Contacts of the helix formed by residues 98 - 121 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B LEU* 3.9 34.8 - - + -
95B GLN* 2.9 35.0 + - + +
97B GLU* 1.4 72.5 - - - +
99B PHE* 1.3 65.1 + - - +
100B LEU 3.1 2.9 - - - -
101B ARG* 3.1 52.1 + - - +
102B GLU* 3.4 13.2 + - + +
187B ILE* 5.9 1.8 - - + -
196B SER* 5.6 2.0 - - - -
199B LEU* 4.7 4.9 - - + -
267B TYR* 3.7 18.6 - - + +
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Residues in contact with PHE 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B LYS 3.3 22.6 + - - +
97B GLU* 3.2 10.2 - - - -
98B VAL* 1.3 79.2 - - - +
100B LEU* 1.4 78.5 + - + +
102B GLU* 3.4 3.5 + - - +
103B LEU* 3.1 40.2 + - + +
144B LEU* 3.7 15.5 - - + -
146B ILE* 4.9 0.2 - - + -
196B SER* 3.4 43.8 + - - +
197B ALA* 4.1 1.8 - - - +
199B LEU* 4.9 0.2 - - - +
200B VAL* 3.7 15.3 - - + -
245B LEU* 3.5 32.3 - - + -
254B LEU* 3.4 45.3 - - + -
263B LEU* 5.3 0.4 - - + -
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Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B GLU 3.5 10.9 + - - +
98B VAL 3.1 0.4 - - - -
99B PHE* 1.4 104.2 - - + +
101B ARG* 1.3 62.6 + - - +
103B LEU* 4.0 2.2 - - + +
104B ILE* 3.0 44.9 + - + +
135B ILE* 4.8 8.5 - - + -
144B LEU* 4.6 6.1 - - + -
146B ILE* 4.1 25.4 - - + -
260B LEU* 4.5 9.4 - - + -
263B LEU* 3.8 31.4 - - + -
264B ILE* 3.9 24.9 - - + +
267B TYR* 3.9 5.2 - - + -
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Residues in contact with ARG 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B LEU* 6.1 0.8 - - - +
95B GLN* 6.2 0.2 - - - +
98B VAL* 3.1 43.8 + - - +
100B LEU* 1.3 77.8 - - - +
102B GLU* 1.3 70.6 + - - +
104B ILE* 4.1 2.4 - - - +
105B SER* 3.2 27.3 + - - -
185B SER* 5.7 7.1 - - - +
267B TYR* 3.5 54.3 - - + +
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Residues in contact with GLU 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B VAL* 3.8 11.3 - - + +
99B PHE 3.6 7.2 - - - +
100B LEU 3.2 0.2 - - - -
101B ARG* 1.3 92.6 + - - +
103B LEU* 1.3 60.6 + - + +
105B SER* 3.2 8.0 + - - -
106B ASN* 2.9 38.2 + - - +
185B SER 5.8 0.2 - - - +
187B ILE* 3.9 25.9 - - + +
188B GLY* 3.4 25.8 + - - -
193B GLY* 3.6 25.6 - - - +
196B SER* 3.6 15.5 - - - +
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Residues in contact with LEU 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B PHE* 3.1 36.6 + - + +
100B LEU* 3.4 4.9 + - + +
102B GLU* 1.3 71.8 - - + +
104B ILE* 1.3 59.5 + - - +
106B ASN* 3.4 13.8 + - - +
107B ALA* 3.0 29.7 + - - +
146B ILE* 3.7 42.9 - - + +
193B GLY 5.4 0.2 - - - +
194B PHE* 4.1 37.9 - - + +
196B SER* 5.7 0.7 - - - +
197B ALA* 4.7 3.8 - - + -
243B ILE* 4.4 19.2 - - + +
245B LEU* 4.1 16.4 - - + -
1001B BC2 5.3 0.5 + - - -
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Residues in contact with ILE 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B LEU* 3.0 45.3 + - + +
101B ARG 4.1 3.4 - - - +
103B LEU* 1.3 75.4 - - - +
105B SER* 1.4 56.3 + - - +
107B ALA* 3.3 7.3 + - - +
108B ALA* 2.9 27.7 + - - +
133B ILE* 3.8 11.0 - - + +
135B ILE* 4.3 23.6 - - + -
146B ILE* 5.2 2.0 - - + -
264B ILE* 4.8 11.9 - - + -
267B TYR* 4.1 24.5 - - + +
271B ILE* 3.7 28.9 - - + -
275B ILE* 3.8 16.8 - - + -
