Contacts of the helix formed by residues 76 - 99 (chain B) in PDB entry 4M83
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 THR 76 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B SER* 1.3 88.6 - - - +
77B LEU* 1.3 55.3 + - - +
78B LEU* 3.4 5.7 + - - +
79B ASP* 3.0 33.9 + - - +
80B ASN* 2.8 38.2 + - - -
157B ARG* 5.4 0.9 + - - -
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Residues in contact with LEU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B SER 4.3 0.4 + - - -
76B THR* 1.3 72.5 + - - +
78B LEU* 1.3 59.3 + - - +
80B ASN* 3.0 12.6 + - + +
81B VAL* 2.9 45.1 + - + +
148B MET* 3.2 57.0 - - + +
149B TRP* 3.4 46.0 - - + +
152B PRO* 4.1 12.3 - - + -
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Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B THR* 3.4 4.4 + - - +
77B LEU* 1.3 78.1 - - - +
79B ASP* 1.3 60.7 + - - +
81B VAL* 4.4 2.2 - - + -
82B GLU* 3.2 35.6 + - + +
83B PRO* 3.9 0.3 - - - +
149B TRP* 3.7 29.4 - - + -
152B PRO* 4.1 17.4 - - + +
155B THR* 3.9 23.1 - - + +
157B ARG* 3.5 32.9 + - + +
158B GLY* 3.9 11.7 - - - +
161B TYR* 3.9 28.0 - - + -
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Residues in contact with ASP 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B TRP 3.8 22.4 - - - +
74B GLY* 4.5 6.9 - - - -
75B SER* 5.4 0.7 + - - -
76B THR* 3.0 34.1 + - - +
78B LEU* 1.3 76.3 - - - +
80B ASN* 1.3 64.2 + - - +
83B PRO* 3.3 19.4 - - - +
157B ARG* 3.1 28.2 + - - +
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Residues in contact with ASN 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B TRP* 5.5 0.8 - - - -
74B GLY* 3.3 35.0 + - - +
75B SER 4.3 5.4 - - - +
76B THR 2.8 21.6 + - - +
77B LEU* 3.0 12.8 + - + +
79B ASP* 1.3 79.3 - - - +
81B VAL* 1.3 68.4 + - + +
83B PRO* 3.4 5.5 - - - +
84B PHE* 3.2 25.4 - - - -
501B ERY 3.3 51.5 - - + +
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Residues in contact with VAL 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LEU* 2.9 39.9 + - + +
78B LEU* 4.4 2.9 - - + -
80B ASN* 1.3 80.2 - - + +
82B GLU* 1.3 68.1 + - - +
84B PHE* 3.3 20.0 + - - +
85B LEU 3.6 6.8 + - - -
114B TYR* 4.7 2.2 + - - +
149B TRP* 3.4 28.7 - - + +
161B TYR* 3.4 27.9 + - + +
501B ERY 3.9 28.3 - - + +
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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
----------------------------------------------------------
78B LEU* 3.2 19.6 + - + +
81B VAL* 1.3 76.2 - - - +
83B PRO* 1.3 71.2 - - + +
85B LEU* 3.0 12.1 + - - -
86B ASN* 3.2 36.5 + - - +
157B ARG* 3.0 39.9 + - - +
161B TYR* 3.9 43.5 + - + +
164B ARG* 5.8 0.5 + - - -
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Residues in contact with PRO 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B THR* 5.1 1.0 + - - -
63B LEU* 3.2 20.6 - - + +
64B PRO* 4.7 13.9 - - + -
73B TRP* 5.9 5.6 - - + +
78B LEU 3.9 1.1 - - - +
79B ASP* 3.3 26.5 - - - +
80B ASN 3.4 8.5 - - - +
82B GLU* 1.3 93.8 - - + +
84B PHE* 1.3 65.8 + - + +
86B ASN* 3.5 5.2 + - + +
87B ASP* 3.2 18.0 + - - +
157B ARG* 5.7 0.4 - - - +
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Residues in contact with PHE 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ILE* 4.1 13.2 - - + -
63B LEU* 3.8 15.7 - - + -
73B TRP* 3.7 29.2 - + - -
80B ASN 3.2 28.3 - - - -
81B VAL* 3.3 8.7 + - - +
