Contacts of the helix formed by residues 76 - 101 (chain B) in PDB entry 3QU3
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 PRO 76 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU* 1.3 98.1 - - + +
77B PRO* 1.3 66.9 - - + +
78B PRO* 3.4 1.1 - - + -
79B GLU* 3.0 35.3 + - + +
80B ALA* 2.7 31.7 + - - +
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Residues in contact with PRO 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU 3.9 1.1 - - - +
76B PRO* 1.3 84.8 - - + +
78B PRO* 1.3 74.9 - - + +
80B ALA* 3.3 5.6 + - + +
81B GLU* 3.0 24.8 + - - +
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Residues in contact with PRO 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B PRO* 4.2 1.3 - - + -
77B PRO* 1.3 102.9 - - + +
79B GLU* 1.3 72.2 + - - +
81B GLU* 3.6 6.5 + - + +
82B ALA* 3.2 26.2 + - - +
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Residues in contact with GLU 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU* 3.5 18.6 - - + +
76B PRO* 3.0 46.4 + - + +
78B PRO* 1.3 91.6 - - - +
80B ALA* 1.3 62.8 + - - +
82B ALA* 3.5 6.5 + - - +
83B ALA* 3.2 17.3 + - - +
86B ARG* 5.4 1.2 + - - -
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Residues in contact with ALA 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B VAL* 3.4 34.5 - - + +
75B LEU* 3.8 6.2 - - + +
76B PRO 2.7 20.8 + - - +
77B PRO* 3.8 5.4 - - + +
79B GLU* 1.3 71.3 - - - +
81B GLU* 1.3 65.3 + - - +
83B ALA* 3.3 2.9 + - - +
84B GLU* 3.2 32.3 + - - +
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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
----------------------------------------------------------
52B GLU* 4.3 9.6 + - + +
77B PRO 3.0 16.9 + - - +
78B PRO* 3.7 8.1 - - + +
80B ALA* 1.3 78.4 - - - +
82B ALA* 1.3 56.9 + - - +
84B GLU* 3.3 3.7 + - - +
85B ARG* 3.0 55.3 + - - -
88B ARG* 2.9 32.8 + - - +
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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
----------------------------------------------------------
78B PRO 3.2 14.9 + - - +
79B GLU* 3.8 8.1 - - - +
80B ALA 3.3 0.2 - - - -
81B GLU* 1.3 82.4 + - - +
83B ALA* 1.3 61.3 + - - +
85B ARG* 3.5 7.7 + - - +
86B ARG* 3.2 44.1 + - - +
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Residues in contact with ALA 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B TRP* 4.4 9.0 - - + -
73B VAL* 4.4 8.7 - - + -
75B LEU* 4.1 15.9 - - + -
79B GLU 3.2 14.0 + - - +
80B ALA* 3.5 9.2 - - - +
81B GLU 3.2 0.4 - - - -
82B ALA* 1.3 77.3 - - - +
84B GLU* 1.3 59.6 - - - +
86B ARG* 3.4 25.5 + - - +
87B GLU* 3.0 24.9 + - - +
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Residues in contact with GLU 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B GLU* 4.7 9.9 - - - +
59B LYS* 4.2 18.7 + - - +
68B TRP* 3.4 37.2 + - + -
72B GLY* 4.4 10.2 - - - -
73B VAL* 4.8 3.1 + - + +
80B ALA* 3.2 16.8 + - - +
81B GLU* 3.8 3.4 - - - +
83B ALA* 1.3 72.0 - - - +
85B ARG* 1.3 65.5 + - - +
86B ARG 3.1 2.0 - - - -
87B GLU* 2.9 19.6 + - - +
88B ARG* 3.0 42.6 + - - +
91B TRP* 4.1 7.7 - - + -
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Residues in contact with ARG 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ASP* 3.1 49.1 + - + +
50B LEU 3.7 13.9 + - - +
51B ASP* 2.8 31.1 + - - +
52B GLU 5.1 0.2 - - - +
81B GLU* 3.0 43.7 + - - +
82B ALA* 3.6 10.3 - - - +
