Contacts of the helix formed by residues 70 - 91 (chain Y) 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 Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1598 A 3.4 26.3 + - - +
1608 T 4.1 2.1 + - - -
69Y THR* 1.3 76.1 - - - +
71Y PRO* 1.3 69.3 - - - +
73Y ARG* 2.9 32.3 + - - +
90a ILE* 5.5 0.8 - - - +
99a MET* 5.3 0.2 - - - +
111b PHE* 3.6 18.3 - - - -
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Residues in contact with PRO 71 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1598 A 3.7 29.8 - - + +
1608 T 3.6 27.1 - - - +
70Y GLY* 1.3 83.2 - - - +
72Y ASN* 1.3 64.0 + - - +
73Y ARG 3.1 0.2 - - - -
74Y ALA* 3.0 6.4 + - + +
75Y ILE* 3.0 24.4 + - - +
71b PRO* 3.6 19.4 - - + +
74b ALA* 4.8 0.7 - - + -
75b ILE* 3.6 39.0 - - + +
107b TYR* 6.5 0.9 - - + -
111b PHE* 4.6 6.1 - - + -
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Residues in contact with ASN 72 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68Y ILE* 3.5 15.9 - - + -
69Y THR 3.3 14.1 + - - +
70Y GLY 3.0 0.6 - - - -
71Y PRO* 1.3 75.2 - - - +
73Y ARG* 1.3 64.1 + - - +
75Y ILE* 3.3 19.8 + - + +
76Y TYR* 3.1 26.4 - - + -
72b ASN* 3.1 24.3 - - - +
75b ILE* 3.5 11.9 - - - +
111b PHE 3.2 25.9 + - - -
112b ASN* 4.6 10.5 + - - +
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Residues in contact with ARG 73 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1598 A 2.9 39.0 + - - +
60Y SER* 2.7 45.5 + - - +
63Y LEU* 3.5 17.4 - - + +
64Y THR* 3.0 31.3 + - - +
68Y ILE* 2.8 57.4 + - + +
69Y THR* 3.8 8.5 - - - +
70Y GLY 2.9 14.1 + - - +
72Y ASN* 1.3 76.4 - - - +
74Y ALA* 1.3 58.1 + - - +
76Y TYR 3.1 3.5 + - - -
77Y GLN* 2.8 32.2 + - - +
89a ARG 4.6 0.4 + - - -
90a ILE* 3.7 26.2 + - - +
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Residues in contact with ALA 74 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1917 A 4.1 24.6 - - + +
1588 T 4.3 5.6 - - - +
1598 A 3.8 37.8 + - + +
70Y GLY 3.7 0.6 + - - -
71Y PRO 3.0 12.3 + - - +
73Y ARG* 1.3 81.0 - - - +
75Y ILE* 1.3 60.9 - - - +
77Y GLN* 3.6 8.9 - - - +
78Y GLY* 2.9 21.1 + - - -
71b PRO* 4.8 3.6 - - + -
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Residues in contact with ILE 75 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1917 A 5.9 0.2 - - - -
71Y PRO 3.0 15.0 + - - +
72Y ASN* 3.4 22.7 - - + +
73Y ARG 3.2 0.4 - - - -
74Y ALA* 1.3 76.7 - - - +
76Y TYR* 1.3 71.8 + - + +
78Y GLY* 3.3 1.3 + - - -
79Y PHE* 3.2 16.8 + - - +
107Y TYR* 3.5 31.1 - - + -
111Y PHE* 4.8 11.2 - - + +
113Y ALA* 4.2 19.7 - - + -
71b PRO* 3.5 27.4 - - + -
72b ASN* 3.5 35.7 - - - +
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Residues in contact with TYR 76 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59Y VAL* 4.3 5.9 - - - +
63Y LEU* 3.6 32.1 - - + -
68Y ILE* 4.0 18.9 - - + +
72Y ASN* 3.1 26.4 + - + -
73Y ARG 3.1 3.7 + - - +
75Y ILE* 1.3 78.7 - - + +
77Y GLN* 1.3 61.1 + - - +
79Y PHE* 3.2 7.5 + - - +
80Y GLY* 2.9 25.6 + - - -
112Y ASN 5.2 0.2 + - - -
113Y ALA* 4.0 8.0 - - + -
114Y ASN* 2.9 38.7 + - - +
117Y VAL* 3.7 26.4 - - + +
118Y LEU* 3.6 31.0 - - + -
121Y VAL* 4.4 8.9 - - + +
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Residues in contact with GLN 77 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1588 T 3.2 32.8 + - + +