82B GLU 3.1 0.8 - - - -
83B PRO* 1.3 82.1 - - + +
85B LEU* 1.3 61.3 + - - +
87B ASP* 3.4 4.9 - - - +
88B ALA 3.3 14.2 + - - -
112B THR* 3.6 36.0 - - + +
114B TYR* 3.7 25.9 - - + +
501B ERY 3.5 56.1 - - + -
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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
----------------------------------------------------------
81B VAL 3.6 2.5 + - - +
82B GLU* 3.0 8.0 + - - +
84B PHE* 1.3 75.2 - - - +
86B ASN* 1.3 74.9 + - - +
87B ASP 2.9 1.8 - - - -
88B ALA* 2.8 21.5 + - + +
89B ILE* 3.2 26.7 + - + +
114B TYR* 3.7 12.9 - - + -
161B TYR* 3.6 46.0 - - + +
164B ARG* 4.4 7.9 - - + -
165B PHE* 4.0 44.9 - - + +
168B TRP* 4.3 10.1 - - + -
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Residues in contact with ASN 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B THR* 4.5 4.7 + - - +
82B GLU* 3.2 32.1 + - - +
83B PRO* 4.3 4.7 - - + +
85B LEU* 1.3 86.1 - - - +
87B ASP* 1.3 59.2 + - - +
89B ILE* 3.5 6.1 + - - +
90B GLN* 2.9 23.8 + - - +
164B ARG* 2.8 43.1 + - - +
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Residues in contact with ASP 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ILE* 4.6 2.4 - - - +
59B TYR* 4.6 11.0 + - - -
61B SER* 3.7 8.2 - - - -
62B THR* 3.4 16.8 + - - +
63B LEU* 3.4 35.5 - - + +
83B PRO 3.2 13.7 + - - +
84B PHE 3.4 11.2 - - - +
85B LEU 2.9 0.2 - - - -
86B ASN* 1.3 74.3 - - - +
88B ALA* 1.3 66.0 + - - +
90B GLN* 2.5 43.4 + - - +
91B ALA* 3.0 16.7 + - - +
115B PRO* 6.0 1.2 - - - +
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Residues in contact with ALA 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B PHE 3.3 2.6 + - - -
85B LEU* 2.8 16.4 + - + +
87B ASP* 1.3 73.7 - - - +
89B ILE* 1.3 57.7 + - - +
91B ALA 3.2 0.2 + - - -
92B LEU* 2.8 34.1 + - - +
114B TYR* 3.4 39.5 - - + -
115B PRO* 3.9 14.3 - - + +
168B TRP* 3.6 18.6 - - + -
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Residues in contact with ILE 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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85B LEU* 3.2 15.3 + - + +
86B ASN* 3.5 7.2 + - - +
87B ASP 3.2 1.0 - - - -
88B ALA* 1.3 77.1 - - - +
90B GLN* 1.3 60.5 + - + +
92B LEU* 4.4 1.6 - - - +
93B PRO* 3.4 18.5 - - - +
164B ARG* 3.7 36.8 - - + +
168B TRP* 3.4 52.9 - - + +
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Residues in contact with GLN 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B HIS* 2.7 34.9 + - + +
62B THR* 3.5 27.6 + - + +
86B ASN 2.9 8.8 + - - +
87B ASP* 2.5 50.3 + - - +
89B ILE* 1.3 78.9 - - + +
91B ALA* 1.3 55.1 + - - +
93B PRO* 4.3 5.7 - - - +
94B GLN* 2.7 33.4 - - - +
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Residues in contact with ALA 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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59B TYR* 4.0 27.4 - - + -
87B ASP* 3.0 20.4 + - - +
88B ALA 3.7 2.5 - - - +
90B GLN* 1.3 80.9 - - - +
92B LEU* 1.3 55.9 + - - +
93B PRO* 3.3 2.5 - - - -
94B GLN* 2.6 38.4 + - - +
95B LEU* 3.2 10.9 + - + +
115B PRO* 3.8 16.6 - - + -
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Residues in contact with LEU 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ALA 2.8 20.3 + - - +
89B ILE* 4.4 2.0 - - + +
91B ALA* 1.3 71.6 - - - +
93B PRO* 1.3 83.5 - - + +
95B LEU* 3.5 3.0 + - - +
96B ALA* 3.2 20.4 + - - +
