Contacts of the helix formed by residues 70 - 91 (chain X) in PDB entry 3J9X
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 GLY 70 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2147 T 3.5 24.8 + - - +
2157 A 4.4 2.0 + - - -
111U PHE* 3.5 19.4 - - - -
90V ILE* 5.6 0.8 - - - +
99V MET* 5.3 0.2 - - - +
69X THR* 1.3 75.3 - - - +
71X PRO* 1.3 67.1 - - - +
73X ARG* 2.9 36.1 + - - +
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Residues in contact with PRO 71 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2147 T 3.6 23.1 - - + +
2157 A 3.9 32.8 - - - +
71U PRO* 3.6 19.2 - - + +
74U ALA* 4.8 2.9 - - + -
75U ILE* 3.5 37.2 - - + +
107U TYR* 6.5 0.9 - - + -
111U PHE* 4.6 6.5 - - + -
69X THR 4.4 0.2 - - - +
70X GLY* 1.3 83.5 - - - +
72X ASN* 1.3 64.3 + - - +
73X ARG 3.1 0.7 - - - -
74X ALA* 3.1 4.7 + - - +
75X ILE* 3.0 24.8 + - - +
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Residues in contact with ASN 72 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72U ASN* 3.1 24.4 - - - +
75U ILE* 3.5 11.5 - - - +
111U PHE 3.3 25.1 + - - -
112U ASN* 4.8 8.5 + - - +
68X ILE* 3.5 16.4 - - + -
69X THR 3.3 14.5 + - - +
70X GLY 3.0 0.8 - - - -
71X PRO* 1.3 75.4 - - - +
73X ARG* 1.3 65.5 + - - +
75X ILE* 3.3 19.2 + - + +
76X TYR* 3.0 25.5 - - + -
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Residues in contact with ARG 73 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2147 T 3.0 35.4 + - - +
89V ARG 4.6 1.2 + - - -
90V ILE* 3.7 26.8 + - - +
60X SER* 2.7 46.9 + - - +
63X LEU* 3.5 16.7 - - + +
64X THR* 2.9 31.9 + - - +
68X ILE* 2.8 56.3 + - + +
69X THR* 3.8 7.6 - - - +
70X GLY 2.9 15.0 + - - +
72X ASN* 1.3 76.8 - - - +
74X ALA* 1.3 58.4 + - - +
76X TYR* 3.0 5.2 + - - -
77X GLN* 2.8 30.1 + - - +
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Residues in contact with ALA 74 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2137 A 4.1 16.9 - - + +
2147 T 3.0 41.4 + - + +
1358 A 4.7 4.9 - - + -
1368 T 4.4 5.5 - - - +
71U PRO* 4.8 3.6 - - + -
70X GLY 3.6 0.6 + - - -
71X PRO 3.1 8.8 + - - +
73X ARG* 1.3 77.4 - - - +
75X ILE* 1.3 65.0 + - - +
77X GLN* 3.6 10.3 - - - +
78X GLY* 2.9 21.7 + - - -
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Residues in contact with ILE 75 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1368 T 5.8 0.2 - - - -
71U PRO* 3.6 27.1 - - + +
72U ASN* 3.5 35.9 - - - +
71X PRO 3.0 14.0 + - - +
72X ASN* 3.4 22.2 - - - +
74X ALA* 1.3 77.7 - - - +
76X TYR* 1.3 68.2 + - + +
78X GLY* 3.4 0.5 + - - -
79X PHE* 3.1 21.7 + - - +
107X TYR* 3.5 31.2 - - + -
111X PHE* 4.6 11.2 - - + +
112X ASN 5.9 0.4 - - - +
113X ALA* 4.1 19.7 - - + -
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Residues in contact with TYR 76 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59X VAL* 4.4 3.1 - - - +
63X LEU* 3.6 28.5 - - + -
68X ILE* 4.0 18.5 - - + +
72X ASN* 3.0 27.6 - - + -
73X ARG 3.0 6.1 + - - +
75X ILE* 1.3 80.8 - - + +
77X GLN* 1.3 59.5 + - - +
79X PHE* 3.3 6.4 + - - +
80X GLY* 2.8 27.4 + - - -
112X ASN 5.0 0.3 + - - -
113X ALA* 3.9 9.5 - - + -
114X ASN* 2.9 38.5 + - - +
117X VAL* 3.7 30.5 - - + +
118X LEU* 3.7 30.7 - - + -
121X VAL* 4.2 12.3 - - + +
