Contacts of the helix formed by residues 77 - 102 (chain Q) in PDB entry 1OCR
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 GLU 77 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407N ASP* 4.5 2.8 - - - +
408N THR* 2.7 31.6 + - - +
411N LYS* 3.1 35.1 + - - +
75Q THR* 3.3 18.4 + - - +
76Q ASN* 1.3 76.3 - - - +
78Q TRP* 1.3 65.1 + - - +
80Q THR* 2.8 18.7 + - - -
81Q VAL* 3.0 19.4 + - + -
10X HIS* 3.3 33.6 - - + +
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Residues in contact with TRP 78 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75Q THR 4.0 18.3 + - - -
76Q ASN* 4.3 4.6 + - - +
77Q GLU* 1.3 79.3 - - - +
79Q LYS* 1.3 90.0 + - + +
81Q VAL* 2.9 9.8 + - - +
82Q VAL* 2.8 49.3 + - + +
18X LEU* 4.0 25.1 - - + -
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Residues in contact with LYS 79 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76Q ASN* 3.0 39.3 + - + +
78Q TRP* 1.3 117.7 - - + +
80Q THR* 1.3 64.2 + - - +
83Q GLY* 2.9 24.3 + - - -
14X GLY* 3.4 18.8 - - - +
15X ASN* 3.0 50.1 + - - +
18X LEU* 3.7 16.6 - - + +
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Residues in contact with THR 80 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408N THR* 4.4 11.9 - - + -
412N ILE* 5.1 2.5 - - + -
76Q ASN 3.9 0.5 + - - -
77Q GLU 2.8 7.7 + - - -
79Q LYS* 1.3 78.4 - - - +
81Q VAL* 1.3 58.0 + - - +
84Q ALA* 2.9 37.7 + - + +
9X PHE* 3.7 26.3 - - + -
10X HIS* 2.8 32.9 + - + +
14X GLY* 3.8 14.6 + - - -
17X VAL* 3.6 18.0 - - + +
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Residues in contact with VAL 81 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408N THR* 4.0 16.2 - - + +
411N LYS* 4.1 40.4 - - + +
412N ILE* 4.1 10.3 - - - +
415N ALA* 4.9 7.0 - - + -
77Q GLU* 3.0 30.9 + - + +
78Q TRP* 2.9 11.9 + - - +
80Q THR* 1.3 75.3 - - - +
82Q VAL* 1.3 68.9 + - + +
84Q ALA* 4.1 0.3 - - - -
85Q ALA* 3.0 25.5 + - - +
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Residues in contact with VAL 82 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415N ALA* 6.2 0.7 - - - -
78Q TRP* 2.8 39.8 + - + +
81Q VAL* 1.3 75.6 - - + +
83Q GLY* 1.3 62.7 + - - +
85Q ALA* 3.3 6.7 + - + +
86Q MET* 2.9 42.0 + - + +
18X LEU* 3.8 18.8 - - + -
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Residues in contact with GLY 83 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79Q LYS 2.9 17.0 + - - -
82Q VAL* 1.3 78.5 - - - +
84Q ALA* 1.3 56.1 + - - +
86Q MET* 3.2 6.6 + - - +
87Q PHE* 2.9 28.9 + - - +
17X VAL* 3.8 10.1 - - - -
18X LEU* 3.7 27.9 - - - +
21X GLY* 3.9 3.7 - - - -
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Residues in contact with ALA 84 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409N TRP* 5.2 1.8 - - + -
412N ILE* 3.4 28.9 - - + -
80Q THR* 2.9 25.2 + - + +
83Q GLY* 1.3 70.4 - - - +
85Q ALA* 1.3 62.2 + - - +
87Q PHE* 3.1 8.1 + - - +
88Q PHE* 2.9 40.0 + - + -
17X VAL* 3.6 10.8 - - + +
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Residues in contact with ALA 85 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412N ILE* 4.3 5.7 - - + +
415N ALA* 4.0 26.0 - - + -
416N ILE* 4.2 15.8 - - + +
81Q VAL 3.0 19.1 + - - +
82Q VAL* 3.4 7.9 - - + +
84Q ALA* 1.3 76.9 - - - +
86Q MET* 1.3 59.3 + - + +
88Q PHE* 3.1 5.4 + - - +
89Q ILE* 2.9 36.8 + - + +
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Residues in contact with MET 86 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82Q VAL* 2.9 36.7 + - + +
