Contacts of the helix formed by residues 67 - 89 (chain A) in PDB entry 1B06
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 LEU 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A LEU* 4.7 9.2 - - + -
55A LEU* 3.8 28.7 - - + -
65A TYR* 3.7 18.6 - - + +
66A ASP* 1.3 71.0 - - - +
68A GLN* 1.3 59.8 + - + +
70A ILE* 2.9 14.4 + - + +
71A LEU* 2.9 51.3 + - + +
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Residues in contact with GLN 68 (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 ASP* 3.1 2.5 + - + -
67A LEU* 1.3 79.3 - - + +
69A GLY* 1.3 57.5 + - - +
71A LEU* 4.2 21.6 - - - +
72A ARG* 3.0 46.1 + - - +
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Residues in contact with GLY 69 (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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48A LEU* 4.8 4.2 - - - +
66A ASP* 2.7 22.4 + - - +
68A GLN* 1.3 74.7 - - - +
70A ILE* 1.3 58.6 + - - -
72A ARG* 4.8 0.8 - - - +
73A GLY* 3.2 19.8 + - - -
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Residues in contact with ILE 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU* 4.0 31.0 - - + +
51A ARG* 4.3 27.8 - - + +
52A LEU* 4.3 17.3 - - + +
55A LEU* 4.2 18.6 - - + -
60A LEU* 5.0 0.7 - - + -
65A TYR* 4.1 25.6 - - + -
66A ASP 3.4 4.9 + - - +
67A LEU* 2.9 16.7 + - + +
69A GLY* 1.3 77.6 - - - +
71A LEU* 1.3 64.6 + - + +
73A GLY* 3.3 1.4 + - - -
74A LEU* 3.1 44.0 + - + +
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Residues in contact with LEU 71 (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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52A LEU* 5.1 10.5 - - + -
67A LEU* 2.9 42.6 + - + +
68A GLN* 4.2 21.8 - - - +
70A ILE* 1.3 78.9 - - + +
72A ARG* 1.3 61.3 + - - +
74A LEU* 3.1 27.6 + - + +
75A THR* 3.3 12.2 + - - +
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Residues in contact with ARG 72 (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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68A GLN* 3.0 30.7 + - - +
69A GLY* 4.8 0.9 - - - +
71A LEU* 1.3 75.1 - - - +
73A GLY* 1.3 65.0 + - - +
75A THR* 3.2 20.3 + - - +
76A PHE* 3.3 14.0 + - - +
156A PHE* 3.6 31.9 - - + -
157A MET* 5.1 5.3 - - - -
131B PRO* 4.3 13.7 - - - +
153B GLU* 2.7 44.8 + - - -
157B MET* 5.9 1.0 - - - -
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Residues in contact with GLY 73 (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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48A LEU* 3.3 19.3 - - - -
69A GLY 3.2 16.2 + - - -
71A LEU 3.2 0.6 - - - -
72A ARG* 1.3 77.7 - - - +
74A LEU* 1.3 56.9 + - - +
76A PHE* 3.6 6.3 - - - +
77A ASN* 3.0 37.0 + - - -
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Residues in contact with LEU 74 (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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45A ALA* 3.9 14.8 - - - +
48A LEU* 3.8 24.5 - - + +
49A LEU* 4.1 14.1 - - + -
52A LEU* 4.0 27.1 - - + -
70A ILE* 3.1 28.8 + - + +
71A LEU* 3.4 16.8 - - + +
72A ARG 3.1 0.4 - - - -
73A GLY* 1.3 76.8 - - - +
75A THR* 1.3 59.6 + - - +
76A PHE 3.2 0.2 - - - -
77A ASN* 4.9 0.7 - - - -
78A ILE* 2.8 62.5 + - + +
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Residues in contact with THR 75 (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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71A LEU 3.3 9.8 + - - +
72A ARG* 3.2 20.8 + - - +
74A LEU* 1.3 76.5 - - - +
