Contacts of the helix formed by residues 70 - 91 (chain v) 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 v).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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707 T 3.5 26.0 + - - +
717 A 4.4 2.4 + - - -
111s PHE* 3.5 19.9 - - - -
90t ILE* 5.6 0.6 - - - +
69v THR* 1.3 75.9 - - - +
71v PRO* 1.3 66.0 - - - +
73v ARG* 2.9 35.6 + - - +
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Residues in contact with PRO 71 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707 T 3.6 23.6 - - + +
717 A 3.9 32.3 - - - +
71s PRO* 3.6 19.3 - - + +
74s ALA* 4.8 3.1 - - + -
75s ILE* 3.5 36.6 - - + +
107s TYR* 6.5 0.9 - - + -
111s PHE* 4.6 7.2 - - + -
69v THR 4.4 0.4 - - - +
70v GLY* 1.3 82.2 - - - +
72v ASN* 1.3 66.0 + - - +
73v ARG 3.1 0.2 - - - -
74v ALA* 3.1 4.5 + - - +
75v ILE* 3.0 24.6 + - - +
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Residues in contact with ASN 72 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72s ASN* 3.1 24.9 - - - +
75s ILE* 3.5 11.0 - - - +
111s PHE* 3.3 25.7 + - - +
112s ASN* 4.8 8.7 + - - +
68v ILE* 3.5 15.9 - - + -
69v THR* 3.3 14.6 + - - +
70v GLY 3.0 1.0 - - - -
71v PRO* 1.3 75.4 - - - +
73v ARG* 1.3 64.6 + - - +
75v ILE* 3.3 17.8 + - + +
76v TYR* 3.0 26.3 - - + -
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Residues in contact with ARG 73 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707 T 3.0 35.6 + - - +
89t ARG 4.6 0.8 + - - -
90t ILE* 3.7 27.7 + - - +
60v SER* 2.7 47.0 + - - +
63v LEU* 3.5 15.9 - - + +
64v THR* 2.9 31.1 + - - +
68v ILE* 2.8 57.6 + - + +
69v THR* 3.9 7.6 - - - +
70v GLY 2.9 15.8 + - - +
72v ASN* 1.3 76.3 - - - +
74v ALA* 1.3 58.5 + - - +
76v TYR* 3.0 5.2 + - - -
77v GLN* 2.8 30.0 + - - +
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Residues in contact with ALA 74 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697 A 4.1 16.9 - - + +
707 T 3.0 40.9 + - + +
2798 A 4.7 5.2 - - + -
2808 T 4.4 5.9 - - - +
71s PRO* 4.8 3.8 - - + -
70v GLY 3.6 1.0 + - - -
71v PRO 3.1 8.8 + - - +
73v ARG* 1.3 76.1 - - - +
75v ILE* 1.3 64.4 + - - +
77v GLN* 3.6 10.6 - - - +
78v GLY* 2.9 21.0 + - - -
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Residues in contact with ILE 75 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71s PRO* 3.6 26.9 - - + +
72s ASN* 3.5 35.4 - - - +
71v PRO 3.0 15.0 + - - +
72v ASN* 3.4 22.2 - - + +
73v ARG 3.2 0.6 - - - -
74v ALA* 1.3 77.2 - - - +
76v TYR* 1.3 67.0 + - + +
78v GLY* 3.4 0.7 + - - -
79v PHE* 3.1 21.3 + - - +
107v TYR* 3.5 30.6 - - + -
111v PHE* 4.6 11.7 - - + +
112v ASN 5.9 0.7 - - - +
113v ALA* 4.1 19.3 - - + -
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Residues in contact with TYR 76 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59v VAL* 4.4 2.9 - - - +
63v LEU* 3.6 28.9 - - + -
68v ILE* 4.0 18.5 - - + +
72v ASN* 3.0 27.8 - - + -
73v ARG 3.0 5.0 + - - +
75v ILE* 1.3 82.1 - - + +
77v GLN* 1.3 60.2 + - - +
79v PHE* 3.5 6.0 - - - +
80v GLY* 2.8 26.9 + - - -
112v ASN 5.0 0.2 + - - -
113v ALA* 3.9 8.8 - - + -
114v ASN* 2.9 37.9 + - - +
117v VAL* 3.7 31.9 - - + +
118v LEU* 3.7 30.3 - - + -
121v VAL* 4.2 11.9 - - + +
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Residues in contact with GLN 77 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697 A 3.4 33.9 + - + +
