Contacts of the helix formed by residues 70 - 91 (chain S) 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 S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1238 A 3.4 26.3 + - - +
1248 T 4.1 1.8 + - - -
69S THR* 1.3 77.0 - - - +
71S PRO* 1.3 69.8 - - - +
73S ARG* 2.9 32.1 + - - +
90U ILE* 5.5 0.6 - - - +
99U MET* 5.3 0.6 - - - +
111V PHE* 3.6 19.0 - - - -
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Residues in contact with PRO 71 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1238 A 3.7 29.8 - - + +
1248 T 3.6 27.4 - - - +
69S THR 4.4 0.4 - - - +
70S GLY* 1.3 82.6 - - - +
72S ASN* 1.3 65.5 + - - +
73S ARG 3.1 0.9 - - - -
74S ALA* 3.0 6.4 + - + +
75S ILE* 3.0 23.9 + - - +
71V PRO* 3.6 19.6 - - + +
74V ALA 4.8 0.9 - - - -
75V ILE* 3.6 37.9 - - + +
107V TYR* 6.5 1.1 - - + -
111V PHE* 4.6 5.8 - - + -
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Residues in contact with ASN 72 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68S ILE* 3.5 15.9 - - + -
69S THR* 3.3 14.6 + - - +
70S GLY 3.0 1.0 - - - -
71S PRO* 1.3 74.8 - - - +
73S ARG* 1.3 64.1 + - - +
75S ILE* 3.3 18.6 + - + +
76S TYR* 3.1 26.3 - - + -
72V ASN* 3.1 24.8 - - - +
75V ILE* 3.5 10.8 - - - +
111V PHE 3.2 26.1 + - - -
112V ASN* 4.6 10.9 + - - +
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Residues in contact with ARG 73 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1238 A 2.9 37.7 + - - +
60S SER* 2.7 46.5 + - - +
63S LEU* 3.5 17.3 - - + +
64S THR* 3.0 31.7 + - - +
68S ILE* 2.8 56.5 + - + +
69S THR* 3.9 8.1 - - - +
70S GLY 2.9 14.1 + - - +
72S ASN* 1.3 76.0 - - - +
74S ALA* 1.3 59.3 + - - +
76S TYR 3.1 3.1 + - - -
77S GLN* 2.8 32.2 + - - +
89U ARG 4.6 0.4 + - - -
90U ILE* 3.7 28.1 + - - +
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Residues in contact with ALA 74 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2277 A 4.1 25.2 - - + +
1228 T 4.3 5.6 - - - +
1238 A 3.8 38.5 + - + +
70S GLY 3.7 0.8 + - - -
71S PRO 3.0 11.1 + - - +
73S ARG* 1.3 80.3 - - - +
75S ILE* 1.3 61.8 + - - +
77S GLN* 3.6 8.9 - - - +
78S GLY* 2.9 21.1 + - - -
71V PRO* 4.8 3.6 - - + -
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Residues in contact with ILE 75 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71S PRO 3.0 13.9 + - - +
72S ASN* 3.4 22.4 - - + +
73S ARG 3.2 0.4 - - - -
74S ALA* 1.3 77.4 - - - +
76S TYR* 1.3 71.0 + - + +
78S GLY* 3.3 0.9 + - - -
79S PHE* 3.2 16.3 + - - +
107S TYR* 3.5 31.7 - - + -
111S PHE* 4.8 11.4 - - + +
112S ASN 6.3 0.2 - - - -
113S ALA* 4.2 19.5 - - + -
71V PRO* 3.5 27.4 - - + -
72V ASN* 3.5 35.4 - - - +
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Residues in contact with TYR 76 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59S VAL* 4.3 5.3 - - - +
63S LEU* 3.6 33.0 - - + -
68S ILE* 4.0 18.4 - - + +
72S ASN* 3.1 27.8 + - + -
73S ARG 3.1 3.6 + - - +
75S ILE* 1.3 80.3 - - + +
77S GLN* 1.3 60.8 + - - +
79S PHE* 3.2 7.3 + - - +
80S GLY* 2.9 25.6 + - - -
112S ASN 5.2 0.3 + - - -
113S ALA* 4.0 7.9 - - + -
114S ASN* 2.9 38.1 + - - +
117S VAL* 3.7 27.7 - - + +
118S LEU* 3.6 31.2 - - + -
121S VAL* 4.4 9.4 - - + +
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Residues in contact with GLN 77 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1228 T 3.2 32.6 + - + +