76A PHE* 1.3 62.4 + - - +
78A ILE* 4.9 2.0 - - - -
79A ASN* 3.0 48.2 + - - +
156A PHE* 3.9 20.5 - - + +
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Residues in contact with PHE 76 (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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41A TYR* 3.9 22.2 - + - -
72A ARG 3.3 14.3 + - - +
73A GLY* 3.6 6.3 - - - +
75A THR* 1.3 81.0 - - - +
77A ASN* 1.3 80.2 + - - +
80A GLY* 3.0 25.1 + - - -
154A ASN* 3.3 26.7 - - - -
155A HIS* 3.5 20.5 - + - +
156A PHE* 3.8 21.7 - + + -
172A PHE* 5.2 0.7 - + - -
131B PRO* 3.8 32.8 - - + -
132B GLY* 3.7 19.1 - - - -
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Residues in contact with ASN 77 (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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40A GLY 4.1 1.4 - - - +
41A TYR* 3.6 43.7 - - - +
44A GLY* 3.9 18.0 - - - -
45A ALA* 3.6 19.7 - - + +
48A LEU* 3.9 8.5 - - - +
73A GLY* 3.0 23.6 + - - +
74A LEU 4.3 0.9 - - - +
76A PHE* 1.3 93.1 - - - +
78A ILE* 1.3 65.7 + - - +
80A GLY* 3.2 1.0 + - - -
81A HIS* 3.0 23.7 + - - +
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Residues in contact with ILE 78 (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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9A TYR* 3.7 41.5 - - + +
45A ALA* 4.2 12.1 - - + -
49A LEU* 5.4 4.3 - - + -
74A LEU* 2.8 49.0 + - + +
75A THR* 4.7 1.6 - - - +
77A ASN* 1.3 71.9 - - - +
79A ASN* 1.3 58.5 + - - +
81A HIS* 3.3 6.3 + - + +
82A LYS* 3.0 54.8 + - + +
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Residues in contact with ASN 79 (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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75A THR* 3.0 39.1 + - - +
78A ILE* 1.3 75.7 - - - +
80A GLY* 1.3 67.5 + - - +
82A LYS* 4.5 7.6 - - - +
83A LEU* 2.9 35.4 + - + +
155A HIS* 3.4 24.7 - - + +
156A PHE* 3.6 18.4 - - - +
159A HIS* 3.6 18.8 + - - -
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Residues in contact with GLY 80 (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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41A TYR* 3.8 14.3 - - - -
76A PHE 3.0 17.8 + - - -
77A ASN 3.2 4.6 + - - -
79A ASN* 1.3 78.7 - - - +
81A HIS* 1.3 60.2 + - - +
83A LEU* 5.0 0.2 - - - -
84A HIS* 2.6 32.1 + - - -
155A HIS* 3.8 24.0 - - - +
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Residues in contact with HIS 81 (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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9A TYR* 3.8 36.5 - + - +
10A GLU 3.8 21.2 + - - -
12A PRO* 4.1 10.3 - - + -
38A HIS* 3.2 35.5 + - - -
41A TYR* 3.8 6.4 - - + +
42A VAL* 3.6 21.8 - - + +
45A ALA* 5.8 1.3 - - + -
77A ASN 3.0 15.1 + - - +
78A ILE* 3.7 5.2 - - - +
80A GLY* 1.3 75.3 - - - +
82A LYS* 1.3 85.5 + - + +
84A HIS 3.2 2.3 + - - -
85A ALA* 3.0 27.0 + - + +
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Residues in contact with LYS 82 (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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9A TYR* 4.2 21.6 + - - -
78A ILE* 3.0 41.0 + - + +
79A ASN* 4.1 7.9 - - - +
81A HIS* 1.3 87.2 + - + +
83A LEU* 1.3 65.4 + - + +
85A ALA* 3.3 8.0 + - - +
86A ILE* 3.2 31.0 + - + +
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Residues in contact with LEU 83 (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 ASN* 2.9 23.6 + - - +
80A GLY 4.4 0.2 - - - +