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Residues in contact with GLN 77 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2137 A 3.4 34.1 + - + +
2147 T 3.1 21.3 + - - +
55X VAL* 5.4 0.5 - - - +
56X ASN* 3.4 23.6 + - - +
59X VAL* 3.3 21.2 - - - +
60X SER* 3.5 26.5 - - - +
63X LEU* 4.0 2.1 - - + +
73X ARG 2.8 21.9 + - - +
74X ALA* 3.6 8.7 - - - +
76X TYR* 1.3 77.0 - - - +
78X GLY* 1.3 57.4 + - - +
80X GLY* 3.3 0.3 + - - -
81X LEU* 2.9 42.2 + - + +
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Residues in contact with GLY 78 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2137 A 5.4 1.1 + - - -
1368 T 5.1 3.8 - - - -
1378 A 4.1 24.7 - - - +
74X ALA 2.9 15.8 + - - -
75X ILE 3.8 2.0 - - - -
77X GLN* 1.3 77.0 - - - +
79X PHE* 1.3 61.1 + - - +
81X LEU* 3.8 4.9 - - - +
82X LYS* 3.0 24.9 + - - +
107X TYR* 3.5 12.7 + - - -
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Residues in contact with PHE 79 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75X ILE 3.1 13.4 + - - +
76X TYR 3.5 8.1 - - - +
78X GLY* 1.3 76.5 - - - +
80X GLY* 1.3 64.3 - - - +
82X LYS* 3.1 5.5 + - - +
83X VAL* 2.9 33.4 + - + +
100X ILE* 5.1 1.8 - - + -
103X LEU* 3.7 24.2 - - + -
104X LYS* 3.8 23.1 - - + -
107X TYR* 3.5 34.1 + + + -
118X LEU* 3.3 53.6 - - + -
121X VAL* 3.8 16.8 - - + -
122X VAL* 3.7 24.2 - - + -
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Residues in contact with GLY 80 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55X VAL* 4.5 6.7 - - - -
59X VAL* 5.0 2.0 - - - -
76X TYR 2.8 17.1 + - - -
77X GLN* 3.8 0.9 - - - -
79X PHE* 1.3 73.4 - - - +
81X LEU* 1.3 62.7 + - - +
83X VAL* 3.1 2.8 + - - -
84X ALA* 3.0 19.8 + - - +
121X VAL* 3.5 26.7 - - - -
125X ILE* 3.1 17.7 - - - +
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Residues in contact with LEU 81 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2127 T 5.5 1.6 - - - +
2137 A 5.6 3.8 - - - +
1378 A 4.1 19.5 - - + +
1388 T 3.4 36.6 - - - +
52X PHE* 3.5 42.4 - - + +
55X VAL* 4.5 6.7 - - + +
56X ASN* 3.4 31.4 - - - +
77X GLN* 2.9 29.8 + - + +
78X GLY* 3.8 4.5 - - - +
80X GLY* 1.3 75.0 - - - +
82X LYS* 1.3 57.9 + - - +
84X ALA* 3.2 3.9 + - - -
85X ARG 2.9 23.7 + - - -
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Residues in contact with LYS 82 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2037 A 4.9 0.2 + - - -
2047 T 3.2 13.7 + - - -
1378 A 3.7 26.4 + - - +
1388 T 3.3 28.1 + - - +
106W TYR* 2.8 34.0 + - - -
78X GLY 3.0 17.7 + - - +
79X PHE* 3.5 5.2 - - - +
81X LEU* 1.3 74.3 - - - +
83X VAL* 1.3 64.6 + - - +
85X ARG* 3.3 11.2 + - - +
86X ALA* 3.1 22.3 + - - +
99X MET* 5.9 2.8 - - - -
103X LEU* 3.5 35.5 - - + +
106X TYR* 5.0 6.5 - - + -
107X TYR* 4.6 3.6 - - + -
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Residues in contact with VAL 83 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79X PHE* 2.9 43.3 + - + +
80X GLY* 3.3 8.7 - - - +
82X LYS* 1.3 75.3 - - - +
84X ALA* 1.3 62.1 + - - +
86X ALA* 3.3 8.2 + - - +
87X LEU* 3.0 20.1 + - + +
96X LEU* 4.5 2.9 - - + +
100X ILE* 4.3 27.6 - - + -
103X LEU* 3.7 18.4 - - + -
122X VAL* 4.6 8.3 - - + -
125X ILE* 3.9 25.6 - - + -
126X THR* 4.5 5.6 - - + -
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Residues in contact with ALA 84 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51X LYS 5.7 0.4 - - - +