1238 A 3.2 20.7 + - - +
55S VAL* 5.2 0.5 - - - +
56S ASN* 3.1 42.4 + - - +
59S VAL* 3.3 24.4 - - - +
60S SER* 3.4 11.7 - - - +
63S LEU* 4.0 3.3 - - + +
73S ARG 2.8 22.6 + - - +
74S ALA* 3.6 7.6 - - - +
76S TYR* 1.3 76.5 - - - +
78S GLY* 1.3 55.9 + - - +
80S GLY* 3.2 1.6 + - - -
81S LEU* 2.9 36.5 + - + +
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Residues in contact with GLY 78 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2277 A 5.6 1.6 - - - -
2287 T 3.7 30.5 + - - +
1228 T 5.3 0.2 + - - -
74S ALA 2.9 14.4 + - - -
75S ILE 3.8 3.6 - - - -
76S TYR 3.2 0.2 - - - -
77S GLN* 1.3 76.3 - - - +
79S PHE* 1.3 62.1 + - - +
81S LEU* 3.3 5.6 + - - +
82S LYS* 3.0 23.4 + - - +
107S TYR* 3.5 11.1 + - - -
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Residues in contact with PHE 79 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75S ILE 3.2 12.2 + - - +
76S TYR 3.4 8.5 - - - +
78S GLY* 1.3 75.7 - - - +
80S GLY* 1.3 65.0 + - - +
82S LYS* 3.2 6.2 + - - +
83S VAL* 3.1 28.8 + - + +
100S ILE* 5.0 1.1 - - + -
103S LEU* 3.6 31.4 - - + -
104S LYS* 3.8 28.5 - - + -
107S TYR* 3.5 26.9 + + + -
118S LEU* 3.3 50.5 - - + -
121S VAL* 3.8 16.4 - - + -
122S VAL* 3.6 25.4 - - + -
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Residues in contact with GLY 80 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55S VAL* 4.1 6.5 - - - -
59S VAL* 4.7 2.2 - - - -
76S TYR 2.9 12.4 + - - -
77S GLN 3.7 2.9 - - - -
79S PHE* 1.3 75.9 - - - +
81S LEU* 1.3 62.4 + - - +
83S VAL* 3.1 3.3 + - - -
84S ALA* 3.1 19.4 + - - +
121S VAL* 3.6 14.4 - - - -
125S ILE* 3.2 29.6 - - - +
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Residues in contact with LEU 81 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2287 T 3.6 24.2 - - + +
2297 A 3.4 31.1 - - - +
1218 A 4.9 6.5 - - + -
1228 T 5.2 2.5 - - - +
52S PHE* 3.7 37.0 - - + +
55S VAL* 4.3 7.1 - - + +
56S ASN* 3.3 30.1 - - - +
77S GLN* 2.9 25.8 + - + +
78S GLY* 3.6 4.7 - - - +
80S GLY* 1.3 75.8 - - - +
82S LYS* 1.3 56.4 + - - +
84S ALA* 3.3 6.7 + - - +
85S ARG* 2.9 27.9 + - - +
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Residues in contact with LYS 82 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2287 T 4.0 12.7 + - - +
2297 A 2.9 31.0 + - - +
1128 T 5.6 1.6 - - - -
1138 A 3.8 11.9 + - - -
78S GLY 3.0 13.6 + - - +
79S PHE* 3.4 10.3 - - - +
81S LEU* 1.3 74.7 - - - +
83S VAL* 1.3 65.5 + - - +
85S ARG* 3.2 11.2 + - - +
86S ALA* 3.1 23.7 + - - +
99S MET* 4.7 17.0 - - + -
103S LEU* 3.5 29.1 - - + +
106S TYR* 5.5 4.8 - - - -
107S TYR* 5.2 1.3 - - + -
106T TYR* 2.7 37.3 + - - -
111T PHE* 6.1 0.2 - - - -
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Residues in contact with VAL 83 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79S PHE* 3.1 35.6 + - + +
80S GLY* 3.1 8.5 + - - +
82S LYS* 1.3 78.0 - - - +
84S ALA* 1.3 62.4 + - - +
86S ALA* 3.4 5.7 + - - +
87S LEU* 3.0 21.1 + - + +
96S LEU* 4.3 4.6 - - + +
99S MET* 6.3 0.7 - - - -
100S ILE* 4.3 18.4 - - + -
103S LEU* 3.6 18.2 - - + -
122S VAL* 4.5 9.4 - - + -
125S ILE* 3.7 28.3 - - + -
126S THR* 4.3 15.5 - - + -
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Residues in contact with ALA 84 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51S LYS 5.5 0.7 - - - +
52S PHE* 3.6 21.1 - - + -
