Contacts of the helix formed by residues 78 - 101 (chain B) in PDB entry 3UNF
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 78 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A PHE* 3.8 33.2 - - + -
16A GLY 5.5 0.4 - - - +
18A LEU* 4.1 18.8 - - + -
21A ILE* 5.6 2.9 - - + -
151A SER* 4.2 13.5 - - - +
26B ALA* 4.0 13.5 - - + -
77B GLY* 1.3 69.8 - - - -
79B THR* 1.3 59.5 + - - +
80B SER* 3.3 24.2 - - - +
81B ASP* 3.3 19.1 + - - +
82B ALA* 3.0 24.9 + - - +
127B ARG* 5.4 0.7 - - - +
130B GLY* 3.1 22.9 + - - +
131B VAL* 3.7 2.3 - - - +
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Residues in contact with THR 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A SER* 5.3 0.2 + - - -
153A ALA* 3.5 24.3 - - - +
155A PHE* 5.9 0.5 - - - -
50B ASN* 6.4 0.2 - - - +
62B GLU* 5.9 3.1 - - + +
63B LYS* 6.0 5.8 - - + -
65B TYR* 5.3 3.8 - - - +
75B VAL* 5.0 11.7 - - + -
77B GLY 3.4 8.0 + - - +
78B ILE* 1.3 71.2 - - - +
80B SER* 1.3 61.1 + - - +
82B ALA* 3.2 9.4 + - - +
83B ASN* 2.8 39.8 + - - +
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Residues in contact with SER 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A GLN* 3.6 15.2 - - - +
121A THR* 5.0 0.9 + - - -
151A SER* 2.9 28.4 + - - -
152A GLY 3.5 25.3 + - - -
153A ALA* 4.0 1.1 - - - +
78B ILE* 3.3 14.8 - - - +
79B THR* 1.3 77.3 + - - +
81B ASP* 1.3 78.4 + - - +
83B ASN* 3.3 8.6 + - - +
84B VAL* 3.1 26.9 + - - +
127B ARG* 5.0 0.3 + - - -
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Residues in contact with ASP 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A GLN* 3.0 13.4 + - - +
78B ILE* 3.3 15.1 + - + +
80B SER* 1.3 85.4 + - - +
82B ALA* 1.3 62.4 + - - +
84B VAL* 3.4 7.4 + - - +
85B LEU* 3.1 28.9 + - - +
127B ARG* 2.5 47.3 + - - -
129B PHE* 3.5 14.2 - - + -
130B GLY 3.2 14.4 + - - -
131B VAL* 3.4 20.6 - - + -
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Residues in contact with ALA 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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65B TYR* 4.1 5.6 - - - +
75B VAL* 3.5 39.9 - - + +
78B ILE 3.0 13.3 + - - +
79B THR* 3.2 11.9 - - - +
81B ASP* 1.3 75.1 - - - +
83B ASN* 1.3 54.3 + - - +
85B LEU* 3.3 4.4 + - - +
86B THR* 2.6 41.2 + - - +
131B VAL* 3.7 12.3 - - + +
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Residues in contact with ASN 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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114A ALA* 6.2 0.2 - - - +
115A SER* 5.9 2.5 - - - +
152A GLY 4.6 4.2 + - - -
153A ALA* 5.6 1.2 - - - +
154A TYR* 3.5 35.0 + - - -
65B TYR* 3.1 29.3 + - - -
79B THR* 2.8 28.2 + - - +
80B SER* 3.3 10.0 + - - +
82B ALA* 1.3 72.9 - - - +
84B VAL* 1.3 63.6 + - + +
86B THR* 3.2 5.8 + - - -
87B ASN* 3.1 26.2 + - - +
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Residues in contact with VAL 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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115A SER* 4.6 15.5 - - - +
118A GLN* 3.4 30.5 - - + +
80B SER 3.1 14.3 + - - +
81B ASP* 3.6 9.6 - - - +
82B ALA 3.3 0.2 - - - -
83B ASN* 1.3 78.1 - - + +
85B LEU* 1.3 63.4 + - + +
87B ASN* 3.9 5.0 - - - +
88B GLU* 3.2 21.6 + - + +
129B PHE* 4.2 23.3 - - + -
