Contacts of the helix formed by residues 70 - 91 (chain z) 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 z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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467 T 3.5 25.0 + - - +
477 A 4.4 2.6 + - - -
111w PHE* 3.5 19.6 - - - -
90x ILE* 5.6 0.2 - - - +
99x MET* 5.3 0.2 - - - +
69z THR* 1.3 76.1 - - - +
71z PRO* 1.3 67.1 - - - +
72z ASN 3.0 0.2 - - - -
73z ARG* 2.9 35.6 + - - +
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Residues in contact with PRO 71 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467 T 3.6 22.9 - - + +
477 A 3.9 32.5 - - - +
71w PRO* 3.6 19.3 - - + +
74w ALA* 4.8 2.9 - - + -
75w ILE* 3.5 37.2 - - + +
107w TYR* 6.5 1.1 - - + -
111w PHE* 4.6 7.0 - - + -
69z THR 4.4 0.2 - - - +
70z GLY* 1.3 82.0 - - - +
72z ASN* 1.3 65.6 + - - +
73z ARG 3.1 0.2 - - - -
74z ALA* 3.1 4.6 + - - +
75z ILE* 3.0 24.6 + - - +
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Residues in contact with ASN 72 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72w ASN* 3.1 25.1 - - - +
75w ILE* 3.5 11.7 - - - +
111w PHE 3.3 24.9 + - - -
112w ASN* 4.8 8.3 + - - +
68z ILE* 3.5 15.7 - - + -
69z THR* 3.3 14.1 + - - +
70z GLY 3.0 1.0 - - - -
71z PRO* 1.3 75.4 - - - +
73z ARG* 1.3 64.9 + - - +
75z ILE* 3.3 18.6 + - + +
76z TYR* 3.0 25.9 - - + -
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Residues in contact with ARG 73 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467 T 3.0 35.0 + - - +
89x ARG 4.6 0.8 + - - -
90x ILE* 3.7 26.3 + - - +
60z SER* 2.7 46.9 + - - +
63z LEU* 3.5 16.3 - - + +
64z THR* 2.9 31.1 + - - +
68z ILE* 2.7 54.6 + - + +
69z THR* 3.9 8.1 - - - +
70z GLY 2.9 15.9 + - - +
72z ASN* 1.3 76.4 - - - +
74z ALA* 1.3 60.4 + - - +
76z TYR* 3.0 5.0 + - - -
77z GLN* 2.8 30.3 + - - +
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Residues in contact with ALA 74 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457 A 4.1 17.0 - - + +
467 T 3.0 40.7 + - + +
3038 A 4.7 4.9 - - + -
3048 T 4.4 5.8 - - - +
71w PRO* 4.8 4.5 - - + -
70z GLY 3.6 0.8 + - - -
71z PRO 3.1 8.2 + - - +
73z ARG* 1.3 77.0 - - - +
75z ILE* 1.3 65.1 + - - +
77z GLN* 3.6 10.3 - - - +
78z GLY* 2.9 22.0 + - - -
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Residues in contact with ILE 75 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3048 T 6.5 0.2 - - - -
71w PRO* 3.6 26.7 - - + +
72w ASN* 3.5 35.0 - - - +
71z PRO 3.0 14.6 + - - +
72z ASN* 3.4 22.9 - - + +
73z ARG 3.2 0.4 - - - -
74z ALA* 1.3 77.3 - - - +
76z TYR* 1.3 66.8 + - + +
78z GLY* 3.4 1.0 + - - -
79z PHE* 3.1 20.8 + - - +
107z TYR* 3.5 31.9 - - + -
111z PHE* 4.6 11.2 - - + +
112z ASN 5.9 0.4 - - - +
113z ALA* 4.1 20.2 - - + -
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Residues in contact with TYR 76 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59z VAL* 4.4 2.9 - - - +
63z LEU* 3.6 28.9 - - + -
68z ILE* 4.0 18.4 - - + +
72z ASN* 3.0 27.8 - - + -
73z ARG 3.0 4.8 + - - +
75z ILE* 1.3 79.9 - - + +
77z GLN* 1.3 62.4 + - - +
79z PHE* 3.3 6.0 + - - +
80z GLY* 2.8 26.5 + - - -
112z ASN 5.0 0.3 + - - -
113z ALA* 3.9 9.1 - - + -
114z ASN* 2.9 38.3 + - - +
117z VAL* 3.7 30.4 - - + +
118z LEU* 3.7 30.5 - - + -
121z VAL* 4.2 12.1 - - + +