1598 A 3.2 20.3 + - - +
55Y VAL* 4.8 0.9 - - - +
56Y ASN* 3.1 41.6 + - - +
59Y VAL* 3.3 24.1 - - - +
60Y SER* 3.4 11.9 - - - +
63Y LEU* 4.0 3.9 - - + +
73Y ARG 2.8 22.2 + - - +
74Y ALA* 3.6 7.9 - - - +
75Y ILE 3.3 0.2 - - - -
76Y TYR* 1.3 76.8 - - - +
78Y GLY* 1.3 55.5 + - - +
80Y GLY* 3.2 1.4 + - - -
81Y LEU* 2.9 36.4 + - + +
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Residues in contact with GLY 78 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1917 A 5.6 1.3 - - - -
1927 T 3.7 30.4 + - - +
1588 T 5.3 0.2 + - - -
74Y ALA 2.9 14.7 + - - -
75Y ILE 3.8 3.6 - - - -
77Y GLN* 1.3 76.5 - - - +
79Y PHE* 1.3 62.1 + - - +
81Y LEU* 3.3 5.5 + - - +
82Y LYS* 3.0 23.6 + - - +
107Y TYR* 3.5 11.2 + - - -
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Residues in contact with PHE 79 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75Y ILE 3.2 12.8 + - - +
76Y TYR 3.4 7.9 - - - +
78Y GLY* 1.3 76.2 - - - +
80Y GLY* 1.3 64.4 + - - +
82Y LYS* 3.2 6.2 + - - +
83Y VAL* 3.1 29.4 + - + +
100Y ILE* 5.0 0.9 - - + -
103Y LEU* 3.6 32.1 - - + -
104Y LYS* 3.8 28.3 - - + -
107Y TYR* 3.5 26.3 + + + -
118Y LEU* 3.3 50.7 - - + -
121Y VAL* 3.8 16.6 - - + -
122Y VAL* 3.6 24.9 - - + -
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Residues in contact with GLY 80 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55Y VAL* 4.1 6.7 - - - -
59Y VAL* 4.7 1.8 - - - -
76Y TYR 2.9 13.0 + - - -
77Y GLN 3.7 2.7 - - - -
79Y PHE* 1.3 76.4 - - - +
81Y LEU* 1.3 62.3 + - - +
83Y VAL* 3.1 3.1 + - - -
84Y ALA* 3.1 18.9 + - - +
121Y VAL* 3.6 13.9 - - - -
125Y ILE* 3.2 30.8 - - - +
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Residues in contact with LEU 81 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1927 T 3.6 23.8 - - + +
1937 A 3.4 30.9 - - - +
1578 A 4.9 7.4 - - + -
1588 T 5.2 2.5 - - - +
52Y PHE* 3.7 37.4 - - + +
55Y VAL* 4.3 6.5 - - + +
56Y ASN* 3.3 30.3 - - - +
77Y GLN* 2.9 25.8 + - + +
78Y GLY* 3.6 4.5 - - - +
80Y GLY* 1.3 75.9 - - - +
82Y LYS* 1.3 57.1 + - - +
84Y ALA* 3.3 7.3 + - - +
85Y ARG* 2.9 28.2 + - - +
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Residues in contact with LYS 82 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1927 T 4.0 14.2 + - - +
1937 A 2.9 31.1 + - - +
1488 T 5.6 1.3 - - - -
1498 A 3.8 14.0 + - - -
78Y GLY 3.0 13.8 + - - +
79Y PHE* 3.4 10.3 - - - +
81Y LEU* 1.3 74.9 - - - +
83Y VAL* 1.3 64.0 + - - +
85Y ARG* 3.2 11.9 + - - +
86Y ALA* 3.1 23.8 + - + +
99Y MET* 4.7 16.6 - - - -
103Y LEU* 3.5 30.7 - - + +
106Y TYR* 5.5 4.4 - - - -
107Y TYR* 5.2 1.1 - - + -
106Z TYR* 2.7 39.1 + - - -
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Residues in contact with VAL 83 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79Y PHE* 3.1 35.7 + - + +
80Y GLY* 3.1 8.3 + - - +
82Y LYS* 1.3 77.4 - - - +
84Y ALA* 1.3 62.4 + - - +
86Y ALA* 3.4 5.9 + - - +
87Y LEU* 3.0 20.9 + - + +
96Y LEU* 4.3 4.4 - - + +
99Y MET* 6.3 0.7 - - - -
100Y ILE* 4.3 18.8 - - + -
103Y LEU* 3.6 18.4 - - + -
122Y VAL* 4.5 8.3 - - + -
125Y ILE* 3.7 27.1 - - + -
126Y THR* 4.3 15.3 - - + -
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Residues in contact with ALA 84 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51Y LYS 5.5 0.9 - - - +