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Residues in contact with LEU 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 ASP 3.1 20.4 + - - +
82B ALA* 3.3 3.6 + - - +
84B VAL* 1.3 76.8 - - + +
86B THR* 1.3 54.2 + - - +
88B GLU* 3.2 3.9 + - + -
89B LEU* 2.8 38.0 + - - +
113B LEU* 3.4 31.9 - - + +
116B ILE* 5.4 4.3 - - + -
117B LYS* 3.8 26.7 - - + -
129B PHE* 3.9 46.0 - - + -
131B VAL* 4.1 8.5 - - + -
133B LEU* 4.0 23.1 - - + -
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Residues in contact with THR 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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65B TYR* 3.6 36.6 - - + -
67B LEU* 4.0 5.6 - - + +
73B CYS* 3.6 31.2 - - - -
75B VAL* 4.8 1.6 - - + -
82B ALA 2.6 25.2 + - - +
83B ASN* 3.2 15.8 + - - -
85B LEU* 1.3 71.7 - - - +
87B ASN* 1.3 58.0 + - - +
89B LEU* 3.3 11.2 + - + +
90B ARG* 3.0 37.0 + - - +
133B LEU* 4.6 5.6 - - + -
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Residues in contact with ASN 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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83B ASN 3.1 19.7 + - - +
84B VAL* 3.9 5.0 - - - +
86B THR* 1.3 76.0 + - - +
88B GLU* 1.3 58.3 + - - +
90B ARG* 3.4 20.2 + - - +
91B LEU* 3.1 39.1 + - - +
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Residues in contact with GLU 88 (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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84B VAL* 3.2 14.0 + - + +
85B LEU* 3.4 10.3 - - + +
87B ASN* 1.3 77.7 + - - +
89B LEU* 1.3 59.2 + - - +
91B LEU* 3.1 13.9 + - - +
92B ILE* 2.9 41.3 + - + +
95B ARG* 3.5 31.4 + - - -
113B LEU* 4.2 6.3 - - + -
116B ILE* 3.8 27.9 - - + +
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Residues in contact with LEU 89 (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 LEU* 3.8 22.7 - - + -
73B CYS* 4.5 0.4 - - - -
85B LEU 2.8 21.8 + - - +
86B THR* 3.4 15.5 - - + +
88B GLU* 1.3 74.2 - - - +
90B ARG* 1.3 59.4 + - - +
92B ILE* 4.5 3.4 - - + -
93B ALA* 3.2 22.0 + - - +
109B LEU* 3.3 43.8 - - + +
113B LEU* 3.8 27.1 - - + +
133B LEU* 3.6 31.0 - - + -
135B TYR* 3.8 20.9 - - + -
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Residues in contact with ARG 90 (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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65B TYR* 4.0 22.5 - - - +
66B LYS* 2.7 35.5 + - - +
67B LEU* 3.7 30.6 - - - +
86B THR* 3.0 20.6 + - - +
87B ASN* 3.5 23.3 - - - +
88B GLU 3.2 0.2 - - - -
89B LEU* 1.3 76.1 - - - +
91B LEU* 1.3 60.7 + - - +
93B ALA* 3.7 2.1 - - - +
94B GLN* 3.3 28.8 + - - +
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Residues in contact with LEU 91 (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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87B ASN* 3.1 31.6 + - - +
88B GLU* 3.1 21.2 + - - +
90B ARG* 1.3 76.7 - - + +
92B ILE* 1.3 61.7 + - - +
94B GLN* 3.1 8.7 + - + +
95B ARG* 2.9 62.7 + - + +
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Residues in contact with ILE 92 (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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88B GLU* 2.9 39.3 + - + +
89B LEU* 4.5 4.7 - - - +
91B LEU* 1.3 74.4 - - - +
93B ALA* 1.3 62.6 + - - +
95B ARG* 3.3 25.0 + - + +
96B TYR* 3.1 23.6 + - + +
104B ILE* 4.4 11.2 - - + -
109B LEU* 4.1 14.1 - - + -
