Contacts of the helix formed by residues 103 - 126 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A LEU 3.5 0.6 + - - -
102A PRO* 1.3 86.9 - - + +
104A GLN* 1.3 59.5 + - - +
105A ASN 3.3 2.9 - - - -
106A LYS* 2.9 35.0 + - + +
107A LEU* 2.8 47.8 + - + -
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Residues in contact with GLN 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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93A PHE 2.9 29.1 + - - +
94A LEU* 3.6 8.8 - - + -
95A ASP 4.0 0.4 + - - -
96A ARG* 2.6 38.9 + - - +
99A MET* 3.1 19.7 + - - +
100A THR* 3.3 8.5 - - - -
101A LEU* 3.0 42.0 + - + +
102A PRO 2.7 8.6 + - - -
103A ILE* 1.3 72.9 - - - +
105A ASN* 1.3 60.7 + - - +
107A LEU* 4.4 4.3 - - - +
108A ALA* 2.8 37.2 + - - +
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Residues in contact with ASN 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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94A LEU* 3.9 20.1 - - - +
96A ARG* 5.5 4.1 + - - +
103A ILE 3.2 1.2 + - - -
104A GLN* 1.3 78.6 - - - +
106A LYS* 1.3 63.6 + - + +
109A PRO* 3.3 17.0 - - - +
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Residues in contact with LYS 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ILE* 2.9 34.2 + - + +
105A ASN* 1.3 86.1 - - + +
107A LEU* 1.3 65.6 + - - +
108A ALA 3.5 0.2 - - - -
109A PRO* 3.2 14.8 - - - +
110A PHE* 3.8 8.0 + - - +
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Residues in contact with LEU 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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101A LEU* 4.6 6.3 - - + -
102A PRO* 2.9 30.7 - - + +
103A ILE* 2.8 31.4 + - + +
104A GLN* 4.1 3.1 - - - +
106A LYS* 1.3 76.8 - - - +
108A ALA* 1.3 66.9 + - - +
110A PHE* 2.7 27.6 + - + +
111A ILE* 2.8 26.6 + - + +
503A CHD 4.0 47.8 - - + -
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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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90A LEU* 3.9 3.8 - - + -
93A PHE* 3.8 32.8 - - + +
94A LEU* 3.4 24.2 - - + -
101A LEU* 5.3 1.9 - - - +
104A GLN* 2.8 23.3 + - + +
107A LEU* 1.3 71.9 - - - +
109A PRO* 1.3 70.3 - - + +
111A ILE* 3.2 5.3 + - - +
112A ALA* 2.9 23.7 + - - +
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Residues in contact with PRO 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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86A HIS* 4.3 8.0 + - + +
90A LEU* 3.3 26.4 - - + -
94A LEU* 4.8 1.8 - - + -
105A ASN 3.3 22.0 - - - +
106A LYS* 3.2 18.2 - - - +
108A ALA* 1.3 94.3 - - + +
110A PHE* 1.3 54.0 + - - +
112A ALA* 3.4 3.1 + - + +
113A LYS* 3.0 28.4 + - - +
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Residues in contact with PHE 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 LYS 4.0 9.2 - - - +
107A LEU* 2.7 27.3 + - + +
109A PRO* 1.3 74.5 - - - +
111A ILE* 1.3 75.5 + - + +
113A LYS* 3.1 8.3 + - + +
114A ARG* 3.1 43.8 + - + +
503A CHD 3.8 34.1 - - + -
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Residues in contact with ILE 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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93A PHE* 4.0 16.8 - - + -
101A LEU* 4.3 24.2 - - + -
107A LEU* 2.8 32.7 + - + +
108A ALA* 3.9 5.4 - - - +
110A PHE* 1.3 84.1 - - + +
112A ALA* 1.3 61.2 + - - +
114A ARG* 3.2 8.7 - - + +
115A LEU* 3.1 43.5 + - + +
502A CHD 4.5 20.4 - - + +
503A CHD 4.3 31.4 - - + -
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Residues in contact with ALA 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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86A HIS* 3.9 11.2 - - - +
89A LEU* 3.7 17.3 - - + +
90A LEU* 3.6 32.8 - - + +
93A PHE* 4.4 3.3 - - + -
108A ALA 2.9 17.1 + - - +
109A PRO* 3.5 6.3 - - + +
111A ILE* 1.3 78.0 - - - +
113A LYS* 1.3 53.2 + - - +
115A LEU 3.3 0.2 + - - -
116A THR* 2.5 39.7 + - - -
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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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86A HIS* 4.1 15.0 - - + +
109A PRO 3.0 14.3 + - - +
110A PHE* 3.1 13.0 + - + +
112A ALA* 1.3 77.1 - - - +
114A ARG* 1.3 58.9 + - - +
116A THR* 3.6 7.3 - - - -
117A PRO* 3.3 19.1 - - - +
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Residues in contact with ARG 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 PHE* 3.1 34.4 + - + +
111A ILE* 3.2 19.3 - - - +
113A LYS* 1.3 77.6 - - - +
115A LEU* 1.3 60.6 + - - +
116A THR 3.4 0.2 - - - -
117A PRO* 3.6 10.8 - - - +
118A LYS* 5.0 2.8 + - - +
502A CHD 2.8 52.4 + - - -
503A CHD 4.1 28.7 + - - +
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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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89A LEU* 3.9 14.1 - - + -