83B ALA 3.3 0.2 - - - -
84B GLU* 1.3 75.9 - - - +
86B ARG* 1.3 62.3 + - + +
87B GLU 3.2 0.9 + - - -
88B ARG* 3.3 31.2 + - - +
89B ARG* 4.6 12.3 + - - -
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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
----------------------------------------------------------
75B LEU* 6.2 0.4 - - - +
79B GLU 5.4 1.2 + - - -
82B ALA* 3.2 32.5 + - - +
83B ALA* 3.6 25.4 - - - +
84B GLU 3.1 0.4 - - - -
85B ARG* 1.3 77.3 - - + +
87B GLU* 1.3 66.5 + - - +
88B ARG 3.6 0.2 - - - -
89B ARG* 5.1 5.0 + - - +
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Residues in contact with GLU 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B TRP* 3.8 25.4 - - + -
83B ALA 3.0 19.0 - - - +
84B GLU* 2.9 8.8 + - - +
86B ARG* 1.3 86.6 + - - +
88B ARG* 1.3 60.3 - - - +
89B ARG 3.4 1.8 - - - -
90B GLY* 3.3 6.8 + - - -
91B TRP* 3.1 49.3 + - + -
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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
----------------------------------------------------------
50B LEU* 3.0 47.4 + - + +
51B ASP 3.6 10.1 - - - -
52B GLU* 3.7 30.7 + - - +
55B ALA* 3.7 17.7 - - + +
58B PHE* 4.5 1.2 - - - -
81B GLU* 2.9 34.5 + - - +
84B GLU* 3.0 47.5 + - - +
85B ARG* 3.3 33.0 + - - +
87B GLU* 1.3 73.6 - - - +
89B ARG* 1.3 66.5 + - - +
91B TRP* 3.5 16.3 - - + +
92B LYS* 2.9 23.7 + - - +
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Residues in contact with ARG 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B GLY 5.2 3.8 + - - -
47B ARG* 3.2 25.3 + - - +
48B ARG 3.6 7.8 + - - -
49B ASP* 2.9 40.0 + - - +
50B LEU* 3.7 18.3 - - + +
85B ARG 4.6 15.0 + - - -
86B ARG* 5.1 3.6 + - - +
87B GLU 3.4 0.6 - - - -
88B ARG* 1.3 76.3 - - - +
90B GLY* 1.3 64.7 + - - +
92B LYS* 3.2 19.1 + - - +
93B THR* 3.0 26.9 + - - +
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Residues in contact with GLY 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ARG 5.5 1.2 + - - -
87B GLU 3.3 7.5 + - - -
89B ARG* 1.3 78.5 - - - +
91B TRP* 1.3 56.9 + - - +
93B THR* 3.2 7.6 + - - -
94B ASN* 2.8 32.2 + - - +
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Residues in contact with TRP 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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55B ALA* 4.7 3.6 - - + -
58B PHE* 3.7 19.9 - - + +
59B LYS* 3.9 29.2 - - + -
61B TRP* 5.1 0.3 - - - -
62B ALA* 3.3 28.0 - - + +
65B ARG* 4.5 6.5 + - - +
67B ARG* 5.2 6.5 + - + +
68B TRP* 3.4 54.9 - + + +
84B GLU* 4.1 14.6 - - + -
87B GLU* 3.1 35.9 + - + +
88B ARG* 3.5 35.9 - - + +
90B GLY* 1.3 76.5 - - - +
92B LYS* 1.3 56.7 + - - +
94B ASN* 3.5 5.3 + - - +
95B PHE* 2.9 31.4 + - - +
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Residues in contact with LYS 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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45B PHE* 3.7 35.0 - - + -
50B LEU* 4.2 4.3 - - + -
58B PHE* 3.6 25.1 - - + -
88B ARG 2.9 13.0 + - - +
89B ARG* 3.3 27.9 + - - +
91B TRP* 1.3 77.3 - - - +
93B THR* 1.3 82.1 + - - +
95B PHE* 3.2 1.6 + - - +
96B ARG* 2.8 63.7 + - - +
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Residues in contact with THR 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ARG 3.0 11.9 + - - -
90B GLY* 3.6 10.8 - - - -
92B LYS* 1.3 91.5 + - - +
94B ASN* 1.3 69.4 + - - +
96B ARG* 5.0 2.7 - - - -