52Y PHE* 3.6 20.4 - - + -
55Y VAL* 4.0 20.9 - - + -
80Y GLY 3.1 8.1 + - - +
81Y LEU* 3.5 8.5 - - - +
83Y VAL* 1.3 80.2 - - - +
85Y ARG* 1.3 64.3 + - - +
87Y LEU* 3.1 11.4 + - + +
88Y ASN* 2.9 27.5 + - - +
125Y ILE* 4.5 8.1 - - + -
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Residues in contact with ARG 85 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1937 A 3.0 35.0 + - - +
1947 T 3.1 34.6 + - - +
1488 T 3.8 34.4 + - - +
1498 A 3.9 21.3 + - - -
52Y PHE* 3.6 10.3 - - - -
81Y LEU 2.9 13.3 + - - +
82Y LYS* 3.2 16.6 + - + +
84Y ALA* 1.3 76.1 - - - +
86Y ALA* 1.3 64.0 + - - +
88Y ASN* 3.1 5.4 + - - +
89Y ARG* 3.0 52.5 + - - +
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Residues in contact with ALA 86 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1488 T 5.4 3.4 - - - +
82Y LYS* 3.1 11.6 + - - +
83Y VAL* 3.7 9.6 - - - +
85Y ARG* 1.3 77.6 - - - +
87Y LEU* 1.3 57.8 + - - +
89Y ARG* 4.5 2.9 - - - +
90Y ILE* 2.7 51.7 + - + +
96Y LEU* 3.9 10.3 - - + -
99Y MET* 3.8 32.8 - - + -
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Residues in contact with LEU 87 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574 GLU* 5.8 3.8 - - - +
584 ASN* 6.2 0.2 - - - +
83Y VAL* 3.0 14.7 + - + +
84Y ALA* 3.1 13.4 + - + +
86Y ALA* 1.3 76.3 - - - +
88Y ASN* 1.3 65.2 + - - +
91Y GLY* 2.7 31.4 + - - +
92Y SER* 3.6 33.0 - - - +
96Y LEU* 3.8 23.7 - - + +
125Y ILE* 4.8 22.2 - - + +
126Y THR* 6.1 2.5 - - + -
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Residues in contact with ASN 88 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574 GLU* 5.2 4.3 - - - +
1947 T 5.9 0.9 - - - +
7X SER* 3.8 18.7 + - - +
48Y ASN* 4.9 5.4 + - - +
51Y LYS* 3.9 30.8 + - - +
52Y PHE* 3.3 34.5 - - + -
84Y ALA* 2.9 13.4 + - - +
85Y ARG* 3.6 8.1 - - - +
87Y LEU* 1.3 86.0 - - - +
89Y ARG* 1.3 63.8 + - + +
90Y ILE 5.0 0.3 - - - -
91Y GLY 4.8 0.5 + - - -
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Residues in contact with ARG 89 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1947 T 3.8 18.4 + - - -
1957 A 4.3 14.5 + - - -
1468 T 4.7 4.2 + - - -
1478 A 3.6 26.4 + - - +
1488 T 3.5 36.4 + - - +
60W SER* 4.7 2.1 + - - -
73W ARG* 4.6 4.0 + - - -
7X SER* 3.6 37.1 - - - +
8X ARG* 5.5 3.6 - - - +
85Y ARG* 3.0 52.8 + - - +
86Y ALA* 4.2 2.2 - - - +
88Y ASN* 1.3 80.2 - - + +
90Y ILE* 1.3 62.0 + - + +
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Residues in contact with ILE 90 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1478 A 5.4 1.1 - - - +
1488 T 4.4 11.0 - - - +
60W SER* 4.7 2.8 + - - -
64W THR* 2.6 37.3 + - + +
69W THR* 4.4 18.2 - - + -
70W GLY 5.5 0.4 - - - +
73W ARG* 3.7 19.1 + - - +
86Y ALA* 2.7 28.0 + - + +
88Y ASN 5.0 0.2 - - - -
89Y ARG* 1.3 80.4 - - + +
91Y GLY* 1.3 68.3 + - - +
95Y ALA* 3.5 25.4 - - + +
96Y LEU* 4.2 4.3 - - - +
99Y MET* 3.7 31.2 - - + -
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Residues in contact with GLY 91 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64W THR* 3.8 1.4 - - - +
86Y ALA 3.6 0.4 + - - -
87Y LEU* 2.7 31.0 + - - -
88Y ASN 4.6 0.4 - - - -
90Y ILE* 1.3 89.2 - - - +
92Y SER* 1.3 68.6 + - - +
96Y LEU* 3.6 10.4 - - - +
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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