707 T 3.1 21.1 + - - +
55v VAL* 5.4 0.5 - - - +
56v ASN* 3.4 24.4 + - - +
59v VAL* 3.3 21.4 - - - +
60v SER* 3.5 26.3 - - - +
63v LEU* 4.0 2.5 - - + +
73v ARG 2.8 22.0 + - - +
74v ALA* 3.2 10.1 + - - +
76v TYR* 1.3 77.6 - - - +
78v GLY* 1.3 57.8 + - - +
80v GLY* 3.3 0.7 + - - -
81v LEU* 2.9 41.8 + - + +
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Residues in contact with GLY 78 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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697 A 5.4 0.8 + - - -
2808 T 5.1 3.1 - - - -
2818 A 4.1 25.3 - - - +
74v ALA 2.9 15.8 + - - -
75v ILE 3.8 2.0 - - - -
77v GLN* 1.3 77.4 - - - +
79v PHE* 1.3 60.8 + - - +
81v LEU* 3.8 5.4 - - - +
82v LYS* 3.0 24.8 + - - +
107v TYR* 3.5 14.0 + - - -
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Residues in contact with PHE 79 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75v ILE 3.1 13.8 + - - +
76v TYR 3.5 7.9 - - - +
77v GLN 3.3 0.2 - - - -
78v GLY* 1.3 76.0 - - - +
80v GLY* 1.3 64.8 + - - +
82v LYS* 3.1 5.7 + - - +
83v VAL* 2.9 32.7 + - + +
100v ILE* 5.1 1.3 - - + -
103v LEU* 3.7 24.5 - - + -
104v LYS* 3.8 24.0 - - + -
107v TYR* 3.5 33.7 + + + -
118v LEU* 3.3 52.7 - - + -
121v VAL* 3.8 16.6 - - + -
122v VAL* 3.7 24.2 - - + -
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Residues in contact with GLY 80 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55v VAL* 4.5 5.8 - - - -
59v VAL* 5.0 2.0 - - - -
76v TYR 2.8 17.0 + - - -
77v GLN 3.8 0.7 - - - -
79v PHE* 1.3 74.0 - - - +
81v LEU* 1.3 63.6 + - - +
83v VAL* 3.1 3.0 + - - -
84v ALA* 3.0 19.2 + - - +
121v VAL* 3.5 26.7 - - - -
125v ILE* 3.1 18.4 - - - +
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Residues in contact with LEU 81 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687 T 5.5 2.0 - - - +
697 A 5.6 3.4 - - - +
2818 A 4.1 18.8 - - + +
2828 T 3.4 37.7 - - - +
52v PHE* 3.5 43.0 - - + +
55v VAL* 4.5 6.3 - - + -
56v ASN* 3.4 31.4 - - - +
77v GLN* 2.9 28.9 + - + +
78v GLY* 3.8 5.4 - - - +
80v GLY* 1.3 76.2 - - - +
82v LYS* 1.3 58.2 + - - +
84v ALA* 3.2 3.5 + - - -
85v ARG 2.9 23.2 + - - -
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Residues in contact with LYS 82 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607 T 3.2 14.3 + - - -
2818 A 3.7 25.5 + - - +
2828 T 3.3 27.4 + - - +
106u TYR* 2.8 33.3 + - - -
78v GLY 3.0 17.7 + - - +
79v PHE* 3.5 5.4 - - - +
81v LEU* 1.3 73.4 - - - +
83v VAL* 1.3 65.6 + - - +
85v ARG* 3.3 11.2 + - - +
86v ALA* 3.1 22.0 + - - +
99v MET* 5.9 3.1 - - - -
103v LEU* 3.5 36.0 - - + +
106v TYR* 5.0 6.3 - - + -
107v TYR* 4.6 3.6 - - + -
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Residues in contact with VAL 83 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79v PHE* 2.9 43.4 + - + +
80v GLY* 3.3 8.7 - - - +
82v LYS* 1.3 77.7 - - - +
84v ALA* 1.3 62.3 + - - +
86v ALA* 3.3 7.7 + - - +
87v LEU* 3.0 20.4 + - + +
96v LEU* 4.5 2.7 - - + +
100v ILE* 4.3 27.6 - - + -
103v LEU* 3.7 19.1 - - + -
122v VAL* 4.6 8.5 - - + -
125v ILE* 3.9 26.7 - - + -
126v THR* 4.5 5.4 - - + -
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Residues in contact with ALA 84 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51v LYS 5.7 0.4 - - - +
