Contacts of the helix formed by residues 70 - 91 (chain p) 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 p).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1067 T 3.5 24.8 + - - +
1077 A 4.4 2.4 + - - -
111m PHE* 3.5 19.0 - - - -
90n ILE* 5.6 0.8 - - - +
99n MET* 5.3 0.2 - - - +
69p THR* 1.3 75.5 - - - +
71p PRO* 1.3 66.9 - - - +
73p ARG* 2.9 36.0 + - - +
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Residues in contact with PRO 71 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1067 T 3.6 23.1 - - + +
1077 A 3.9 33.2 - - - +
71m PRO* 3.6 19.0 - - + +
74m ALA* 4.8 3.1 - - + -
75m ILE* 3.5 37.2 - - + +
107m TYR* 6.5 0.7 - - + -
111m PHE* 4.6 7.2 - - + -
69p THR 4.4 0.2 - - - +
70p GLY* 1.3 83.0 - - - +
72p ASN* 1.3 64.1 + - - +
73p ARG 3.1 0.7 - - - -
74p ALA* 3.1 4.7 + - - +
75p ILE* 3.0 24.8 + - - +
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Residues in contact with ASN 72 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72m ASN* 3.1 24.3 - - - +
75m ILE* 3.5 12.5 - - - +
111m PHE 3.3 24.9 + - - -
112m ASN* 4.8 8.3 + - - +
68p ILE* 3.5 16.2 - - + -
69p THR 3.3 14.7 + - - +
70p GLY 3.0 0.8 - - - -
71p PRO* 1.3 75.2 - - - +
73p ARG* 1.3 66.2 + - - +
75p ILE* 3.3 19.0 + - + +
76p TYR* 3.0 25.4 - - + -
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Residues in contact with ARG 73 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1067 T 3.0 35.8 + - - +
89n ARG 4.6 0.8 + - - -
90n ILE* 3.7 27.0 + - - +
60p SER* 2.7 46.3 + - - +
63p LEU* 3.5 16.8 - - + +
64p THR* 2.9 31.5 + - - +
68p ILE* 2.7 56.1 + - + +
69p THR* 3.8 7.6 - - - +
70p GLY 2.9 15.2 + - - +
72p ASN* 1.3 76.3 - - - +
74p ALA* 1.3 59.2 + - - +
76p TYR* 3.0 5.5 + - - -
77p GLN* 2.8 29.6 + - - +
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Residues in contact with ALA 74 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1057 A 4.1 16.9 - - + +
1067 T 3.0 41.2 + - + +
2438 A 4.7 5.2 - - + -
2448 T 4.4 5.7 - - - +
71m PRO* 4.8 3.4 - - + -
70p GLY 3.6 0.6 + - - -
71p PRO 3.1 8.6 + - - +
73p ARG* 1.3 77.9 - - - +
75p ILE* 1.3 64.1 + - - +
77p GLN* 3.6 10.1 - - - +
78p GLY* 2.9 22.2 + - - -
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Residues in contact with ILE 75 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2448 T 5.8 0.2 - - - -
71m PRO* 3.6 26.9 - - + +
72m ASN* 3.5 36.1 - - - +
71p PRO 3.0 14.8 + - - +
72p ASN* 3.4 22.4 - - - +
73p ARG 3.2 0.4 - - - -
74p ALA* 1.3 76.3 - - - +
76p TYR* 1.3 67.6 + - + +
78p GLY* 3.4 0.7 + - - -
79p PHE* 3.1 21.5 + - - +
107p TYR* 3.5 31.5 - - + -
111p PHE* 4.6 11.4 - - + +
112p ASN 5.9 0.4 - - - +
113p ALA* 4.1 19.7 - - + -
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Residues in contact with TYR 76 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59p VAL* 4.4 3.2 - - - +
63p LEU* 3.6 29.4 - - + -
68p ILE* 4.0 18.5 - - + +
72p ASN* 3.0 28.0 - - + -
73p ARG 3.0 5.2 + - - +
75p ILE* 1.3 83.0 - - + +
77p GLN* 1.3 59.9 + - - +
79p PHE* 3.3 6.2 + - - +
80p GLY* 2.8 27.0 + - - -
112p ASN 5.0 0.3 + - - -
113p ALA* 4.0 8.9 - - + -
114p ASN* 2.9 38.8 + - - +
117p VAL* 3.7 30.7 - - + +
118p LEU* 3.7 30.3 - - + -
121p VAL* 4.2 11.7 - - + +
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Residues in contact with GLN 77 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1057 A 3.4 33.7 + - + +