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Residues in contact with SER 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B ARG 3.2 16.2 + - - -
102B GLU* 3.2 16.5 + - - -
104B ILE* 1.4 76.2 - - - +
106B ASN* 1.4 58.7 + - - +
108B ALA* 3.3 9.2 + - - +
109B ASP* 3.0 27.8 + - - +
271B ILE* 4.6 7.6 - - - +
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Residues in contact with ASN 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B GLU* 2.9 28.2 + - - +
103B LEU* 3.4 15.6 + - + +
105B SER* 1.4 73.2 + - - +
107B ALA* 1.4 60.2 + - - +
109B ASP* 3.3 8.1 + - - +
110B ALA* 3.1 28.4 + - - +
188B GLY* 6.1 0.7 - - - -
193B GLY* 5.4 0.7 - - - -
194B PHE* 4.1 30.6 + - - +
243B ILE* 5.8 0.9 - - + -
1001B BC2 3.8 63.4 + - + +
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Residues in contact with ALA 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B LEU 3.0 18.3 + - - +
104B ILE 3.4 5.6 - - - +
106B ASN* 1.4 74.3 - - - +
108B ALA* 1.4 57.2 + - - +
110B ALA* 3.3 4.0 + - - +
111B LEU* 3.0 34.9 + - - +
133B ILE* 3.8 28.3 - - + -
146B ILE* 4.9 4.5 - - + -
148B ASP* 3.8 18.2 - - + +
1001B BC2 3.9 11.8 + - - +
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Residues in contact with ALA 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B ILE 2.9 14.5 + - - +
105B SER 3.3 9.2 + - - +
107B ALA* 1.4 73.9 - - - +
109B ASP* 1.4 55.9 + - - +
111B LEU* 3.4 1.5 + - - -
112B GLU* 2.9 26.6 + - - +
133B ILE* 4.1 8.2 - - + +
271B ILE* 3.8 24.2 - - + -
272B GLN 5.9 0.2 - - - +
273B PHE* 3.5 25.6 - - + -
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Residues in contact with ASP 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B SER 3.0 13.4 + - - +
106B ASN* 3.6 9.0 - - - +
107B ALA 3.3 0.2 - - - -
108B ALA* 1.4 74.1 - - - +
110B ALA* 1.4 63.0 + - - +
112B GLU* 3.4 7.2 + - - +
113B LYS* 2.9 60.0 + - - +
1001B BC2 2.7 32.8 - - - +
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Residues in contact with ALA 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B ASN 3.1 10.6 + - - +
107B ALA 3.3 8.9 + - - +
109B ASP* 1.4 74.7 + - - +
111B LEU* 1.3 61.3 + - - +
113B LYS 3.5 1.0 + - - -
114B ILE 3.4 11.1 + - - -
148B ASP* 3.8 12.8 - - - +
150B GLY* 3.9 0.2 - - - -
151B ILE* 3.0 32.4 + - + +
152B GLY 5.1 0.7 - - - +
1001B BC2 3.6 44.6 - - + +
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Residues in contact with LEU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B ALA 3.0 17.8 + - - +
108B ALA 3.6 5.2 - - - +
109B ASP 3.3 0.2 - - - -
110B ALA* 1.3 74.7 - - - +
112B GLU* 1.3 58.7 + - - +
114B ILE* 3.4 4.9 - - - +
115B ARG* 2.9 29.6 + - - +
131B LEU* 3.8 13.6 - - + +
132B GLU 3.5 31.9 - - - +
133B ILE* 3.6 32.3 - - + -
148B ASP* 4.4 2.2 - - + -
149B THR* 3.4 30.3 - - - +
150B GLY* 4.0 5.8 - - - +
273B PHE* 3.7 31.3 - - + -
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Residues in contact with GLU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B ALA 2.9 16.9 + - - +
109B ASP* 3.4 8.7 + - - +
111B LEU* 1.3 74.0 - - - +
113B LYS* 1.3 57.2 + - + +
115B ARG* 3.0 36.1 + - - -
116B PHE* 2.8 40.2 + - + +
272B GLN* 4.9 10.7 + - - +
273B PHE* 3.6 21.2 - - + -
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Residues in contact with LYS 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B ASP* 2.9 51.1 + - - +