97B CYS* 3.1 39.0 + - - +
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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
----------------------------------------------------------
61B TRP* 2.7 32.6 + - - -
65B ARG* 2.9 37.7 - - - +
90B GLY 2.8 21.6 + - - +
91B TRP* 3.7 4.7 - - - +
93B THR* 1.3 74.6 - - - +
95B PHE* 1.3 62.6 + - - +
97B CYS* 4.1 2.6 - - - +
98B ALA* 3.1 23.2 + - - +
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Residues in contact with PHE 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PHE* 3.4 34.4 - + - -
15B TRP* 4.2 1.6 - + - -
16B LEU* 3.8 15.9 - - + -
40B VAL* 4.2 15.3 - - + -
41B PRO 5.6 0.4 - - - -
42B TRP* 5.2 2.7 - + - -
57B ILE* 3.7 41.7 - - + -
58B PHE* 3.6 28.9 - + + -
61B TRP* 3.9 16.8 - - + +
91B TRP 2.9 19.4 + - - +
92B LYS 3.5 3.1 - - - +
94B ASN* 1.3 77.1 + - - +
96B ARG* 1.3 71.3 + - + +
98B ALA* 3.2 5.2 + - - +
99B LEU* 3.1 40.1 + - + +
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Residues in contact with ARG 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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41B PRO 4.5 1.6 + - - -
42B TRP* 3.7 52.2 - - + +
43B LYS 2.8 41.8 + - - +
44B HIS* 4.3 8.7 + - - +
45B PHE* 3.7 10.5 - - - +
58B PHE* 3.9 13.1 - - + -
92B LYS* 2.8 51.8 + - + +
93B THR* 4.3 3.1 - - - +
95B PHE* 1.3 84.2 - - + +
97B CYS* 1.3 60.4 + - - +
99B LEU* 3.3 6.7 + - - +
100B HIS* 2.8 40.0 + - + +
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Residues in contact with CYS 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B THR* 3.1 35.7 + - - +
94B ASN* 4.1 3.1 - - - +
96B ARG* 1.3 77.2 - - - +
98B ALA* 1.3 60.0 + - - +
100B HIS* 3.0 13.7 + - - +
101B SER* 2.8 35.8 + - - +
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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
----------------------------------------------------------
12B PHE* 3.5 31.0 - - + +
61B TRP* 4.1 10.8 - - + +
94B ASN* 3.1 18.8 + - - +
95B PHE 3.5 5.2 - - - +
97B CYS* 1.3 75.3 - - - +
99B LEU* 1.3 52.5 + - - +
101B SER* 3.6 6.2 + - - +
102B THR* 2.7 32.7 + - - -
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Residues in contact with LEU 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PHE* 3.5 13.9 - - + -
16B LEU* 3.8 25.6 - - + -
40B VAL* 4.1 13.2 - - + -
42B TRP* 4.1 14.8 - - + -
95B PHE* 3.1 28.9 + - + +
96B ARG* 3.5 10.5 - - - +
98B ALA* 1.3 75.6 - - - +
100B HIS* 1.3 64.2 + - - +
101B SER 3.2 0.2 - - - -
102B THR* 3.2 12.7 + - - -
105B PHE* 4.2 11.6 - - + -
122B TYR* 3.4 42.8 - - + +
135B NA 2.9 20.7 - - - -
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Residues in contact with HIS 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B TRP* 3.7 30.9 - + - -
96B ARG* 2.8 32.6 + - + +
97B CYS* 3.0 14.8 + - - +
99B LEU* 1.3 77.4 - - - +
101B SER* 1.3 61.1 + - - +
102B THR 3.2 2.0 + - - -
103B GLY* 4.9 1.4 + - - -
120B LYS* 4.7 7.4 - - - -
122B TYR* 4.6 8.7 + - - -
135B NA 4.0 8.9 - - - -
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Residues in contact with SER 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B CYS* 2.8 17.8 + - - +
98B ALA* 3.9 5.6 - - - -
99B LEU 3.2 0.2 - - - -
100B HIS* 1.3 77.7 - - - +
102B THR* 1.3 59.3 + - - +
103B GLY* 3.5 4.9 + - - -
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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