112B ALA* 3.8 34.1 - - + -
113B LEU* 4.3 9.6 - - + +
116B ILE* 4.2 13.2 - - + -
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Residues in contact with ALA 93 (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 LEU 4.1 10.5 - - - +
68B ASN* 3.4 26.8 - - + +
89B LEU 3.2 19.5 + - - +
90B ARG 3.7 6.1 - - - +
92B ILE* 1.3 77.5 - - - +
94B GLN* 1.3 60.0 + - + +
96B TYR* 3.6 3.3 + - - +
97B LEU* 3.2 24.9 + - - +
104B ILE* 3.9 20.9 + - + +
109B LEU* 3.9 6.9 - - + +
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Residues in contact with GLN 94 (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 LEU 5.7 0.6 - - - +
68B ASN* 5.4 4.0 - - - +
90B ARG 3.3 17.4 + - - +
91B LEU* 3.1 10.4 + - + +
93B ALA* 1.3 79.2 - - + +
95B ARG* 1.3 60.6 + - + +
97B LEU* 3.5 31.8 - - - +
98B LEU* 2.9 30.8 + - - +
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Residues in contact with ARG 95 (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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88B GLU* 3.5 25.9 + - - -
91B LEU* 2.9 47.2 + - + +
92B ILE* 3.3 28.7 + - + +
94B GLN* 1.3 73.1 - - + +
96B TYR* 1.3 64.8 + - - +
98B LEU* 3.4 12.9 + - + +
99B GLN* 3.1 25.2 + - - +
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Residues in contact with TYR 96 (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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92B ILE* 3.1 16.4 + - + +
93B ALA 3.8 4.9 - - - +
95B ARG* 1.3 74.5 - - - +
97B LEU* 1.3 59.2 + - - +
99B GLN* 3.2 2.7 + - - -
100B TYR* 2.9 69.6 + + + +
102B GLU* 3.3 32.4 + - + -
103B PRO 3.8 3.1 - - - -
104B ILE* 3.6 40.4 - - + -
105B PRO* 3.4 23.9 - - + +
108B GLN* 3.9 21.0 + - - -
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Residues in contact with LEU 97 (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 ALA 3.2 12.8 + - - +
94B GLN* 3.5 38.4 - - - +
96B TYR* 1.3 79.0 - - - +
98B LEU* 1.3 56.9 + - - +
101B GLN* 2.7 51.7 + - - +
102B GLU* 3.9 30.3 - - - +
103B PRO* 4.9 7.6 - - + -
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Residues in contact with LEU 98 (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 GLN* 2.9 17.3 + - - +
95B ARG* 3.7 11.4 - - + +
97B LEU* 1.3 76.6 - - - +
99B GLN* 1.3 62.2 + - - +
101B GLN* 3.1 22.6 + - - +
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Residues in contact with GLN 99 (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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95B ARG 3.1 17.4 + - - +
96B TYR* 3.8 4.8 - - - +
97B LEU 3.2 0.2 - - - -
98B LEU* 1.3 80.6 - - - +
100B TYR* 1.3 93.7 + - + +
101B GLN* 3.6 1.6 - - - +
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Residues in contact with TYR 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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96B TYR* 2.9 75.9 + + + +
99B GLN* 1.3 105.4 + - + +
101B GLN* 1.3 68.6 + - - +
102B GLU* 3.4 17.4 + - + +
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Residues in contact with GLN 101 (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 LEU* 2.7 49.6 + - - +
98B LEU* 3.1 29.0 + - - +
99B GLN 5.1 1.6 - - - +
100B TYR* 1.3 73.8 - - - +
102B GLU* 1.3 59.7 + - - +
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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