83Q GLY* 3.7 3.4 - - - +
85Q ALA* 1.3 74.1 - - + +
87Q PHE* 1.3 60.7 + - - +
89Q ILE* 4.2 12.3 - - + -
90Q GLY 2.9 22.9 + - - -
18X LEU* 5.7 0.2 - - - -
21X GLY 4.1 5.8 - - - +
22X ALA* 3.8 31.2 - - + +
25X CYS* 3.1 38.3 - - + +
26X VAL* 5.0 6.7 - - + -
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Residues in contact with PHE 87 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83Q GLY 2.9 13.4 + - - +
84Q ALA* 3.3 11.7 - - - +
85Q ALA 3.1 0.2 - - - -
86Q MET* 1.3 77.9 - - - +
88Q PHE* 1.3 91.4 + + - +
90Q GLY 3.1 1.9 + - - -
91Q PHE* 2.9 35.2 + + + +
20X SER 6.0 0.2 - - - -
21X GLY* 4.1 15.4 + - - -
24X PHE* 3.4 43.8 - + + -
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Residues in contact with PHE 88 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409N TRP* 3.7 26.7 - + - -
412N ILE* 4.4 3.8 - - + -
416N ILE* 3.6 28.7 - - + -
463N THR* 3.9 12.3 - - + +
467N LEU* 4.5 5.8 - - + -
84Q ALA* 2.9 34.4 + - + -
85Q ALA 3.7 0.7 - - - +
87Q PHE* 1.3 98.3 - + - +
89Q ILE* 1.3 60.2 + - - +
91Q PHE* 3.3 9.3 + + - +
92Q THR* 3.0 25.5 + - - -
19Z LEU* 3.8 26.9 - - + -
23Z PHE* 3.8 35.4 - + - -
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Residues in contact with ILE 89 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416N ILE* 4.7 12.3 - - + -
419N VAL* 4.2 32.8 - - + -
423N MET* 6.4 0.4 - - + -
460N ILE* 4.3 27.1 - - + -
85Q ALA* 2.9 26.0 + - + +
86Q MET* 3.8 12.1 - - + +
87Q PHE 3.2 0.2 - - - -
88Q PHE* 1.3 73.8 - - - +
90Q GLY* 1.3 63.8 + - - +
92Q THR* 3.1 20.4 + - - -
25X CYS* 3.8 12.6 - - - -
29X TRP* 2.8 32.1 + - + +
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Residues in contact with GLY 90 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86Q MET 2.9 15.8 + - - -
87Q PHE 3.6 3.4 - - - -
89Q ILE* 1.3 75.3 - - - +
91Q PHE* 1.3 65.7 + - - +
93Q ALA* 2.9 20.8 + - - +
94Q LEU 3.8 1.9 + - - -
24X PHE* 3.7 10.0 - - - -
25X CYS* 3.8 20.0 - - - -
28X VAL* 4.0 8.6 - - - +
29X TRP* 3.7 10.3 - - - -
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Residues in contact with PHE 91 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463N THR* 4.5 10.1 - - + -
466N MET* 4.8 2.7 - - + -
87Q PHE* 2.9 25.5 + + + +
88Q PHE* 3.4 17.7 - + - +
89Q ILE 3.2 0.4 - - - -
90Q GLY* 1.3 75.5 - - - +
92Q THR* 1.3 67.2 + - - +
94Q LEU* 3.1 34.4 + - + +
95Q LEU* 3.7 31.2 + - + -
24X PHE* 3.5 13.5 - + + -
23Z PHE* 3.6 39.7 - + + -
27Z LEU* 4.5 8.5 - - + -
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Residues in contact with THR 92 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459N PHE* 3.7 40.8 - - + +
460N ILE* 3.7 16.7 - - + +
463N THR* 2.7 24.5 + - - +
88Q PHE 3.0 12.3 + - - -
89Q ILE* 3.2 15.8 + - - -
90Q GLY 3.1 0.4 - - - -
91Q PHE* 1.3 79.7 - - - +
93Q ALA* 1.3 56.0 + - - +
95Q LEU* 2.8 26.6 + - + +
96Q LEU* 3.1 16.6 + - + +
29X TRP* 4.8 1.1 - - + -
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Residues in contact with ALA 93 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89Q ILE 3.5 1.8 + - - -
90Q GLY 2.9 13.2 + - - +
92Q THR* 1.3 78.0 - - - +
94Q LEU* 1.3 56.0 + - - +
96Q LEU* 3.4 14.2 - - - +
97Q ILE* 2.9 34.0 + - - +
28X VAL* 3.7 19.5 - - + +
29X TRP* 3.4 33.4 - - + +
32X MET* 4.0 6.1 - - - +
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Residues in contact with LEU 94 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90Q GLY 4.4 2.7 - - - +
91Q PHE* 3.3 28.7 - - + +