1067 T 3.1 21.3 + - - +
55p VAL* 5.4 0.7 - - - +
56p ASN* 3.4 23.9 + - - +
59p VAL* 3.3 20.9 - - - +
60p SER* 3.5 26.7 - - - +
63p LEU* 4.0 2.1 - - + +
73p ARG 2.8 22.1 + - - +
74p ALA* 3.6 9.0 - - - +
76p TYR* 1.3 77.8 - - - +
78p GLY* 1.3 56.6 + - - +
80p GLY* 3.3 0.7 + - - -
81p LEU* 2.9 41.7 + - + +
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Residues in contact with GLY 78 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1057 A 5.4 1.2 + - - -
2448 T 5.1 3.6 - - - -
2458 A 4.1 24.3 - - - +
74p ALA 2.9 15.4 + - - -
75p ILE 3.8 1.8 - - - -
76p TYR 3.3 0.2 - - - -
77p GLN* 1.3 77.0 - - - +
79p PHE* 1.3 61.8 + - - +
81p LEU* 3.8 5.3 - - - +
82p LYS* 3.0 24.9 + - - +
107p TYR* 3.5 13.3 + - - -
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Residues in contact with PHE 79 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75p ILE 3.1 13.1 + - - +
76p TYR 3.5 7.9 - - - +
78p GLY* 1.3 76.3 - - - +
80p GLY* 1.3 63.1 - - - +
82p LYS* 3.1 5.3 + - - +
83p VAL* 2.9 34.0 + - + +
100p ILE* 5.1 1.8 - - + -
103p LEU* 3.7 24.2 - - + -
104p LYS* 3.8 23.1 - - + -
107p TYR* 3.5 34.5 + + + -
118p LEU* 3.3 52.9 - - + -
121p VAL* 3.8 16.8 - - + -
122p VAL* 3.7 23.8 - - + -
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Residues in contact with GLY 80 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55p VAL* 4.5 6.3 - - - -
59p VAL* 5.0 2.0 - - - -
76p TYR 2.8 17.3 + - - -
77p GLN* 3.8 0.9 - - - -
79p PHE* 1.3 73.6 - - - +
81p LEU* 1.3 63.1 + - - +
83p VAL* 3.1 2.5 + - - -
84p ALA* 3.0 19.9 + - - +
121p VAL* 3.5 26.9 - - - -
125p ILE* 3.1 17.4 - - - +
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Residues in contact with LEU 81 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1047 T 5.5 1.6 - - - +
1057 A 5.6 3.6 - - - +
2458 A 4.1 19.7 - - + +
2468 T 3.4 36.6 - - - +
52p PHE* 3.5 42.8 - - + +
55p VAL* 4.5 6.5 - - + +
56p ASN* 3.4 31.4 - - - +
77p GLN* 2.9 29.2 + - + +
78p GLY* 3.8 4.5 - - - +
80p GLY* 1.3 74.5 - - - +
82p LYS* 1.3 57.5 + - - +
84p ALA* 3.2 3.6 + - - -
85p ARG 2.9 23.7 + - - -
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Residues in contact with LYS 82 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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957 A 4.9 0.2 + - - -
967 T 3.2 13.9 + - - -
2458 A 3.7 26.4 + - - +
2468 T 3.3 29.1 + - - +
106o TYR* 2.8 33.8 + - - -
78p GLY 3.0 17.5 + - - +
79p PHE* 3.1 5.4 + - - +
81p LEU* 1.3 74.5 - - - +
83p VAL* 1.3 63.9 + - - +
85p ARG* 3.3 10.3 + - - +
86p ALA* 3.1 22.3 + - - +
99p MET* 5.9 2.9 - - - -
103p LEU* 3.5 34.9 - - + +
106p TYR* 5.0 6.3 - - - -
107p TYR* 4.6 4.0 - - + -
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Residues in contact with VAL 83 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79p PHE* 2.9 42.6 + - + +
80p GLY* 3.1 8.9 + - - +
82p LYS* 1.3 76.4 - - - +
84p ALA* 1.3 61.3 + - - +
86p ALA* 3.3 8.1 + - - +
87p LEU* 3.0 20.3 + - + +
96p LEU* 4.5 2.9 - - + +
99p MET* 6.5 0.2 - - - -
100p ILE* 4.3 26.7 - - + -
103p LEU* 3.7 18.6 - - + -
122p VAL* 4.6 8.5 - - + -
125p ILE* 3.8 26.7 - - + -
126p THR* 4.5 6.1 - - + -
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Residues in contact with ALA 84 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51p LYS 5.7 0.2 - - - +
