Contacts of the helix formed by residues 82 - 105 (chain B) in PDB entry 4B8Z
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 TYR 82 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B MET* 4.6 4.0 - - + -
78B ARG* 3.0 49.1 + - + +
79B ASN 3.5 3.3 + - - -
81B LYS* 1.4 112.6 - - + +
83B ASN* 1.3 57.1 + - - +
84B LEU 3.3 3.1 - - - +
85B ASP* 3.3 29.8 + - + +
86B PHE* 3.0 33.6 + + + -
183B GLU* 5.8 0.3 + - - -
184B ASP* 5.2 3.6 - - - -
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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
----------------------------------------------------------
79B ASN* 2.8 24.2 + - - +
80B ILE* 3.7 13.1 + - - +
81B LYS 3.9 2.0 + - - -
82B TYR* 1.3 73.9 - - - +
84B LEU* 1.4 56.4 + - - +
86B PHE* 4.4 4.4 - - - +
87B TRP* 3.1 28.2 + - - +
138B ASN 4.2 2.0 + - - -
139B SER 3.5 11.7 + - - -
140B ASN* 3.4 7.4 - - - -
141B PHE* 3.3 46.6 + - + -
142B GLY* 3.2 25.5 + - - +
143B TYR 4.5 0.9 + - - -
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Residues in contact with LEU 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B TYR* 3.3 1.0 - - - -
83B ASN* 1.4 75.3 - - - +
85B ASP* 1.3 64.3 + - - +
87B TRP* 3.3 13.2 + - + +
88B ARG* 2.8 65.7 + - + +
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Residues in contact with ASP 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B MET* 3.6 18.8 - - + -
82B TYR* 3.3 32.1 + - + +
84B LEU* 1.3 84.3 - - - +
86B PHE* 1.4 58.7 + - - +
88B ARG* 4.7 2.2 - - - +
89B LYS* 3.0 51.1 + - + +
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Residues in contact with PHE 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B MET* 3.3 53.4 - - + -
73B VAL* 4.0 0.7 - - - -
74B GLY* 3.6 20.2 - - - -
78B ARG* 3.6 44.4 - - + -
79B ASN* 3.4 32.5 - - - +
82B TYR* 3.0 31.3 + - + +
83B ASN* 4.0 5.4 - - - +
85B ASP* 1.4 75.9 - - - +
87B TRP* 1.3 55.7 + - - +
90B ASN* 2.7 34.6 + - - +
143B TYR* 3.7 26.9 - + + +
146B ALA* 4.0 2.3 - - - +
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Residues in contact with TRP 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 20.1 + - - +
84B LEU* 3.6 14.1 - - + +
86B PHE* 1.3 75.8 - - - +
88B ARG* 1.4 84.6 + - + +
91B VAL* 3.1 66.2 + - + +
141B PHE* 6.4 0.2 - - + -
142B GLY* 3.6 20.6 - - - +
145B TYR* 3.6 20.4 - - + -
146B ALA* 3.5 30.4 - - - +
149B MET* 4.2 13.5 - - + -
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Residues in contact with ARG 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B LEU* 2.8 44.8 + - + +
85B ASP* 4.4 2.2 - - - +
87B TRP* 1.4 87.0 - - + +
89B LYS* 1.3 64.4 + - + +
91B VAL* 3.9 3.1 - - - +
92B HIS* 2.7 64.5 + - + -
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Residues in contact with LYS 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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49B THR* 3.7 17.2 - - + +
72B MET* 3.8 29.8 - - + -
85B ASP* 3.0 34.6 + - + +
88B ARG* 1.3 72.7 - - + +
90B ASN* 1.3 60.4 + - - +
92B HIS* 3.7 2.4 + - - -
93B MET* 3.2 41.7 + - + +
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Residues in contact with ASN 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ALA* 3.4 12.6 - - + +
72B MET* 2.6 48.4 + - - +
86B PHE* 2.7 25.8 + - - +
87B TRP 3.7 0.6 + - - -
88B ARG 3.3 0.2 - - - -
89B LYS* 1.3 73.9 - - - +
91B VAL* 1.4 54.8 + - - +
93B MET* 3.3 6.5 + - - +
94B ASN* 2.8 46.7 + - - +
143B TYR* 3.5 22.6 - - - +