55S VAL* 4.0 20.4 - - + -
80S GLY 3.1 8.2 + - - +
81S LEU* 3.5 7.9 - - - +
83S VAL* 1.3 79.5 - - - +
85S ARG* 1.3 65.2 + - - +
87S LEU* 3.1 11.7 + - + +
88S ASN* 2.9 27.2 + - - +
125S ILE* 4.5 8.9 - - + +
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Residues in contact with ARG 85 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2297 A 3.0 36.5 + - - +
2307 T 3.1 33.9 + - - +
1128 T 3.8 34.8 + - - +
1138 A 3.9 20.3 + - - -
52S PHE* 3.6 10.3 - - - -
81S LEU 2.9 14.2 + - - +
82S LYS* 3.4 15.7 - - + +
84S ALA* 1.3 76.5 - - - +
86S ALA* 1.3 63.1 - - - +
88S ASN* 3.1 5.5 + - - +
89S ARG* 3.0 53.1 + - - +
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Residues in contact with ALA 86 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1128 T 5.4 3.4 - - - +
82S LYS* 3.1 12.4 + - - +
83S VAL* 3.7 9.2 - - - +
85S ARG* 1.3 77.3 - - - +
87S LEU* 1.3 58.9 + - - +
89S ARG* 4.5 2.9 - - - +
90S ILE* 2.7 50.9 + - + +
96S LEU* 3.9 9.0 - - + -
99S MET* 3.8 32.5 - - + -
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Residues in contact with LEU 87 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83S VAL* 3.0 14.1 + - + +
84S ALA* 3.1 12.3 + - + +
86S ALA* 1.3 76.7 - - - +
88S ASN* 1.3 66.0 + - - +
91S GLY* 2.7 31.6 + - - +
92S SER* 3.6 32.5 - - - +
96S LEU* 3.8 23.5 - - + +
125S ILE* 4.8 22.7 - - + +
126S THR* 6.1 2.5 - - + -
57x GLU* 5.8 3.8 - - - +
58x ASN* 6.2 0.2 - - - +
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Residues in contact with ASN 88 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2307 T 5.9 1.1 - - - +
7R SER* 3.8 17.4 + - - +
48S ASN* 4.9 5.6 + - - -
51S LYS* 3.9 29.8 + - - +
52S PHE* 3.3 34.5 - - + -
84S ALA* 2.9 13.3 + - - +
85S ARG* 3.1 7.8 + - - +
87S LEU* 1.3 85.2 - - - +
89S ARG* 1.3 63.4 + - + +
90S ILE 3.7 0.3 + - - -
91S GLY* 4.8 0.7 + - - -
57x GLU* 5.2 4.3 - - - +
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Residues in contact with ARG 89 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2307 T 3.8 18.7 + - - +
2317 A 4.3 14.6 + - - -
1108 T 4.7 3.8 + - - -
1118 A 3.6 25.6 + - - +
1128 T 3.5 36.8 + - - +
60Q SER* 4.7 2.3 + - - -
73Q ARG* 4.6 3.8 + - - -
7R SER* 3.6 36.1 - - - +
8R ARG* 5.5 3.6 - - - +
85S ARG* 3.0 54.0 + - - +
86S ALA* 4.2 1.8 - - - +
88S ASN* 1.3 80.2 - - + +
90S ILE* 1.3 62.3 + - + +
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Residues in contact with ILE 90 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1118 A 5.4 0.9 - - - +
1128 T 4.4 10.5 - - - +
60Q SER* 4.7 2.5 + - - -
64Q THR* 2.6 36.0 + - - +
69Q THR* 4.4 18.2 - - + -
70Q GLY 5.5 0.4 - - - +
73Q ARG* 3.7 20.1 + - - +
86S ALA* 2.7 27.8 + - + +
88S ASN 5.0 0.4 - - - -
89S ARG* 1.3 80.4 - - - +
91S GLY* 1.3 68.6 + - - +
95S ALA* 3.5 26.2 - - + +
96S LEU* 4.2 4.7 - - - +
99S MET* 3.7 31.0 - - + -
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Residues in contact with GLY 91 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64Q THR* 3.8 1.8 - - - +
86S ALA 3.6 0.6 + - - -
87S LEU* 2.7 30.8 + - - -
88S ASN 4.6 0.2 - - - -
90S ILE* 1.3 90.2 - - - +
92S SER* 1.3 67.7 + - - +
96S 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) + - + + + + + -
------------------------------------------------------------
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