82A LYS* 1.3 75.9 - - + +
84A HIS* 1.3 61.2 + - - +
86A ILE* 3.4 16.9 + - + +
87A TYR* 3.0 27.0 + - - +
135A TRP* 3.7 49.1 - - + +
137A VAL* 5.6 0.7 - - + -
152A VAL* 5.2 0.4 - - + -
155A HIS* 3.7 25.1 - - + +
159A HIS* 4.1 23.1 - - + +
165A VAL* 4.8 7.9 - - + -
168A ILE* 4.0 19.1 - - + +
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Residues in contact with HIS 84 (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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33A HIS* 3.1 20.5 + + - -
37A HIS* 5.0 0.2 - - - +
38A HIS* 3.6 26.9 - + + +
41A TYR* 3.4 26.3 - + - -
80A GLY 2.6 25.8 + - - +
81A HIS 3.2 3.0 + - - +
83A LEU* 1.3 76.0 - - - +
85A ALA* 1.3 66.3 + - - +
87A TYR* 3.2 7.0 + + - +
88A TRP* 3.0 43.4 + + - +
135A TRP* 3.5 20.7 - + - -
155A HIS* 3.9 6.3 - + - -
170A ASP* 3.3 3.5 + - - -
174A HIS* 3.8 0.4 + - - -
322A FE 2.2 32.2 - - - -
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Residues in contact with ALA 85 (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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12A PRO* 4.6 12.1 - - + -
38A HIS* 3.7 13.4 - - + +
81A HIS* 3.0 18.9 + - + +
82A LYS* 3.4 12.6 - - - +
84A HIS* 1.3 79.6 - - - +
86A ILE* 1.3 61.4 + - + +
88A TRP* 3.9 6.1 + - - +
89A ASN* 3.0 31.0 + - - +
203A ARG* 5.6 0.2 - - - -
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Residues in contact with ILE 86 (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 LYS* 3.2 20.9 + - + +
83A LEU* 3.7 14.6 - - + +
84A HIS 3.2 0.2 - - - -
85A ALA* 1.3 75.4 - - + +
87A TYR* 1.3 55.4 + - - +
89A ASN* 3.1 4.7 + - - +
90A ASN* 2.8 36.2 + - + +
165A VAL* 4.1 34.1 - - + -
168A ILE* 3.9 18.4 - - + -
203A ARG* 3.7 42.3 + - - +
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Residues in contact with TYR 87 (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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25A ILE* 4.0 16.1 - - - +
30A ILE* 6.0 0.6 - - + +
33A HIS* 3.6 22.6 + + - -
83A LEU 3.0 18.2 + - - +
84A HIS* 3.4 8.1 - + - +
86A ILE* 1.3 75.5 - - - +
88A TRP* 1.3 100.6 + + - +
90A ASN* 3.1 9.4 + - - +
91A MET* 3.5 38.3 + - + +
135A TRP* 3.9 12.6 - + + -
168A ILE* 3.9 26.9 - - + +
169A VAL* 4.3 1.8 - - - -
170A ASP* 3.6 29.6 - - + +
175A ALA* 4.6 2.3 + - - +
187A TYR* 2.8 22.8 + - - -
191A TRP* 4.5 3.5 - - - -
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Residues in contact with TRP 88 (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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12A PRO* 5.4 2.7 - - + -
13A GLN 5.7 2.0 - - - -
14A LEU* 3.9 18.2 - - + -
15A PRO* 3.8 21.5 - - + +
16A TYR* 2.7 30.3 + + - +
30A ILE* 4.2 16.8 - - + -
33A HIS* 3.5 38.1 - + + -
34A TYR* 3.8 35.2 - + + -
38A HIS* 2.9 31.5 + + - -
84A HIS* 3.0 34.4 + + + +
85A ALA* 4.2 6.5 - - - +
86A ILE 3.3 0.2 - - - -
87A TYR* 1.3 99.0 - + - +
89A ASN* 1.3 61.7 + - - +
91A MET* 3.4 20.9 + - + +
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Residues in contact with ASN 89 (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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15A PRO* 3.4 24.0 - - - +
85A ALA* 3.0 21.0 + - - +
86A ILE* 3.1 7.4 + - - +
88A TRP* 1.3 74.5 - - - +
90A ASN* 1.3 56.8 + - - +
91A MET 3.1 6.6 + - - +
196A ASN* 3.3 19.6 + - - -
199A ASP* 3.1 28.2 - - - +
203A ARG* 4.1 9.2 - - - +
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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