146B ALA* 3.7 14.4 - - + +
147B LYS* 4.7 3.7 - - - +
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Residues in contact with VAL 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 TRP* 3.1 65.4 + - + +
88B ARG* 3.4 5.1 + - - +
90B ASN* 1.4 73.5 - - - +
92B HIS* 1.3 63.0 + - + +
94B ASN* 3.9 5.9 - - - +
95B ASP* 3.0 34.0 + - + +
146B ALA* 4.0 11.7 - - + +
149B MET* 5.3 4.7 - - + -
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Residues in contact with HIS 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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48B LEU 4.1 0.2 - - - -
49B THR* 4.0 28.9 - - - +
51B THR* 6.1 0.9 - - - -
88B ARG* 2.7 69.6 + - + +
89B LYS* 3.8 6.1 - - - +
91B VAL* 1.3 80.1 - - + +
93B MET* 1.3 56.6 + - - +
95B ASP* 4.0 2.5 - - - +
96B ASN* 3.0 39.9 + - - +
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Residues in contact with MET 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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48B LEU* 3.4 32.1 + - + -
49B THR* 3.8 8.5 - - + -
68B HIS* 4.3 2.5 - - + -
70B ALA* 3.9 14.1 - - - +
71B ALA* 3.8 15.0 - - - -
72B MET* 3.7 27.1 - - + +
89B LYS* 3.2 36.1 + - + +
90B ASN* 3.3 5.4 + - - +
92B HIS* 1.3 76.3 - - - +
94B ASN* 1.3 57.7 + - - +
96B ASN* 4.0 0.9 - - - +
97B VAL* 3.1 35.2 + - - +
900B NAP 3.5 37.7 - - - +
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Residues in contact with ASN 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B HIS* 2.8 31.6 + - + +
70B ALA 4.4 4.7 - - - +
71B ALA* 5.5 0.7 - - - +
90B ASN* 2.8 34.7 + - - +
91B VAL* 3.9 5.4 - - - +
93B MET* 1.3 69.3 - - - +
95B ASP* 1.3 59.5 + - - +
97B VAL* 4.0 0.5 - - - +
98B LEU* 2.9 42.2 + - + +
146B ALA 3.5 26.0 + - - +
147B LYS* 5.0 5.6 + - - +
150B ILE* 3.5 31.6 - - + +
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Residues in contact with ASP 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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91B VAL* 3.0 23.1 + - + +
92B HIS* 4.0 3.6 - - - +
94B ASN* 1.3 75.3 - - - +
96B ASN* 1.3 63.4 + - - +
98B LEU* 4.7 3.8 - - - +
99B HIS* 3.0 39.7 + - - +
157B TYR* 4.9 3.8 + - - -
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Residues in contact with ASN 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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48B LEU 2.9 27.1 + - - +
49B THR 3.1 23.2 + - - -
50B ASP 3.7 0.2 - - - -
51B THR* 3.2 41.9 + - + +
54B THR* 3.4 13.9 - - + +
92B HIS* 3.0 21.2 + - - +
93B MET 4.0 0.2 - - - +
95B ASP* 1.3 82.4 - - - +
97B VAL* 1.3 57.2 + - - +
99B HIS* 5.3 0.9 - - - -
100B SER* 2.7 37.2 + - - -
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Residues in contact with VAL 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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13B THR* 4.2 9.0 - - + -
48B LEU* 3.7 32.3 - - + -
54B THR* 4.3 2.0 - - + -
58B PHE* 3.6 21.7 - - + -
66B VAL* 4.3 7.9 - - + -
68B HIS* 3.5 45.1 - - + +
93B MET 3.1 21.4 + - - +
94B ASN 4.1 1.3 - - - +
96B ASN* 1.3 73.6 - - - +
98B LEU* 1.3 60.6 + - + +
100B SER 3.5 0.3 + - - -
101B ALA* 3.1 29.1 + - - +
109B VAL* 5.2 2.7 - - + -
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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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68B HIS* 5.5 2.2 - - + -
94B ASN* 2.9 28.6 + - + +
95B ASP* 4.3 3.6 - - - +
97B VAL* 1.3 79.0 - - + +
