Contacts of the helix formed by residues 64 - 87 (chain B) 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 LYS 64 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63B GLY* 1.3 67.0 - - - -
65B TRP* 1.3 58.0 + - - +
66B ARG 3.5 0.4 - - - -
67B GLU* 3.8 14.3 - - + -
68B GLN* 3.1 51.6 + - + +
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Residues in contact with TRP 65 (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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65A TRP* 5.1 9.2 - + - -
116A PHE* 3.8 47.5 - + + -
63B GLY* 3.6 26.0 - - - +
64B LYS* 1.3 73.1 - - - +
66B ARG* 1.3 109.1 + - + +
67B GLU 3.1 1.6 - - - -
68B GLN* 3.2 4.2 + - - +
69B LEU* 3.0 45.3 + - + +
113B ILE* 5.1 10.8 - - + -
116B PHE* 4.0 25.6 - + - -
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Residues in contact with ARG 66 (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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63B GLY 3.6 14.6 - - - +
65B TRP* 1.3 122.6 - - + +
67B GLU* 1.3 60.0 + - + +
69B LEU* 4.1 0.8 - - - +
70B GLY* 3.2 21.8 + - - -
113B ILE* 3.8 28.7 + - + +
114B ARG* 4.0 18.7 + - - +
115B THR 3.4 2.0 + - - -
116B PHE* 3.2 35.2 - - - -
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Residues in contact with GLU 67 (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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63B GLY 4.8 2.0 - - - +
64B LYS* 3.9 20.2 - - + +
65B TRP 3.1 0.4 - - - -
66B ARG* 1.3 83.2 - - + +
68B GLN* 1.3 64.2 + - - +
70B GLY* 5.2 0.2 - - - -
71B GLN* 2.6 49.4 + - - +
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Residues in contact with GLN 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A GLU* 5.4 4.9 - - - +
64B LYS* 3.1 49.3 + - + +
65B TRP* 3.2 4.8 + - - +
67B GLU* 1.3 77.5 - - - +
69B LEU* 1.3 64.8 + - - +
71B GLN* 3.2 10.0 + - + +
72B LYS* 3.2 41.3 + - + +
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Residues in contact with LEU 69 (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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109A VAL* 4.3 22.4 - - + +
112A GLU* 3.3 36.3 + - + +
113A ILE* 4.5 14.4 - - + -
116A PHE* 6.6 0.4 - - + -
65B TRP* 3.0 30.1 + - + +
66B ARG* 4.3 3.1 - - - +
68B GLN* 1.3 78.9 - - - +
70B GLY* 1.3 55.8 + - - +
72B LYS* 2.8 22.9 + - + +
73B PHE* 3.0 31.8 + - + -
113B ILE* 4.1 24.0 - - + -
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Residues in contact with GLY 70 (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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66B ARG 3.2 16.3 + - - -
67B GLU* 4.4 1.1 - - - -
69B LEU* 1.3 78.8 - - - +
71B GLN* 1.3 64.1 + - - +
73B PHE* 3.4 13.3 + - - +
74B GLU* 3.1 25.7 + - - +
110B GLU* 3.9 7.2 - - - +
113B ILE* 5.0 4.1 - - - +
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Residues in contact with GLN 71 (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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67B GLU* 2.6 48.4 + - + +
68B GLN* 3.2 10.6 + - + +
69B LEU 3.2 1.0 - - - -
70B GLY* 1.3 78.9 - - - +
72B LYS* 1.3 58.7 + - + +
74B GLU* 3.6 14.9 + - - +
75B GLU* 2.9 29.3 + - - +
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Residues in contact with LYS 72 (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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105A LEU* 4.0 17.1 - - + +
108A GLU* 2.8 27.8 + - - +
109A VAL* 3.6 24.7 - - + -
112A GLU* 3.0 25.3 + - - +
