Contacts of the helix formed by residues 93 - 116 (chain A) in PDB entry 1PD3
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 93 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A ILE* 3.9 5.9 - - - +
90A THR* 2.8 41.7 + - - -
91A GLU 3.6 0.2 - - - -
92A ASN* 1.4 78.5 - - - +
94A PHE* 1.3 65.8 + - - +
95A GLU* 3.5 11.8 + - - +
96A GLN* 3.0 22.2 + - - +
97A ILE* 3.1 21.7 + - - +
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Residues in contact with PHE 94 (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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92A ASN 3.6 2.0 + - - -
93A SER* 1.3 73.1 - - - +
95A GLU* 1.3 70.2 + - + +
97A ILE* 3.8 11.8 - - + +
98A THR* 2.8 50.8 + - - -
82B GLU* 3.8 40.8 - - + -
83B VAL* 5.0 1.1 - - - -
86B ARG* 3.4 58.6 - - + +
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Residues in contact with GLU 95 (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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87A LEU* 5.0 0.9 - - + -
89A ILE* 4.2 23.9 - - + +
93A SER* 2.9 13.1 - - - +
94A PHE* 1.3 88.1 - - + +
96A GLN* 1.3 57.3 + - - +
98A THR* 3.4 1.7 + - - -
99A PHE* 3.0 44.2 + - + -
83B VAL* 3.0 43.0 - - + +
86B ARG* 3.8 22.5 - - - +
87B LEU* 4.2 17.0 - - - +
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Residues in contact with GLN 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ARG* 2.9 39.0 + - - +
89A ILE* 3.5 8.3 - - + +
90A THR 3.2 22.9 - - - +
91A GLU* 3.5 35.9 + - - +
93A SER* 3.0 11.0 + - - +
95A GLU* 1.3 67.5 - - - +
97A ILE* 1.3 67.3 + - - +
98A THR 3.2 0.3 + - - -
99A PHE* 3.2 4.3 + - - +
100A MET* 2.9 63.7 + - + +
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Residues in contact with ILE 97 (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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91A GLU 4.7 4.0 - - - +
92A ASN* 3.5 34.8 - - - +
93A SER 3.1 20.9 + - - +
94A PHE* 3.9 10.3 - - + +
96A GLN* 1.3 74.6 - - - +
98A THR* 1.4 59.0 + - - +
100A MET* 3.5 14.3 + - + +
101A GLN* 3.0 45.9 + - + +
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Residues in contact with THR 98 (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 PHE* 2.8 38.6 + - + -
97A ILE* 1.4 73.7 - - - +
99A PHE* 1.3 61.9 + - - +
101A GLN* 3.1 12.8 + - - +
102A ALA* 3.0 21.1 + - - +
79B LEU* 3.5 38.1 - - + +
82B GLU* 4.1 11.4 - - + +
83B VAL* 3.3 26.9 - - + -
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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
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80A ILE* 3.8 39.9 - - + -
83A VAL* 4.0 17.9 - - + -
84A ARG* 3.8 35.2 - - + +
87A LEU* 3.6 30.7 - - + -
89A ILE* 4.6 0.7 - - + -
95A GLU* 3.0 34.3 + - + +
96A GLN* 3.7 5.4 - - - +
98A THR* 1.3 72.6 - - - +
100A MET* 1.3 64.2 + - + +
102A ALA* 3.1 7.1 + - + +
103A LEU* 2.9 34.3 + - + +
80B ILE* 6.0 2.7 - - + -
83B VAL* 3.2 34.1 - - + -
99B PHE* 4.0 3.4 - + - -
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Residues in contact with MET 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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91A GLU* 4.5 15.0 - - + +
96A GLN* 2.9 54.4 + - + +
97A ILE* 3.7 13.0 - - + +
99A PHE* 1.3 77.2 - - + +
101A GLN* 1.3 64.0 + - - +
103A LEU* 3.4 10.3 + - + +
104A GLN* 2.9 40.5 + - - +
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Residues in contact with GLN 101 (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 ILE* 3.0 34.5 + - - +
98A THR* 3.1 8.1 + - - +
100A MET* 1.3 79.7 - - + +
102A ALA* 1.4 61.1 + - - +
104A GLN* 3.5 10.6 + - - +
105A LEU* 3.1 25.0 + - + +
75B GLU* 4.1 8.3 + - - -
79B LEU* 3.6 31.2 - - + +
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Residues in contact with ALA 102 (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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80A ILE* 5.3 5.8 - - + -
98A THR 3.0 11.7 + - - +
99A PHE* 3.5 10.8 - - + +
101A GLN* 1.4 73.9 - - - +
103A LEU* 1.3 68.4 + - + +
105A LEU* 3.2 3.3 + - - +
106A LEU* 3.0 27.2 + - - +
76B ILE* 4.7 7.1 - - + +
79B LEU* 4.1 24.8 - - + +
80B ILE* 4.4 21.3 - - + -
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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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77A ARG* 3.6 28.7 - - + -
80A ILE* 3.9 26.7 - - + -
81A GLU* 3.8 31.6 - - + +
84A ARG* 5.6 4.0 - - + -
99A PHE* 2.9 27.1 + - + +
100A MET* 3.8 9.4 - - + +
102A ALA* 1.3 74.5 - - - +
104A GLN* 1.3 64.7 + - + +
105A LEU 3.3 0.2 + - - -
106A LEU* 3.3 7.0 + - + +
107A LEU* 2.9 33.8 + - + +
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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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100A MET* 2.9 29.8 + - - +
101A GLN* 4.0 7.5 - - - +
103A LEU* 1.3 80.2 - - + +
105A LEU* 1.3 56.2 + - - +
107A LEU* 3.5 10.2 + - + +
108A GLU* 3.1 29.1 + - - +
