Contacts of the helix formed by residues 103 - 126 (chain B) in PDB entry 2PO5
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 ILE 103 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B LEU 3.4 1.2 + - - -
102B PRO* 1.3 85.9 - - + +
104B GLN* 1.3 59.9 + - - +
105B ASN* 3.3 2.9 - - - -
106B LYS* 3.0 36.1 + - + +
107B LEU* 2.9 47.4 + - + -
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Residues in contact with GLN 104 (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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93B PHE 2.8 28.4 + - - +
94B LEU* 3.6 11.0 - - + -
95B ASP 3.7 2.2 + - - -
96B ARG* 3.4 35.0 + - - +
99B MET* 3.0 25.2 + - - +
100B THR* 3.5 3.3 - - - -
101B LEU* 3.1 42.1 + - + +
102B PRO 2.8 8.0 + - - -
103B ILE* 1.3 72.3 - - - +
105B ASN* 1.3 60.9 + - - +
106B LYS 2.9 0.2 + - - -
107B LEU* 4.4 2.5 - - - +
108B ALA* 2.8 35.8 + - + +
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Residues in contact with ASN 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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94B LEU* 3.8 21.8 - - + +
96B ARG* 5.2 6.4 + - - +
103B ILE 3.3 0.8 - - - -
104B GLN* 1.3 78.1 - - - +
106B LYS* 1.3 67.8 + - + +
109B PRO* 3.2 19.0 - - - +
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Residues in contact with LYS 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ILE* 3.0 38.5 + - + +
104B GLN 3.0 0.6 - - - -
105B ASN* 1.3 88.0 - - + +
107B LEU* 1.3 65.1 + - + +
108B ALA 3.4 0.4 - - - -
109B PRO* 3.2 14.9 - - - +
110B PHE* 3.9 8.1 + - - +
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Residues in contact with LEU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LEU* 4.9 5.6 - - + -
102B PRO* 3.0 28.9 - - + +
103B ILE* 2.9 29.4 + - + +
104B GLN* 4.1 3.4 - - - +
106B LYS* 1.3 77.9 - - + +
108B ALA* 1.3 65.2 + - - +
110B PHE* 3.0 13.9 + - + +
111B ILE* 2.8 39.2 + - + +
503B CHD 3.9 49.1 - - + -
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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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90B LEU* 4.0 3.5 - - + +
93B PHE* 3.9 31.1 - - + +
94B LEU* 3.5 28.3 - - + -
101B LEU* 5.5 1.3 - - - +
104B GLN* 2.8 24.3 + - + +
107B LEU* 1.3 73.1 - - - +
109B PRO* 1.3 68.9 - - + +
111B ILE* 3.2 5.3 + - - +
112B ALA* 3.0 23.9 + - - +
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Residues in contact with PRO 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B HIS* 4.4 7.3 + - + -
90B LEU* 3.5 24.7 - - + -
94B LEU* 5.0 0.7 - - + -
105B ASN 3.2 24.0 - - - +
106B LYS* 3.2 18.2 - - - +
108B ALA* 1.3 92.9 - - + +
110B PHE* 1.3 60.6 + - - +
112B ALA* 3.4 3.4 + - + +
113B LYS* 3.1 22.7 + - - +
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Residues in contact with PHE 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 LYS 4.0 9.0 - - - +
107B LEU* 3.0 19.6 + - + +
109B PRO* 1.3 81.3 - - - +
111B ILE* 1.3 72.9 + - + +
113B LYS* 3.1 16.9 + - + +
114B ARG* 3.2 46.0 + - + +
503B CHD 5.3 15.5 - - + -
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Residues in contact with ILE 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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93B PHE* 3.8 35.7 - - + -
101B LEU* 4.4 21.8 - - + -
107B LEU* 2.8 35.8 + - + +
108B ALA 3.7 4.3 - - - +
110B PHE* 1.3 81.9 - - + +
112B ALA* 1.3 61.7 + - - +
114B ARG* 3.2 10.3 - - - +
115B LEU* 3.1 31.0 + - + +
502B CHD 4.4 18.2 - - + +
503B CHD 4.2 29.8 - - + -
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Residues in contact with ALA 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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86B HIS* 4.0 11.9 - - - +
89B LEU* 3.6 17.1 - - + +
90B LEU* 3.6 34.3 - - + +
93B PHE* 4.7 2.2 - - - -
108B ALA 3.0 16.8 + - - +
109B PRO 3.6 5.4 - - - +
111B ILE* 1.3 78.0 - - - +
113B LYS* 1.3 53.2 + - - +
115B LEU* 3.4 0.4 + - - -
116B THR* 2.6 38.8 + - - -
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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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86B HIS* 4.1 15.0 + - + +
109B PRO 3.1 13.4 + - - +
110B PHE* 3.1 13.2 + - + +
112B ALA* 1.3 79.0 - - - +
114B ARG* 1.3 60.3 + - - +
116B THR* 3.7 5.8 + - - -
117B PRO* 3.4 17.7 - - - +
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Residues in contact with ARG 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 PHE* 3.2 39.7 + - + +
111B ILE* 3.2 20.0 - - - +
113B LYS* 1.3 79.2 - - - +
115B LEU* 1.3 62.7 + - - +
116B THR 3.4 0.2 - - - -
117B PRO* 3.6 10.4 - - - +
118B LYS* 4.9 3.3 + - - +
502B CHD 3.2 42.8 + - - -
503B CHD 5.2 9.9 - - - +
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Residues in contact with LEU 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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89B LEU* 3.7 13.9 - - + -
93B PHE* 3.6 37.2 - - + -
111B ILE* 3.1 23.5 + - + +
114B ARG* 1.3 80.1 - - + +