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Residues in contact with GLN 77 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457 A 3.4 34.1 + - + +
467 T 3.1 21.5 + - - +
55z VAL* 5.4 0.7 - - - +
56z ASN* 3.4 24.1 + - - +
59z VAL* 3.3 21.3 - - - +
60z SER* 3.5 25.9 - - - +
63z LEU* 4.0 2.1 - - + +
73z ARG 2.8 22.3 + - - +
74z ALA* 3.6 9.4 - - - +
76z TYR* 1.3 77.7 - - - +
78z GLY* 1.3 57.5 + - - +
80z GLY* 3.3 0.9 + - - -
81z LEU* 2.9 41.2 + - + +
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Residues in contact with GLY 78 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457 A 5.4 1.2 + - - -
3048 T 5.1 2.9 - - - -
3058 A 4.1 24.8 - - - +
74z ALA 2.9 16.0 + - - -
75z ILE 3.8 1.8 - - - -
77z GLN* 1.3 76.2 - - - +
79z PHE* 1.3 62.0 + - - +
81z LEU* 3.4 5.8 + - - +
82z LYS* 3.0 24.4 + - - +
107z TYR* 3.5 13.1 + - - -
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Residues in contact with PHE 79 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75z ILE 3.1 13.7 + - - +
76z TYR 3.5 8.1 - - - +
78z GLY* 1.3 76.5 - - - +
80z GLY* 1.3 64.8 + - - +
82z LYS* 3.1 5.1 + - - +
83z VAL* 2.9 32.2 + - + +
100z ILE* 5.1 2.2 - - + -
103z LEU* 3.7 23.6 - - + -
104z LYS* 3.8 24.7 - - + -
107z TYR* 3.5 33.9 + + + -
118z LEU* 3.3 53.4 - - + -
121z VAL* 3.8 16.4 - - + -
122z VAL* 3.7 24.5 - - + -
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Residues in contact with GLY 80 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55z VAL* 4.5 5.4 - - - -
59z VAL* 5.0 2.2 - - - -
76z TYR 2.8 16.3 + - - -
77z GLN 3.8 1.3 - - - -
79z PHE* 1.3 73.8 - - - +
81z LEU* 1.3 62.3 - - - +
83z VAL* 3.1 2.5 + - - -
84z ALA* 3.0 19.4 + - - +
121z VAL* 3.5 27.1 - - - -
125z ILE* 3.1 18.1 - - - +
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Residues in contact with LEU 81 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447 T 5.5 1.8 - - - +
457 A 5.6 2.9 - - - +
3058 A 4.1 19.3 - - + +
3068 T 3.4 36.2 - - - +
52z PHE* 3.5 43.1 - - + +
55z VAL* 4.5 6.3 - - + +
56z ASN* 3.4 31.9 - - - +
77z GLN* 2.9 29.2 + - + +
78z GLY* 3.8 4.9 - - - +
80z GLY* 1.3 75.6 - - - +
82z LYS* 1.3 57.6 + - - +
84z ALA* 3.2 3.5 + - - -
85z ARG 2.9 24.1 + - - -
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Residues in contact with LYS 82 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367 T 3.2 13.5 + - - -
3058 A 3.7 25.8 + - - +
3068 T 3.3 28.7 + - - +
106y TYR* 2.8 33.3 + - - -
78z GLY 3.0 18.0 + - - +
79z PHE* 3.1 5.1 + - - +
81z LEU* 1.3 74.3 - - - +
83z VAL* 1.3 64.6 + - - +
85z ARG* 3.3 11.6 + - - +
86z ALA* 3.1 22.2 + - - +
99z MET* 5.9 2.6 - - - -
103z LEU* 3.5 35.1 - - + +
106z TYR* 5.0 6.1 - - - -
107z TYR* 4.6 3.8 - - + -
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Residues in contact with VAL 83 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79z PHE* 2.9 43.3 + - + +
80z GLY* 3.3 8.1 - - - +
82z LYS* 1.3 76.8 - - - +
84z ALA* 1.3 61.9 + - - +
86z ALA* 3.3 8.0 + - - +
87z LEU* 3.0 20.0 + - + +
96z LEU* 4.5 2.8 - - + +
99z MET* 6.5 0.2 - - - -
100z ILE* 4.3 27.8 - - + -
103z LEU* 3.7 18.1 - - + +
122z VAL* 4.6 8.5 - - + -
125z ILE* 3.9 26.9 - - + -
126z THR* 4.5 5.2 - - + -
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Residues in contact with ALA 84 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51z LYS 5.7 0.4 - - - +