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Residues in contact with LEU 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 GLN* 3.1 16.2 + - + +
102A ALA 3.2 4.7 + - - +
104A GLN* 1.3 75.7 - - - +
106A LEU* 1.3 57.5 + - - +
108A GLU* 3.2 23.0 + - - +
109A VAL* 2.8 33.6 + - - +
72B LYS* 4.0 26.5 - - + +
75B GLU* 3.6 34.1 - - + -
76B ILE* 3.6 25.4 - - + -
79B LEU* 4.0 11.4 - - + -
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Residues in contact with LEU 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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73A PHE* 3.8 31.7 - - + +
76A ILE* 3.8 18.4 - - + -
77A ARG* 4.0 25.4 - - + +
80A ILE* 3.6 30.5 - - + -
102A ALA 3.0 17.1 + - - +
103A LEU* 3.4 8.5 - - + +
105A LEU* 1.3 76.5 - - - +
107A LEU* 1.4 61.7 + - - +
109A VAL* 3.4 2.5 + - - +
110A GLU* 3.2 25.0 + - - +
76B ILE* 3.6 28.9 - - + +
106B LEU* 4.7 2.7 - - + -
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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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77A ARG* 3.5 43.7 - - - +
103A LEU* 2.9 29.0 + - + +
104A GLN* 3.9 8.1 - - + +
106A LEU* 1.4 66.5 - - - +
108A GLU* 1.3 60.7 + - - +
110A GLU* 3.5 8.6 + - + +
111A GLN* 2.8 36.8 + - + +
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Residues in contact with GLU 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 GLN 3.1 18.0 + - - +
105A LEU* 3.2 23.0 + - - +
107A LEU* 1.3 76.9 - - - +
109A VAL* 1.3 64.0 + - - +
111A GLN* 3.1 10.9 + - + +
112A GLU* 3.0 29.5 + - + +
72B LYS* 2.8 32.7 + - - -
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Residues in contact with VAL 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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73A PHE* 3.6 28.7 - - + -
105A LEU* 2.8 19.9 + - + +
106A LEU* 3.8 5.6 - - - +
107A LEU 3.3 0.2 - - - -
108A GLU* 1.3 78.1 - - + +
110A GLU* 1.3 61.4 + - - +
112A GLU* 3.1 9.7 + - - +
113A ILE* 3.0 23.2 + - + +
69B LEU* 4.3 10.3 - - + -
72B LYS* 3.6 41.1 - - + -
73B PHE* 3.6 16.2 - - + -
76B ILE* 4.3 9.4 - - + -
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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
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70A GLY* 3.7 19.1 - - - +
73A PHE* 3.7 35.8 - - + +
74A GLU* 2.8 23.3 - - - +
77A ARG* 2.8 24.7 + - - -
106A LEU* 3.2 16.7 + - - +
107A LEU* 3.7 11.4 - - + +
109A VAL* 1.3 76.0 - - - +
111A GLN* 1.3 65.2 + - - +
112A GLU 3.2 0.5 + - - -
113A ILE* 3.5 4.1 + - - +
114A ARG* 3.3 20.1 + - - +
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Residues in contact with GLN 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 LEU* 2.8 31.0 + - + +
108A GLU* 3.1 9.8 + - + +
110A GLU* 1.3 74.3 - - - +
112A GLU* 1.3 62.1 + - + +
114A ARG* 2.0 54.1 + - - +
115A THR* 3.2 18.9 + - - -
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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 GLU* 3.0 24.5 + - + +
109A VAL* 3.1 10.2 + - - +
111A GLN* 1.3 74.4 - - + +
113A ILE* 1.3 66.6 + - - +
115A THR* 3.1 9.3 + - + +
116A PHE* 3.0 24.9 + - - +
68B GLN* 5.4 4.0 - - - +
69B LEU* 3.3 27.9 + - + +
72B LYS* 3.0 35.1 + - - +
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Residues in contact with ILE 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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65A TRP* 5.9 1.8 - - + -
66A ARG* 3.4 36.2 + - + +
69A LEU* 4.0 30.7 - - + -
70A GLY* 5.0 4.7 - - - +
73A PHE* 2.9 42.8 - - + -
109A VAL* 3.0 17.1 + - + +
110A GLU* 3.9 5.2 - - - +
112A GLU* 1.3 75.5 - - - +
114A ARG* 1.3 61.3 + - - +
115A THR 3.3 0.3 + - - -
116A PHE* 3.8 8.0 - - - +
69B LEU* 4.5 17.9 - - + -
73B PHE* 5.1 1.3 - - + -
113B ILE* 4.9 4.7 - - + -
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Residues in contact with ARG 114 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A ARG* 3.6 20.0 + - - +
110A GLU* 3.3 10.7 + - - +
111A GLN* 2.0 51.3 + - - +
112A GLU 3.1 0.6 - - - -
113A ILE* 1.3 79.2 - - - +
115A THR* 1.3 71.8 + - - +
116A PHE 3.6 0.4 - - - -
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Residues in contact with THR 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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66A ARG* 4.3 0.2 - - - -
111A GLN* 3.2 16.2 + - - +
112A GLU* 3.1 9.5 + - + +
113A ILE 3.1 0.4 - - - -
114A ARG* 1.3 93.8 + - - +
116A PHE* 1.3 64.6 + - - +
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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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65A TRP* 5.1 16.4 - + - -
66A ARG* 2.8 38.7 + - + +
112A GLU 3.0 16.0 + - - +
113A ILE* 3.8 9.9 - - + +
114A ARG 3.6 0.2 - - - -
115A THR* 1.3 80.3 - - - +
65B TRP* 3.8 62.6 - + + -
69B LEU* 6.6 0.4 - - + -
116B PHE* 5.6 6.3 - + - -
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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