68B GLN* 3.2 32.1 + - + +
69B LEU* 2.8 13.3 + - - +
71B GLN* 1.3 75.7 - - + +
73B PHE* 1.3 55.3 + - - +
75B GLU* 3.0 9.4 + - - +
76B ILE* 2.9 34.7 + - - +
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Residues in contact with PHE 73 (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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73A PHE* 3.4 41.5 - + - -
109A VAL* 3.6 17.0 - - + -
113A ILE* 5.1 0.2 - - + -
69B LEU* 3.0 31.1 + - + -
70B GLY* 3.9 7.0 - - - +
72B LYS* 1.3 73.6 - - - +
74B GLU* 1.3 64.0 + - - +
76B ILE* 3.9 15.2 - - + +
77B ARG* 3.0 26.2 + - - +
106B LEU* 4.3 13.6 - - + +
109B VAL* 3.7 12.1 - - + -
110B GLU* 3.6 39.7 - - + +
113B ILE* 3.9 29.8 - - + -
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Residues in contact with GLU 74 (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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70B GLY 3.1 16.7 + - - +
71B GLN* 3.6 20.9 - - - +
73B PHE* 1.3 73.7 - - - +
75B GLU* 1.3 64.5 + - - +
77B ARG* 2.8 37.5 + - - +
78B TRP* 2.9 26.1 + - - +
110B GLU* 2.5 23.1 + - - +
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Residues in contact with GLU 75 (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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101A GLN* 4.1 8.0 + - - -
105A LEU* 3.6 20.2 - - + -
71B GLN 2.9 15.5 + - - +
72B LYS* 3.0 9.6 + - - +
74B GLU* 1.3 77.7 - - - +
76B ILE* 1.3 62.2 + - - +
78B TRP* 3.6 16.4 - - - +
79B LEU* 2.9 52.4 + - + +
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Residues in contact with ILE 76 (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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102A ALA* 4.7 6.0 - - + +
105A LEU* 3.6 25.8 - - + +
106A LEU* 3.6 46.9 - - + +
109A VAL* 4.3 7.0 - - + -
72B LYS 2.9 23.1 + - - +
73B PHE* 3.9 21.3 - - + +
74B GLU 3.3 0.2 - - - -
75B GLU* 1.3 72.3 - - - +
77B ARG* 1.3 59.9 + - - +
79B LEU* 3.1 11.8 + - - +
80B ILE* 2.8 48.0 + - + +
106B LEU* 3.8 15.7 - - + -
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Residues in contact with ARG 77 (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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73B PHE 3.0 16.8 + - - +
74B GLU* 2.8 46.6 + - - +
76B ILE* 1.3 77.9 - - - +
78B TRP* 1.3 66.8 + - - +
80B ILE* 3.1 4.4 + - - +
81B GLU* 2.9 32.4 + - - +
103B LEU* 3.8 20.3 - - + +
106B LEU* 3.8 20.2 - - + -
107B LEU* 3.7 38.4 - - - +
110B GLU* 3.3 17.0 + - - -
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Residues in contact with TRP 78 (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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74B GLU 2.9 18.2 + - - +
75B GLU* 3.6 26.2 - - - +
77B ARG* 1.3 77.6 - - - +
79B LEU* 1.3 60.2 + - + +
81B GLU* 3.1 12.6 + - + +
82B GLU* 2.8 72.6 + - + +
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Residues in contact with LEU 79 (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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98A THR* 3.5 31.8 - - + +
101A GLN* 3.6 24.7 - - + +
102A ALA* 4.1 21.8 - - + +
105A LEU* 4.0 17.3 - - + -
75B GLU* 2.9 53.9 + - + +
76B ILE* 3.6 6.3 - - - +
78B TRP* 1.3 77.5 - - + +
80B ILE* 1.4 63.6 + - - +
82B GLU* 3.1 28.2 + - - +
83B VAL* 3.1 12.7 + - - +
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Residues in contact with ILE 80 (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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76A ILE* 5.2 0.2 - - + -