52z PHE* 3.6 20.4 - - + -
55z VAL* 4.2 20.2 - - + -
80z GLY 3.0 11.9 + - - +
81z LEU* 3.5 8.3 - - - +
83z VAL* 1.3 74.3 - - - +
85z ARG* 1.3 66.5 + - - +
87z LEU* 3.1 12.0 + - + +
88z ASN* 3.0 26.0 + - - +
125z ILE* 4.4 11.6 - - + +
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Residues in contact with ARG 85 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357 A 3.8 36.5 + - - -
367 T 2.9 32.9 + - - +
3068 T 3.0 35.8 + - - +
3078 A 3.4 31.2 + - - +
52z PHE* 3.5 11.4 - - - -
81z LEU 2.9 13.2 + - - +
82z LYS* 3.3 20.6 - - - +
84z ALA* 1.3 74.8 - - - +
86z ALA* 1.3 64.3 + - - +
88z ASN* 3.0 5.6 + - - +
89z ARG* 3.0 45.4 + - - +
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Residues in contact with ALA 86 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357 A 5.6 2.2 - - - -
82z LYS 3.1 9.3 + - - +
83z VAL* 3.6 9.4 - - - +
85z ARG* 1.3 77.6 - - - +
87z LEU* 1.3 58.7 + - - +
89z ARG* 4.5 3.1 - - - +
90z ILE* 2.7 47.5 + - + +
96z LEU* 3.8 16.8 - - + -
99z MET* 3.8 26.9 - - + -
100z ILE* 6.0 0.2 - - + -
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Residues in contact with LEU 87 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83z VAL* 3.0 14.0 + - + +
84z ALA* 3.1 12.5 + - + +
86z ALA* 1.3 76.1 - - - +
88z ASN* 1.3 64.0 + - - +
91z GLY* 2.7 30.9 + - - +
92z SER* 3.6 28.9 - - - +
96z LEU* 3.6 25.0 - - + +
125z ILE* 4.5 25.8 - - + +
126z THR* 6.0 2.5 - - + -
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Residues in contact with ASN 88 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71 SER* 4.6 13.1 - - - +
3078 A 5.4 1.7 + - - +
48z ASN* 4.9 4.8 + - - -
51z LYS* 3.8 31.4 + - - +
52z PHE* 3.4 34.2 - - - -
84z ALA* 3.0 12.1 + - - +
85z ARG* 3.5 7.6 - - - +
87z LEU* 1.3 85.6 - - - +
89z ARG* 1.3 65.6 + - + +
90z ILE 4.8 0.2 - - - -
91z GLY* 4.5 1.4 + - - -
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Residues in contact with ARG 89 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71 SER* 4.1 33.8 - - - +
81 ARG* 6.2 0.2 - - - +
602 SER* 4.5 6.4 + - - -
732 ARG* 4.6 1.9 + - - -
337 A 4.6 10.1 + - - -
347 T 3.6 28.2 + - - +
357 A 3.3 31.7 + - - +
3078 A 4.1 17.3 + - - +
3088 T 4.3 15.8 + - - -
85z ARG* 3.0 44.7 + - + +
86z ALA* 4.3 2.0 - - - +
88z ASN* 1.3 80.2 - - + +
90z ILE* 1.3 61.2 + - + +
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Residues in contact with ILE 90 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602 SER* 4.9 1.4 + - - -
612 ALA* 5.8 0.7 - - - -
642 THR* 2.6 36.4 + - + +
692 THR* 4.4 10.5 - - + -
732 ARG* 3.7 19.4 + - - +
347 T 5.6 0.4 - - - +
357 A 4.5 11.4 - - - +
86z ALA* 2.7 28.0 + - + +
88z ASN 4.8 0.7 - - - -
89z ARG* 1.3 79.5 - - - +
91z GLY* 1.3 67.4 + - - +
95z ALA* 3.6 26.5 - - + +
96z LEU* 4.0 4.7 - - + +
99z MET* 3.8 38.4 - - + -
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Residues in contact with GLY 91 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642 THR* 3.6 1.1 - - - +
86z ALA 3.6 0.2 + - - -
87z LEU* 2.7 31.5 + - - -
88z ASN 4.5 0.6 - - - -
90z ILE* 1.3 90.4 - - - +
92z SER* 1.3 67.1 + - - +
96z LEU* 3.4 9.9 - - - +
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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