52X PHE* 3.6 20.2 - - + -
55X VAL* 4.2 19.7 - - + -
80X GLY 3.0 12.1 + - - +
81X LEU* 3.5 8.3 - - - +
83X VAL* 1.3 73.4 - - - +
85X ARG* 1.3 68.0 + - - +
87X LEU* 3.1 12.6 + - + +
88X ASN* 3.0 24.9 + - - +
125X ILE* 4.4 11.0 - - + +
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Residues in contact with ARG 85 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2037 A 3.8 35.3 + - - -
2047 T 2.9 33.7 + - - +
1388 T 3.0 35.9 + - - +
1398 A 3.4 29.7 + - - +
52X PHE* 3.5 11.3 - - - -
81X LEU 2.9 13.5 + - - +
82X LYS* 3.3 20.8 - - - +
83X VAL 3.2 0.4 - - - -
84X ALA* 1.3 74.8 - - - +
86X ALA* 1.3 63.6 - - - +
88X ASN* 3.0 6.5 + - - +
89X ARG* 3.0 45.1 + - - +
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Residues in contact with ALA 86 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2037 A 5.6 3.1 - - - +
82X LYS* 3.1 8.7 + - + +
83X VAL* 3.6 10.1 - - - +
85X ARG* 1.3 78.6 - - - +
87X LEU* 1.3 58.5 + - - +
89X ARG* 4.5 2.7 - - - +
90X ILE* 2.7 46.9 + - + +
96X LEU* 3.8 17.0 - - + -
99X MET* 3.8 27.6 - - + -
100X ILE* 6.0 0.2 - - + -
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Residues in contact with LEU 87 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83X VAL* 3.0 14.7 + - + +
84X ALA* 3.1 13.0 + - + +
86X ALA* 1.3 75.6 - - - +
88X ASN* 1.3 64.2 + - - +
91X GLY* 2.7 30.8 + - - +
92X SER* 3.6 29.6 - - - +
96X LEU* 3.6 24.1 - - + +
125X ILE* 4.5 25.1 - - + +
126X THR* 6.0 2.7 - - + -
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Residues in contact with ASN 88 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1398 A 5.4 1.7 + - - +
48X ASN* 4.9 5.8 + - - +
51X LYS* 3.8 31.7 + - - +
52X PHE* 3.4 33.5 - - - -
84X ALA* 3.0 12.6 + - - +
85X ARG* 3.0 7.4 + - - +
87X LEU* 1.3 86.1 - - - +
89X ARG* 1.3 63.9 + - + +
90X ILE 4.8 0.3 - - - -
91X GLY* 4.5 1.2 + - - -
7Y SER* 4.6 12.6 - - - +
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Residues in contact with ARG 89 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2017 A 4.6 10.1 + - - -
2027 T 3.6 28.2 + - - +
2037 A 3.3 32.0 + - - +
1398 A 4.1 17.3 + - - +
1408 T 4.3 15.6 + - - -
85X ARG* 3.0 45.6 + - - +
86X ALA* 4.3 2.5 - - - +
88X ASN* 1.3 79.6 - - + +
90X ILE* 1.3 61.9 + - + +
7Y SER* 4.1 32.8 - - - +
60Z SER* 4.5 5.9 + - - -
73Z ARG* 4.6 1.7 + - - -
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Residues in contact with ILE 90 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2027 T 5.6 0.7 - - - +
2037 A 4.5 10.8 - - - +
86X ALA* 2.7 29.5 + - + +
88X ASN 4.8 1.1 - - - -
89X ARG* 1.3 77.8 - - - +
91X GLY* 1.3 68.4 + - - +
95X ALA* 3.6 25.6 - - + +
96X LEU* 4.0 5.6 - - + +
99X MET* 3.8 37.9 - - + -
60Z SER* 4.9 1.6 + - - -
61Z ALA* 5.8 0.5 - - - -
64Z THR* 2.6 36.6 + - - +
69Z THR* 4.4 10.8 - - + -
70Z GLY 5.6 0.4 - - - +
73Z ARG* 3.7 19.5 + - - +
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Residues in contact with GLY 91 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86X ALA 3.6 0.4 + - - -
87X LEU* 2.7 31.6 + - - -
88X ASN 4.5 0.9 - - - -
90X ILE* 1.3 89.7 - - - +
92X SER* 1.3 67.8 + - - +
96X LEU* 3.4 9.6 - - - +
64Z THR* 3.6 1.5 - - - +
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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