4 - - + -
146A ILE* 4.1 25.1 - - + -
260A LEU* 4.5 9.0 - - + -
263A LEU* 3.8 31.2 - - + -
264A ILE* 3.9 24.5 - - + +
267A TYR* 3.9 9.9 - - + -
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Residues in contact with ARG 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LEU* 6.1 1.0 - - - +
98A VAL* 3.1 44.3 + - - +
100A LEU* 1.3 76.7 - - - +
102A GLU* 1.3 71.8 + - - +
104A ILE* 4.1 2.9 - - - +
105A SER* 3.2 26.9 + - - -
185A SER* 5.7 8.5 - - - +
267A TYR* 3.5 54.5 - - + +
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Residues in contact with GLU 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A VAL* 3.8 11.3 - - + +
99A PHE 3.6 7.0 - - - +
100A LEU 3.2 0.6 - - - -
101A ARG* 1.3 91.1 + - - +
103A LEU* 1.3 61.3 + - + +
105A SER* 3.2 8.4 + - - -
106A ASN* 2.9 38.8 + - - +
185A SER 5.7 1.0 - - - +
187A ILE* 3.9 27.0 - - + +
188A GLY* 3.4 25.5 + - - -
193A GLY* 3.6 25.3 - - - +
196A SER* 3.6 14.8 - - - +
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Residues in contact with LEU 103 (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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99A PHE* 3.1 37.7 + - + +
100A LEU* 3.4 3.8 + - - +
102A GLU* 1.3 72.8 - - + +
104A ILE* 1.3 60.0 + - - +
106A ASN* 3.4 14.1 + - - +
107A ALA* 3.0 29.3 + - - +
146A ILE* 3.7 43.3 - - + +
194A PHE* 4.1 38.4 - - + +
196A SER* 5.7 0.9 - - - +
197A ALA* 4.7 3.8 - - + -
243A ILE* 4.4 17.9 - - + +
245A LEU* 4.0 16.8 - - + -
1001A BC2 5.3 0.3 + - - -
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Residues in contact with ILE 104 (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 LEU* 3.0 45.0 + - + +
101A ARG 4.1 2.7 - - - +
103A LEU* 1.3 74.8 - - - +
105A SER* 1.4 57.4 + - - +
107A ALA* 3.3 7.7 + - - +
108A ALA* 2.9 27.7 + - - +
133A ILE* 3.8 9.7 - - + +
135A ILE* 4.3 23.6 - - + -
146A ILE* 5.3 2.2 - - + -
264A ILE* 4.8 8.1 - - + -
267A TYR* 4.1 24.2 - - + +
271A ILE* 3.7 28.9 - - + -
275A ILE* 3.8 20.6 - - + -
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Residues in contact with SER 105 (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 ARG* 3.2 16.2 + - - -
102A GLU* 3.2 15.8 + - - -
104A ILE* 1.4 73.2 - - - +
106A ASN* 1.3 66.2 + - - +
108A ALA* 3.3 8.6 + - - +
109A ASP* 3.0 22.6 + - - +
271A ILE* 4.6 7.8 - - - +
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Residues in contact with ASN 106 (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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102A GLU* 2.9 27.0 + - - +
103A LEU* 3.6 16.3 - - + +
105A SER* 1.3 78.5 - - - +
107A ALA* 1.4 55.8 + - - +
109A ASP* 3.2 9.8 + - - +
110A ALA* 3.0 27.7 + - - +
188A GLY* 6.0 1.2 - - - -
193A GLY* 5.3 1.2 - - - -
194A PHE* 4.0 30.6 + - - +
243A ILE* 5.8 1.1 - - + -
1001A BC2 3.8 62.9 + - + +
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Residues in contact with ALA 107 (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 LEU 3.0 17.9 + - - +
104A ILE 3.3 5.8 + - - +
106A ASN* 1.4 73.0 - - - +
108A ALA* 1.4 57.7 + - - +
110A ALA* 3.3 3.3 + - - +
111A LEU* 3.0 34.9 + - - +
133A ILE* 3.8 27.8 - - + -
146A ILE* 4.9 4.5 - - + -
148A ASP* 3.8 19.2 - - + +
1001A BC2 3.9 12.2 + - - +
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Residues in contact with ALA 108 (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 2.9 16.5 + - - +
105A SER* 3.3 6.9 + - - +
107A ALA* 1.4 74.0 - - - +
109A ASP* 1.4 56.5 + - - +
111A LEU* 3.4 3.4 + - - -
112A GLU* 3.0 27.0 + - - +
133A ILE* 4.1 5.6 - - + +
271A ILE* 3.9 24.9 - - + -
272A GLN 5.9 0.4 - - - +
273A PHE* 3.5 26.1 - - + -
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Residues in contact with ASP 109 (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 3.0 13.4 + - - +
106A ASN* 3.2 9.8 + - - +
108A ALA* 1.4 73.5 - - - +
110A ALA* 1.4 63.1 + - - +
112A GLU* 3.4 6.7 + - - +
113A LYS* 2.9 59.4 + - - +
1001A BC2 2.7 31.8 - - - +
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Residues in contact with ALA 110 (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 ASN 3.0 10.7 + - - +
107A ALA 3.6 8.1 - - - +
109A ASP* 1.4 73.0 + - - +
111A LEU* 1.3 62.4 + - - +
113A LYS 3.5 0.7 + - - -
114A ILE 3.4 10.7 + - - -
148A ASP* 3.8 13.2 - - - +
150A GLY* 3.9 0.2 - - - -
151A ILE* 3.0 32.6 + - + +