99B HIS* 1.4 59.8 + - - +
101B ALA* 3.6 2.1 + - - +
102B PHE* 3.2 17.5 + - - +
109B VAL* 3.7 14.1 - - + -
111B SER* 3.7 21.3 - - - +
150B ILE* 4.5 14.8 - - + +
153B GLN* 3.8 28.9 - - + -
154B ASN* 3.9 11.4 - - - +
157B TYR* 3.9 13.9 - - + +
165B PHE* 3.3 36.7 - - + -
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Residues in contact with HIS 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 ASP* 3.0 27.5 + - - +
96B ASN* 4.8 0.9 - - - +
98B LEU* 1.4 74.5 - - - +
100B SER* 1.4 60.0 + - - +
102B PHE* 3.3 24.4 + + - +
103B GLU* 3.1 57.0 + - - +
157B TYR* 2.7 28.0 + + - +
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Residues in contact with SER 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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51B THR* 5.0 2.1 + - - +
54B THR* 3.7 8.9 - - - +
55B ARG* 3.9 18.5 + - - +
58B PHE* 3.6 31.7 - - - -
96B ASN* 2.7 24.5 + - - -
97B VAL 3.9 0.9 - - - -
98B LEU 3.4 0.2 - - - -
99B HIS* 1.4 75.2 - - - +
101B ALA* 1.4 58.6 + - - +
103B GLU* 3.5 16.6 + - - +
104B VAL* 3.1 29.8 + - - +
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Residues in contact with ALA 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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58B PHE* 3.7 20.6 - - + -
66B VAL* 4.3 1.8 - - + -
97B VAL 3.1 19.1 + - - +
98B LEU 3.7 4.9 - - - +
100B SER* 1.4 74.0 - - - +
102B PHE* 1.3 56.2 + - - +
104B VAL* 3.8 1.6 + - - -
105B GLY 3.2 5.5 + - - -
106B ALA* 2.8 40.3 + - + +
109B VAL* 3.6 30.1 - - + -
165B PHE* 4.3 1.8 - - - -
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Residues in contact with PHE 102 (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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98B LEU 3.2 14.3 + - - +
99B HIS* 3.4 33.2 - + - +
100B SER 3.3 0.2 - - - -
101B ALA* 1.3 76.7 - - - +
103B GLU* 1.4 64.1 + - + +
105B GLY* 3.2 18.1 + - - -
106B ALA 5.0 0.4 - - - +
157B TYR* 3.6 23.8 - + + -
161B TYR* 3.5 63.0 - + + -
163B CYS* 3.7 15.9 - - - -
165B PHE* 4.0 7.8 - - + -
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Residues in contact with GLU 103 (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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55B ARG* 3.2 46.9 + - - +
99B HIS* 3.1 39.3 + - - +
100B SER* 3.5 19.3 + - - +
102B PHE* 1.4 81.7 - - + +
104B VAL* 1.3 58.4 + - - +
105B GLY* 3.3 0.7 + - - -
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Residues in contact with VAL 104 (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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55B ARG* 4.8 7.4 - - - +
58B PHE* 4.1 16.8 - - + +
59B GLU* 5.5 1.3 - - - +
62B GLN* 3.8 29.6 + - - +
63B PRO* 4.7 14.6 - - + +
100B SER 3.1 20.2 + - - +
101B ALA* 4.3 4.7 - - - +
103B GLU* 1.3 75.1 - - - +
105B GLY* 1.3 62.3 + - - +
106B ALA* 5.1 0.7 - - + +
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Residues in contact with GLY 105 (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 PRO 4.6 3.1 - - - +
64B THR* 5.3 1.4 - - - +
101B ALA 3.2 0.6 + - - -
102B PHE 3.2 15.4 + - - -
103B GLU 3.3 0.8 - - - -
104B VAL* 1.3 81.6 - - - +
106B ALA* 1.3 64.4 + - - +
107B ARG* 3.6 2.8 + - - +
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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
------------------------------------------------------------
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