115B PRO* 4.1 15.0 - - + +
118B VAL* 3.5 18.8 - - + -
119B LEU* 4.6 8.1 - - + +
122B ARG* 4.0 12.6 - - - +
168B TRP* 3.5 36.1 - - + +
172B ASN* 3.2 30.1 - - - +
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Residues in contact with PRO 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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89B ILE 3.4 17.9 - - - +
90B GLN* 4.3 7.0 - - - +
91B ALA 3.6 2.2 - - - -
92B LEU* 1.3 104.8 - - + +
94B GLN* 1.3 60.2 + - + +
96B ALA* 3.7 8.3 - - + +
97B ASP* 2.9 29.8 + - - +
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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
----------------------------------------------------------
58B LEU 5.1 2.3 - - - +
59B TYR* 3.8 13.7 - - + +
60B HIS* 2.8 59.8 - - - +
90B GLN* 2.7 31.2 + - - +
91B ALA* 2.6 16.4 + - - +
93B PRO* 1.3 74.9 - - + +
95B LEU* 1.3 57.8 + - - +
97B ASP* 3.7 8.4 - - - +
98B ALA* 3.5 20.4 + - - +
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Residues in contact with LEU 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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12B PHE* 3.4 31.0 - - + -
40B ALA* 4.2 10.3 - - + -
57B VAL* 5.0 5.2 - - + +
58B LEU 5.0 1.1 - - - +
59B TYR* 3.5 46.2 - - + -
91B ALA* 3.2 12.5 + - + +
92B LEU 4.0 2.7 - - - +
93B PRO 3.1 0.4 - - - -
94B GLN* 1.3 75.9 - - - +
96B ALA* 1.3 66.5 + - - +
97B ASP 3.2 1.1 - - - -
98B ALA* 3.8 3.1 - - - +
99B TYR* 3.0 34.0 + - + +
113B SER* 5.4 1.1 - - - +
115B PRO* 3.6 30.1 - - + -
119B LEU* 3.6 16.4 - - + -
123B TRP* 4.1 1.2 - - - -
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Residues in contact with ALA 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B LEU 3.2 18.1 + - - +
93B PRO* 3.7 9.9 - - + +
95B LEU* 1.3 77.2 - - - +
97B ASP* 1.3 62.7 + - - +
99B TYR 3.9 0.5 - - - -
100B ALA* 3.1 23.9 + - - +
119B LEU* 4.3 9.5 - - + +
122B ARG* 3.6 28.0 - - - +
123B TRP* 4.7 5.5 + - - +
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Residues in contact with ASP 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B PRO 2.9 18.1 + - - +
94B GLN* 3.7 10.5 - - - +
96B ALA* 1.3 76.7 - - - +
98B ALA* 1.3 64.8 + - - +
100B ALA* 3.0 20.1 - - - +
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Residues in contact with ALA 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B VAL* 3.5 31.2 - - + -
58B LEU 5.3 2.9 - - - +
94B GLN 3.5 14.4 + - - +
95B LEU* 3.5 4.9 + - - +
96B ALA 3.4 0.4 - - - -
97B ASP* 1.3 77.5 - - - +
99B TYR* 1.3 60.1 + - + +
100B ALA* 2.8 12.2 + - - +
101B ASP 4.3 2.1 + - - -
102B ASP* 5.4 1.2 + - - +
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Residues in contact with TYR 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B HIS* 3.9 12.1 - + - -
10B ALA* 3.5 15.5 - - + +
12B PHE* 3.6 22.9 - + - -
38B THR* 2.8 38.3 + - + -
40B ALA* 3.8 16.2 + - + +
57B VAL* 3.5 30.9 - - + +
95B LEU* 3.0 17.4 + - + +
96B ALA 3.9 1.3 - - - -
98B ALA* 1.3 76.7 - - + +
100B ALA* 1.3 64.0 + - - +
101B ASP 3.1 3.2 + - - -
102B ASP* 3.2 35.9 + - + +
103B ILE* 3.7 7.8 + - - +
104B PRO* 4.2 5.4 - - + -
123B TRP* 3.4 33.6 - + + -
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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
------------------------------------------------------------
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