152A GLY 5.1 1.1 - - - +
1001A BC2 3.6 44.2 - - + +
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Residues in contact with LEU 111 (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 ALA 3.0 20.4 + - - +
108A ALA 3.6 4.7 - - - +
110A ALA* 1.3 73.7 - - - +
112A GLU* 1.4 59.6 + - - +
114A ILE* 3.3 5.6 - - - +
115A ARG* 2.8 29.6 + - - +
131A LEU* 3.7 13.4 - - + +
132A GLU* 3.5 29.4 - - - +
133A ILE* 3.6 28.0 - - + -
148A ASP* 4.5 2.0 - - + -
149A THR 3.4 31.2 - - - +
150A GLY* 4.0 5.4 - - - +
273A PHE* 3.7 34.0 - - + -
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Residues in contact with GLU 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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108A ALA 3.0 17.9 + - - +
109A ASP* 3.4 8.5 + - - +
111A LEU* 1.4 75.0 - - - +
113A LYS* 1.3 56.9 + - - +
115A ARG* 3.0 36.3 + - - -
116A PHE* 2.8 39.4 + - + +
272A GLN* 5.4 6.9 + - - +
273A PHE* 3.6 20.6 - - + -
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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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109A ASP* 2.9 51.2 + - - +
110A ALA 3.7 7.9 - - - +
111A LEU 3.3 0.4 - - - -
112A GLU* 1.3 77.5 - - - +
114A ILE* 1.3 60.2 + - - +
116A PHE* 3.7 7.6 + - - +
117A LEU* 3.4 25.8 + - - +
151A ILE* 3.9 18.4 - - + -
1001A BC2 3.9 37.7 - - + +
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Residues in contact with ILE 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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110A ALA 3.4 2.0 + - - +
111A LEU 3.3 13.2 - - - +
113A LYS* 1.3 76.4 - - - +
115A ARG* 1.4 59.9 + - - +
117A LEU* 3.5 7.8 + - + +
118A SER* 3.1 26.3 + - - -
124A VAL* 3.8 32.8 - - + +
125A LEU* 4.7 5.1 - - + +
131A LEU* 3.9 17.9 - - + -
149A THR 4.0 1.3 - - - +
150A GLY* 3.6 11.0 - - - -
151A ILE* 3.6 42.5 - - + +
211A ASN* 4.3 5.8 - - - +
239A ARG* 3.6 30.1 - - - +
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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 LEU 2.8 17.7 + - - +
112A GLU* 3.0 35.2 + - - +
114A ILE* 1.4 74.1 - - - +
116A PHE* 1.3 65.3 + - - +
118A SER* 2.7 25.2 + - - +
119A LEU* 3.4 47.8 - - + +
131A LEU* 4.2 22.4 - - + -
273A PHE* 3.8 19.3 - - + -
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Residues in contact with PHE 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A GLU* 2.8 28.8 + - + +
113A LYS* 3.9 6.1 - - - +
115A ARG* 1.3 76.8 - - - +
117A LEU* 1.4 77.1 + - + +
119A LEU* 3.5 33.6 + - + +
120A SER* 4.0 6.4 + - - -
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Residues in contact with LEU 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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113A LYS 3.4 10.6 + - - +
114A ILE* 3.9 12.6 - - + +
115A ARG 3.4 0.4 - - - -
116A PHE* 1.4 91.4 - - + +
118A SER* 1.4 55.2 + - - +
119A LEU 3.2 0.4 - - - -
120A SER* 3.0 27.3 + - - +
121A ASP* 3.1 12.3 + - - +
124A VAL* 4.1 20.2 - - + +
151A ILE* 3.9 28.3 - - + -
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Residues in contact with SER 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 ILE 3.1 15.3 + - - -
115A ARG* 2.7 26.2 + - - +
117A LEU* 1.4 75.1 - - - +
119A LEU* 1.3 62.2 + - - +
121A ASP 3.4 11.2 - - - -
122A GLU* 3.2 27.6 + - - +
124A VAL* 3.6 10.5 - - - +
125A LEU* 4.1 25.8 - - - +
131A LEU* 5.1 2.3 - - - +
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Residues in contact with LEU 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* 3.4 49.1 - - + +
116A PHE* 3.5 26.2 - - + +
117A LEU 3.2 0.4 - - - -
118A SER* 1.3 79.3 - - - +
120A SER* 1.3 61.7 + - - +
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Residues in contact with SER 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A PHE* 4.1 9.4 + - - -
117A LEU* 3.0 14.7 + - - +
118A SER 4.3 0.2 - - - -
119A LEU* 1.3 81.7 - - - +
121A ASP* 1.4 60.7 + - - +
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Residues in contact with ASP 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 LEU 3.1 6.5 + - - +
118A SER* 3.4 5.2 - - - -
120A SER* 1.4 77.7 - - - +
122A GLU* 1.4 57.9 + - - +
123A SER* 3.0 36.1 + - - -
124A VAL* 3.4 35.5 - - + +
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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