110B ALA 3.7 7.4 - - - +
111B LEU 3.3 0.4 - - - -
112B GLU* 1.3 76.7 - - - +
114B ILE* 1.3 60.4 + - - +
116B PHE* 3.9 7.6 - - - +
117B LEU* 3.4 26.2 + - - +
151B ILE* 3.9 20.1 - - + +
1001B BC2 3.9 37.7 - - + +
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Residues in contact with ILE 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B ALA 3.4 1.6 + - - +
111B LEU 3.4 13.9 - - - +
113B LYS* 1.3 75.5 - - - +
115B ARG* 1.4 62.7 + - - +
117B LEU* 3.5 7.2 + - + +
118B SER* 3.1 22.7 + - - -
124B VAL* 3.9 32.8 - - + +
125B LEU* 4.7 4.5 - - + -
131B LEU* 3.9 16.6 - - + -
149B THR 4.0 1.6 - - - +
150B GLY* 3.6 11.9 - - - -
151B ILE* 3.6 45.0 - - + +
211B ASN* 4.3 5.4 - - - +
239B ARG* 3.6 31.2 - - - +
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Residues in contact with ARG 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B LEU 2.9 19.6 + - - +
112B GLU* 3.0 36.4 + - - +
114B ILE* 1.4 75.2 - - - +
116B PHE* 1.3 64.5 + - - +
118B SER* 2.7 24.9 + - - +
119B LEU* 3.4 47.5 - - + +
131B LEU* 4.2 23.1 - - + -
273B PHE* 3.8 19.3 - - + -
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Residues in contact with PHE 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B GLU* 2.8 28.7 + - + +
113B LYS* 3.9 6.5 - - - +
115B ARG* 1.3 77.4 - - - +
117B LEU* 1.4 77.5 + - + +
119B LEU* 3.5 34.5 + - + +
120B SER* 4.0 3.5 + - - -
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Residues in contact with LEU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B LYS 3.4 12.6 + - - +
114B ILE* 3.9 11.0 - - + +
115B ARG 3.4 0.4 - - - -
116B PHE* 1.4 91.2 - - + +
118B SER* 1.4 55.7 + - - +
119B LEU 3.2 0.4 - - - -
120B SER* 3.0 26.1 + - - -
121B ASP* 3.1 12.6 + - - +
124B VAL* 4.1 20.6 - - + +
151B ILE* 3.8 28.3 - - + -
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Residues in contact with SER 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B ILE 3.1 14.6 + - - -
115B ARG* 2.7 26.5 + - - +
117B LEU* 1.4 74.7 - - - +
119B LEU* 1.3 62.0 + - - +
120B SER 3.3 0.2 - - - -
121B ASP 3.4 11.7 - - - -
122B GLU* 3.2 26.9 + - - +
124B VAL* 3.6 11.1 - - - +
125B LEU* 4.1 26.2 - - - +
131B LEU* 5.1 2.4 - - - +
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Residues in contact with LEU 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ARG* 3.4 50.5 - - + +
116B PHE* 3.5 25.8 - - + +
117B LEU 3.2 0.8 - - - -
118B SER* 1.3 79.6 - - - +
120B SER* 1.4 61.4 + - - +
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Residues in contact with SER 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B PHE 4.0 2.4 + - - -
117B LEU* 3.0 15.7 + - - -
118B SER 4.3 0.2 - - - -
119B LEU* 1.4 80.7 - - - +
121B ASP* 1.4 61.1 + - - +
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Residues in contact with ASP 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LEU 3.1 6.0 + - - +
118B SER* 3.4 4.4 - - - -
120B SER* 1.4 78.1 - - - +
122B GLU* 1.4 58.0 + - - +
123B SER* 3.0 31.7 + - - -
124B VAL* 3.4 35.2 + - + +
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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
------------------------------------------------------------
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