116B THR* 1.3 66.1 + - - +
117B PRO* 3.4 0.4 - - - -
118B LYS* 3.2 12.4 + - + +
119B ILE* 3.0 30.7 + - + +
501B CHD 4.0 19.3 - - + -
502B CHD 3.9 33.0 - - + +
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Residues in contact with THR 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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85B VAL* 3.9 6.5 - - + +
86B HIS* 3.6 35.5 - - + +
89B LEU* 3.6 9.6 - - - +
112B ALA 2.6 21.7 + - - -
113B LYS* 3.7 5.4 - - - -
115B LEU* 1.3 76.2 - - - +
117B PRO* 1.3 66.9 - - + +
119B ILE* 3.2 1.4 + - - +
120B GLN* 2.8 62.9 + - + +
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Residues in contact with PRO 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 12.8 - - - +
114B ARG* 3.6 9.2 - - - +
115B LEU 3.6 3.4 - - - -
116B THR* 1.3 96.1 - - + +
118B LYS* 1.3 60.4 + - - +
120B GLN* 3.5 13.1 + - - +
121B GLU* 3.1 23.9 + - - +
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Residues in contact with LYS 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 ARG 4.9 2.4 + - - +
115B LEU* 3.2 15.9 + - + +
117B PRO* 1.3 80.1 - - - +
119B ILE* 1.3 68.8 + - + +
121B GLU* 3.5 8.0 + - - +
122B GLN* 3.2 28.4 + - - +
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Residues in contact with ILE 119 (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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85B VAL* 3.8 19.1 - - + -
88B PHE* 5.2 5.4 - - + -
89B LEU* 3.9 22.9 - - + -
115B LEU* 3.0 26.3 + - + +
118B LYS* 1.3 78.8 - - + +
120B GLN* 1.3 66.9 + - - +
122B GLN* 3.1 20.3 + - - +
123B TYR* 3.1 51.7 + - + -
501B CHD 4.0 36.8 - - + -
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Residues in contact with GLN 120 (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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82B LEU* 2.9 56.4 + - + +
83B GLY* 4.4 4.2 - - - +
85B VAL* 3.7 16.4 - - + +
86B HIS* 5.5 0.6 - - - +
116B THR* 2.8 42.1 + - + +
117B PRO* 3.8 12.1 - - - +
119B ILE* 1.3 75.6 - - - +
121B GLU* 1.3 58.9 + - - +
123B TYR 3.2 1.4 + - - -
124B ARG* 2.8 27.0 + - - +
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Residues in contact with GLU 121 (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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117B PRO 3.1 17.6 + - - +
118B LYS* 3.5 8.5 - - - +
120B GLN* 1.3 78.4 - - - +
122B GLN* 1.3 62.0 + - + +
124B ARG* 2.6 46.5 + - - +
125B ARG* 3.1 43.7 + - + +
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Residues in contact with GLN 122 (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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118B LYS* 3.2 17.0 + - - +
119B ILE* 3.1 29.6 + - - +
121B GLU* 1.3 79.9 - - + +
123B TYR* 1.3 61.1 + - + +
125B ARG* 3.2 16.7 + - - +
126B ILE 3.5 4.2 + - - -
342B ILE* 3.8 28.6 - - + +
346B TYR* 3.5 50.1 + - + +
501B CHD 4.1 17.4 + - - +
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Residues in contact with TYR 123 (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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78B GLY* 4.6 2.9 - - - -
79B PRO* 3.4 39.2 - - + +
81B THR 6.1 0.7 - - - -
82B LEU* 3.6 20.0 - - + -
85B VAL* 4.3 4.5 - - + -
88B PHE* 4.3 9.2 - + - -
119B ILE* 3.1 48.4 + - + +
120B GLN 3.2 1.1 + - - +
122B GLN* 1.3 75.1 - - - +
124B ARG* 1.3 64.0 + - - +
126B ILE* 3.1 18.6 + - + +
128B GLY 2.7 22.0 + - - -
129B GLY* 3.8 25.1 - - - +
130B SER* 3.9 18.7 - - - -
342B ILE* 3.7 45.5 + - + +
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Residues in contact with ARG 124 (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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82B LEU* 3.8 15.4 - - + +
120B GLN 2.8 16.7 + - - +
121B GLU* 2.6 47.8 + - - +
122B GLN 3.2 0.2 - - - -
123B TYR* 1.3 76.0 - - - +
125B ARG* 1.3 77.9 + - - +
127B GLY* 3.1 13.2 + - - -
128B GLY* 3.8 11.8 + - - +
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Residues in contact with ARG 125 (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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121B GLU* 3.1 40.8 + - + +
122B GLN 3.4 8.5 - - - +
123B TYR 3.2 0.6 - - - -
124B ARG* 1.3 92.5 - - - +
126B ILE* 1.3 57.9 + - - +
127B GLY 3.5 0.2 - - - -
346B TYR* 4.0 26.1 + - + +
350B ILE* 3.5 43.9 - - + +
354B GLN* 5.0 5.7 - - - +
355B VAL* 6.2 0.4 - - - +
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Residues in contact with ILE 126 (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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122B GLN 3.5 4.2 + - - +
123B TYR* 3.1 24.5 - - + +
125B ARG* 1.3 80.4 - - - +
127B GLY* 1.3 57.2 + - - +
129B GLY 3.4 25.1 - - - +
130B SER* 4.9 2.7 - - - -
131B PRO* 4.9 0.2 - - + -
342B ILE* 3.8 21.3 - - + +
345B LEU* 3.6 57.1 - - + +
346B TYR* 3.7 23.1 - - + -
350B ILE* 4.4 1.6 - - + -
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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