92Q THR 2.9 0.8 + - - -
93Q ALA* 1.3 77.0 - - - +
95Q LEU* 1.3 64.1 + - + +
97Q ILE* 3.2 14.2 + - + +
98Q TRP* 2.8 30.0 + - - +
24X PHE* 4.6 14.4 - - + -
28X VAL* 3.4 28.5 - - + -
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Residues in contact with LEU 95 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459N PHE* 4.0 27.7 - - + +
462N LEU* 4.6 4.5 - - + -
463N THR* 4.8 7.9 - - - +
466N MET* 4.6 8.1 - - + -
91Q PHE* 4.2 27.6 - - + +
92Q THR* 2.8 13.0 + - + +
94Q LEU* 1.3 79.1 - - + +
96Q LEU* 1.3 58.2 + - - +
98Q TRP* 3.1 11.9 + - + +
99Q GLU* 2.8 29.6 + - - +
27Z LEU* 3.9 42.8 - - + -
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Residues in contact with LEU 96 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455N SER 5.1 0.7 - - - +
456N MET* 3.4 44.2 - - + +
459N PHE* 4.1 27.8 - - + -
92Q THR* 3.1 9.0 + - + +
93Q ALA* 3.4 11.2 - - - +
94Q LEU 3.1 0.4 - - - -
95Q LEU* 1.3 73.2 - - - +
97Q ILE* 1.3 66.8 + - - +
99Q GLU* 3.0 23.8 + - - +
100Q LYS* 2.9 23.1 + - - +
29X TRP* 3.9 20.4 - - + -
32X MET* 3.6 23.6 - - - -
36X ILE* 5.0 0.2 - - - -
38X ILE* 6.2 0.4 - - + -
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Residues in contact with ILE 97 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93Q ALA 2.9 21.8 + - - +
94Q LEU* 3.5 14.6 - - + +
96Q LEU* 1.3 76.7 - - - +
98Q TRP* 1.3 64.8 + - - +
100Q LYS* 3.2 2.8 + - - +
101Q HIS* 3.1 26.7 + - + +
28X VAL* 4.0 17.3 - - + -
31X TYR* 3.7 30.3 - - + -
32X MET* 3.5 23.6 - - + -
36X ILE* 3.8 27.6 - - + +
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Residues in contact with TRP 98 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94Q LEU 2.8 17.9 + - - +
95Q LEU* 3.3 15.9 - - + +
97Q ILE* 1.3 75.5 - - - +
99Q GLU* 1.3 80.6 + - + +
101Q HIS* 3.3 2.2 + - - -
102Q TYR* 2.9 66.0 + + + -
103Q VAL* 3.2 31.2 - - + -
31Z GLY* 3.7 40.4 - - - -
34Z LEU* 4.5 7.6 - - + -
35Z TYR* 4.4 12.1 - + + -
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Residues in contact with GLU 99 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39N ALA* 4.1 15.1 - - - +
459N PHE* 3.5 31.2 - - + -
95Q LEU 2.8 13.2 + - - +
96Q LEU* 3.4 26.0 - - - +
98Q TRP* 1.3 90.6 - - + +
100Q LYS* 1.3 57.8 + - - +
103Q VAL* 2.9 40.0 + - + +
104Q TYR* 3.0 45.6 + - + -
34Z LEU* 5.7 4.9 - - + +
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Residues in contact with LYS 100 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43N GLN* 3.5 29.9 - - + +
96Q LEU 2.9 12.2 + - - +
97Q ILE 3.6 7.2 - - - +
99Q GLU* 1.3 77.8 + - - +
101Q HIS* 1.3 61.5 + - - +
104Q TYR* 3.5 31.7 + - + +
105Q GLY 4.1 8.1 + - - -
106Q PRO* 5.7 1.0 - - - +
107Q ILE* 5.8 3.2 - - - +
36X ILE* 3.9 31.4 - - + -
37X GLY* 3.6 32.9 + - - +
38X ILE* 4.2 14.8 - - + +
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Residues in contact with HIS 101 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97Q ILE* 3.1 18.7 + - + +
98Q TRP* 3.7 4.3 - - - +
100Q LYS* 1.3 81.8 - - - +
102Q TYR* 1.3 88.7 + + + +
104Q TYR 4.6 4.0 - - - +
36X ILE* 6.3 1.0 - - + +
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Residues in contact with TYR 102 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98Q TRP* 2.9 60.8 + + + +
101Q HIS* 1.3 102.0 + + + +
103Q VAL* 1.3 61.4 + - - +
104Q TYR 5.2 0.4 - - - -
35Z TYR* 3.1 58.1 - + + +
38Z ASP* 5.4 3.3 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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