52v PHE* 3.6 20.0 - - + -
55v VAL* 4.2 20.4 - - + -
80v GLY 3.0 10.8 + - - +
81v LEU* 3.5 8.7 - - - +
83v VAL* 1.3 74.3 - - - +
85v ARG* 1.3 66.6 + - - +
87v LEU* 3.1 12.2 + - + +
88v ASN* 3.0 25.2 + - - +
125v ILE* 4.4 11.0 - - + +
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Residues in contact with ARG 85 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597 A 3.8 35.3 + - - -
607 T 2.9 33.3 + - - +
2828 T 3.0 35.7 + - - +
2838 A 3.4 29.7 + - - +
52v PHE* 3.5 11.3 - - - -
81v LEU 2.9 14.2 + - - +
82v LYS* 3.3 19.7 - - - +
83v VAL 3.2 0.2 - - - -
84v ALA* 1.3 75.0 - - - +
86v ALA* 1.3 63.6 + - - +
88v ASN* 3.0 6.5 + - - +
89v ARG* 3.0 45.6 + - - +
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Residues in contact with ALA 86 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597 A 5.6 2.5 - - - -
82v LYS 3.1 10.0 + - - +
83v VAL* 3.6 10.1 - - - +
85v ARG* 1.3 78.6 - - - +
87v LEU* 1.3 59.0 + - - +
89v ARG* 4.5 2.9 - - - +
90v ILE* 2.7 47.6 + - + +
96v LEU* 3.8 15.3 - - + -
99v MET* 3.8 28.5 - - + -
100v ILE* 6.0 0.2 - - + -
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Residues in contact with LEU 87 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83v VAL* 3.0 13.0 + - + +
84v ALA* 3.2 12.6 - - + +
86v ALA* 1.3 77.5 - - - +
88v ASN* 1.3 64.2 + - - +
91v GLY* 2.7 31.7 + - - +
92v SER* 3.6 29.6 - - - +
96v LEU* 3.6 23.7 - - + +
125v ILE* 4.5 25.4 - - + +
126v THR* 6.0 2.7 - - + -
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Residues in contact with ASN 88 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2838 A 5.4 1.3 + - - +
48v ASN* 4.9 5.2 + - - +
51v LYS* 3.8 31.8 + - - +
52v PHE* 3.4 33.9 - - - -
84v ALA* 3.0 13.0 + - - +
85v ARG* 3.0 8.0 + - - +
87v LEU* 1.3 86.6 - - - +
89v ARG* 1.3 65.0 + - + +
90v ILE 4.8 0.5 - - - -
91v GLY 4.5 1.0 + - - -
7w SER* 4.6 13.1 - - - +
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Residues in contact with ARG 89 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577 A 4.6 10.1 + - - -
587 T 3.6 28.1 + - - +
597 A 3.3 31.8 + - - +
2838 A 4.1 16.5 + - - +
2848 T 4.3 16.2 + - - -
85v ARG* 3.0 46.0 + - - +
86v ALA* 4.3 2.2 - - - +
88v ASN* 1.3 80.5 - - + +
90v ILE* 1.3 61.6 + - + +
7w SER* 4.1 33.5 - - - +
8w ARG* 6.2 0.2 - - - +
60x SER* 4.5 6.1 + - - -
73x ARG* 4.6 1.9 + - - -
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Residues in contact with ILE 90 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587 T 5.6 0.2 - - - +
597 A 4.5 11.0 - - - +
86v ALA* 2.7 29.5 + - + +
88v ASN 4.8 0.9 - - - -
89v ARG* 1.3 78.2 - - - +
91v GLY* 1.3 68.5 + - - +
95v ALA* 3.6 26.0 - - + +
96v LEU* 4.0 4.9 - - + +
99v MET* 3.8 38.6 - - + -
60x SER* 4.9 1.9 + - - -
61x ALA* 5.8 0.7 - - - -
64x THR* 2.6 36.4 + - + +
69x THR* 4.4 11.0 - - + -
73x ARG* 3.7 18.2 + - - +
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Residues in contact with GLY 91 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86v ALA 3.6 0.8 + - - -
87v LEU* 2.7 31.4 + - - -
88v ASN 4.5 0.9 - - - -
90v ILE* 1.3 89.2 - - - +
92v SER* 1.3 66.9 + - - +
96v LEU* 3.4 9.2 - - - +
64x 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
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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