52p PHE* 3.6 20.0 - - + -
55p VAL* 4.2 20.2 - - + -
80p GLY 3.0 11.4 + - - +
81p LEU* 3.5 8.3 - - - +
83p VAL* 1.3 73.2 - - - +
85p ARG* 1.3 66.8 + - - +
87p LEU* 3.1 11.9 + - + +
88p ASN* 3.0 25.2 + - - +
125p ILE* 4.4 11.2 - - + +
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Residues in contact with ARG 85 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
957 A 3.8 36.1 + - - -
967 T 2.9 33.7 + - - +
2468 T 3.0 36.1 + - - +
2478 A 3.4 29.9 + - - +
52p PHE* 3.5 11.1 - - - -
81p LEU 2.9 13.3 + - - +
82p LYS* 3.3 21.2 - - - +
83p VAL 3.2 0.4 - - - -
84p ALA* 1.3 75.3 - - - +
86p ALA* 1.3 63.7 + - - +
88p ASN* 3.0 6.6 + - - +
89p ARG* 3.0 44.7 + - - +
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Residues in contact with ALA 86 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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957 A 5.6 2.7 - - - -
82p LYS* 3.1 8.7 + - + +
83p VAL* 3.3 10.1 + - - +
85p ARG* 1.3 77.8 - - - +
87p LEU* 1.3 59.0 + - - +
89p ARG* 4.5 2.9 - - - +
90p ILE* 2.7 46.9 + - + +
96p LEU* 3.8 17.5 - - + -
99p MET* 3.8 27.6 - - + -
100p ILE* 6.0 0.2 - - + -
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Residues in contact with LEU 87 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83p VAL* 3.0 14.3 + - + +
84p ALA* 3.1 12.8 + - + +
86p ALA* 1.3 76.3 - - - +
88p ASN* 1.3 64.4 + - - +
91p GLY* 2.7 30.7 + - - +
92p SER* 3.6 29.8 - - - +
96p LEU* 3.6 24.3 - - + +
125p ILE* 4.5 25.4 - - + +
126p THR* 6.0 2.2 - - + -
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Residues in contact with ASN 88 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2478 A 5.4 1.7 + - - +
48p ASN* 4.9 5.6 + - - +
51p LYS* 3.8 31.5 + - - +
52p PHE* 3.4 33.5 - - - -
84p ALA* 3.0 13.0 + - - +
85p ARG* 3.0 7.6 + - - +
87p LEU* 1.3 87.2 - - - +
89p ARG* 1.3 63.7 + - + +
90p ILE 4.8 0.2 - - - -
91p GLY* 4.5 1.4 + - - -
7q SER* 4.6 12.4 - - - +
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Residues in contact with ARG 89 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
937 A 4.6 9.9 + - - -
947 T 3.6 28.8 + - - +
957 A 3.3 32.9 + - - +
2478 A 4.1 17.9 + - - +
2488 T 4.3 15.6 + - - -
85p ARG* 3.0 46.0 + - - +
86p ALA* 4.3 2.5 - - - +
88p ASN* 1.3 80.5 - - + +
90p ILE* 1.3 62.1 + - + +
7q SER* 4.1 32.7 - - - +
8q ARG* 6.2 0.2 - - - +
60r SER* 4.5 5.9 + - - -
73r ARG* 4.6 1.7 + - - -
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Residues in contact with ILE 90 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
947 T 5.6 0.2 - - - +
957 A 4.5 11.2 - - - +
86p ALA* 2.7 28.8 + - + +
88p ASN 4.8 1.1 - - - -
89p ARG* 1.3 77.6 - - - +
91p GLY* 1.3 67.6 + - - +
95p ALA* 3.6 26.2 - - + +
96p LEU* 4.0 6.3 - - + +
99p MET* 3.8 38.1 - - + -
60r SER* 4.9 2.1 + - - +
61r ALA* 5.8 0.7 - - - -
64r THR* 2.6 36.5 + - - +
69r THR* 4.4 11.0 - - + -
73r ARG* 3.7 19.4 + - - +
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Residues in contact with GLY 91 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86p ALA 3.6 0.6 + - - -
87p LEU* 2.7 30.4 + - - -
88p ASN 4.5 1.1 - - - -
90p ILE* 1.3 89.3 - - - +
92p SER* 1.3 69.0 + - - +
96p LEU* 3.4 9.2 - - - +
64r THR* 3.6 1.8 - - - +
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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