93A PHE* 3.4 38.1 - - + -
111A ILE* 3.1 25.3 + - + +
114A ARG* 1.3 78.1 - - - +
116A THR* 1.3 66.8 + - - +
117A PRO 3.4 0.2 - - - -
118A LYS* 3.1 12.0 + - + +
119A ILE* 3.0 30.6 + - + +
501A CHD 4.4 13.7 - - + -
502A CHD 3.5 40.6 - - + +
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Residues in contact with THR 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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85A VAL* 4.1 6.5 - - + -
86A HIS* 3.5 33.0 - - + +
89A LEU* 3.7 9.7 - - - +
112A ALA 2.5 26.2 + - - -
113A LYS* 3.6 6.1 - - - -
115A LEU* 1.3 74.9 - - - +
117A PRO* 1.3 65.8 - - + +
119A ILE* 3.2 1.0 + - - +
120A GLN* 2.8 62.2 + - + +
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Residues in contact with PRO 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 3.3 13.7 - - - +
114A ARG* 3.6 9.4 - - - +
115A LEU 3.5 4.3 - - - -
116A THR* 1.3 95.2 - - + +
118A LYS* 1.3 60.8 + - - +
120A GLN* 3.4 12.8 + - - +
121A GLU* 3.1 23.9 + - - +
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Residues in contact with LYS 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 ARG 5.0 2.2 + - - +
115A LEU* 3.1 16.4 + - + +
117A PRO* 1.3 79.8 - - - +
119A ILE* 1.3 68.3 + - + +
121A GLU* 3.4 8.6 - - - +
122A GLN* 3.2 26.4 + - - +
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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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85A VAL* 3.9 16.4 - - + -
88A PHE* 5.3 5.4 - - + -
89A LEU* 4.0 21.1 - - + -
115A LEU* 3.0 25.6 + - + +
116A THR 3.9 2.7 - - - +
118A LYS* 1.3 76.6 - - + +
120A GLN* 1.3 66.3 + - - +
121A GLU 3.1 1.8 - - - -
122A GLN* 3.1 23.2 + - + +
123A TYR* 3.0 52.0 + - + -
501A CHD 3.9 35.4 - - + -
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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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82A LEU* 2.9 55.1 + - + +
83A GLY* 4.4 3.8 + - - +
85A VAL* 3.7 16.2 - - + -
86A HIS 5.5 0.4 - - - +
116A THR* 2.8 45.3 + - + +
117A PRO* 3.7 11.4 - - - +
119A ILE* 1.3 71.9 - - - +
121A GLU* 1.3 52.9 + - - +
123A TYR 3.2 1.1 + - - +
124A ARG* 2.8 31.9 + - - +
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Residues in contact with GLU 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 PRO 3.1 13.9 + - - +
118A LYS* 3.4 13.5 - - - +
120A GLN* 1.3 75.3 - - - +
122A GLN* 1.3 65.5 + - + +
124A ARG* 2.6 46.6 + - - +
125A ARG* 3.0 43.6 + - + +
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Residues in contact with GLN 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 LYS* 3.2 13.8 + - - +
119A ILE* 3.1 31.5 + - - +
121A GLU* 1.3 80.5 - - + +
123A TYR* 1.3 62.1 + - + +
125A ARG* 3.3 15.9 + - - +
126A ILE 3.5 4.7 + - - -
342A ILE* 3.7 29.9 - - + +
346A TYR* 3.4 50.2 + - + +
351A GLU* 5.6 0.2 + - - -
501A CHD 4.1 15.9 + - - -
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Residues in contact with TYR 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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79A PRO* 3.4 34.8 - - + +
81A THR 6.3 0.2 - - - -
82A LEU* 3.7 19.1 - - + -
85A VAL* 4.3 4.3 - - + -
88A PHE* 4.4 6.3 - + - -
119A ILE* 3.0 48.1 + - + -
120A GLN* 3.7 1.6 - - - +
122A GLN* 1.3 73.0 - - + +
124A ARG* 1.3 65.3 + - - +
126A ILE* 3.1 22.5 - - + +
128A GLY 2.8 21.6 + - - -
129A GLY* 3.8 9.0 - - - +
130A SER* 3.8 33.4 - - - -
341A HIS* 2.9 25.6 + + - -
342A ILE* 3.7 28.9 - - + +
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Residues in contact with ARG 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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82A LEU* 3.7 20.8 - - + +
120A GLN 2.8 14.0 + - - +
121A GLU* 2.6 46.9 + - - +
123A TYR* 1.3 76.3 - - - +
125A ARG* 1.3 79.7 + - - +
127A GLY* 3.0 13.2 + - - -
128A GLY* 3.8 8.7 + - - +
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Residues in contact with ARG 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 GLU* 3.0 38.4 + - + +
122A GLN 3.5 9.2 - - - +
123A TYR 3.2 0.4 - - - -
124A ARG* 1.3 94.0 - - - +
126A ILE* 1.3 57.5 + - - +
127A GLY 3.5 0.4 + - - -
346A TYR* 4.0 25.7 + - + +
350A ILE* 3.5 43.8 - - + +
354A GLN* 4.7 6.3 - - - +
355A VAL* 6.0 1.2 - - - +
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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 GLN 3.5 2.9 + - - +
123A TYR* 3.1 28.7 - - + +
125A ARG* 1.3 81.0 - - - +
127A GLY* 1.3 57.1 + - - +
129A GLY 3.6 23.1 - - - +
130A SER* 4.8 2.7 - - - -
342A ILE* 3.8 20.4 - - + +
345A LEU* 3.6 54.2 - - + +
346A TYR* 3.6 22.2 - - + -
350A ILE* 4.3 4.3 - - + -
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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