80A ILE* 3.4 40.8 - - + -
99A PHE* 6.0 2.2 - - + -
102A ALA* 4.4 12.1 - - + -
76B ILE* 2.8 27.6 + - + +
77B ARG 3.7 3.8 - - - +
79B LEU* 1.4 75.2 - - - +
81B GLU* 1.3 56.4 + - - +
83B VAL* 3.5 6.6 + - + +
84B ARG* 2.9 26.2 + - + +
99B PHE* 3.7 26.7 - - + +
102B ALA* 5.3 4.9 - - + -
103B LEU* 3.7 21.3 - - + -
106B LEU* 3.6 23.8 - - + -
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Residues in contact with GLU 81 (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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77B ARG* 2.9 26.1 + - - +
78B TRP* 3.1 16.4 + - + +
80B ILE* 1.3 76.1 - - - +
82B GLU* 1.3 63.7 + - - +
84B ARG* 3.4 8.3 + - + +
85B HIS* 2.9 24.1 + - - +
103B LEU* 3.5 35.9 - - + +
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Residues in contact with GLU 82 (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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94A PHE* 3.8 30.2 - - + -
98A THR* 4.1 5.2 - - + +
78B TRP* 2.8 70.3 + - + +
79B LEU* 3.1 23.3 + - - +
81B GLU* 1.3 76.7 - - - +
83B VAL* 1.3 62.4 + - - +
85B HIS* 3.4 19.1 + - - +
86B ARG* 3.5 13.9 + - - +
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Residues in contact with VAL 83 (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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94A PHE* 5.2 1.3 - - + -
95A GLU* 3.0 40.2 - - + +
98A THR* 3.3 38.4 - - + -
99A PHE* 3.2 43.3 - - + +
79B LEU 3.1 7.9 + - - +
80B ILE* 3.7 4.7 - - + +
82B GLU* 1.3 78.5 - - - +
84B ARG* 1.4 66.3 + - - +
86B ARG* 3.2 9.0 + - - -
87B LEU* 3.6 8.1 - - + +
99B PHE* 3.7 13.7 - - + -
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Residues in contact with ARG 84 (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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80B ILE* 2.9 18.7 + - + +
81B GLU* 3.8 12.8 - - + +
83B VAL* 1.4 77.9 - - - +
85B HIS* 1.3 64.0 + - - +
86B ARG 3.1 0.9 + - - -
87B LEU* 2.9 27.7 + - - -
89B ILE* 3.3 38.7 + - - +
90B THR 6.0 0.2 - - - -
96B GLN* 2.7 33.8 + - - +
99B PHE* 3.8 35.9 - - + -
103B LEU* 5.6 5.6 - - + -
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Residues in contact with HIS 85 (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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81B GLU 2.9 17.9 + - - +
82B GLU* 3.4 11.4 - - - +
83B VAL 3.2 0.4 - - - -
84B ARG* 1.3 80.5 - - - +
86B ARG* 1.3 71.8 + - + +
87B LEU 3.3 4.6 + - - +
88B LYS* 6.1 0.9 - - - -
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Residues in contact with ARG 86 (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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94A PHE* 3.4 57.2 - - + +
95A GLU* 3.8 24.3 - - - +
82B GLU* 3.5 14.5 + - - +
83B VAL 3.2 3.7 + - - +
84B ARG 3.1 1.0 - - - -
85B HIS* 1.3 89.4 - - + +
87B LEU* 1.3 62.2 + - - +
88B LYS* 4.1 7.3 + - - +
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Residues in contact with LEU 87 (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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87A LEU* 4.1 35.4 - - + -
89A ILE* 6.1 2.5 - - + -
95A GLU* 4.2 17.9 - - - +
83B VAL 3.6 11.2 - - - +
84B ARG* 2.9 26.5 + - - +
85B HIS 4.0 3.6 - - - +
86B ARG* 1.3 81.7 - - - +
88B LYS* 1.4 63.6 + - - +
89B ILE* 4.0 22.7 - - + -
95B GLU* 4.6 4.0 - - + -
99B PHE* 3.5 36.3 - - + -
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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