Contacts of the helix formed by residues 70 - 91 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518 A 3.4 27.5 + - - +
528 T 4.1 2.1 + - - -
69G THR* 1.3 75.7 - - - +
71G PRO* 1.3 68.5 - - - +
72G ASN 3.0 0.2 - - - -
73G ARG* 2.9 31.7 + - - +
90I ILE* 5.5 0.8 - - - +
99I MET* 5.3 0.4 - - - +
111J PHE* 3.6 18.3 - - - -
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Residues in contact with PRO 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518 A 3.7 30.1 - - + +
528 T 3.6 26.7 - - - +
69G THR 4.4 0.2 - - - +
70G GLY* 1.3 83.0 - - - +
72G ASN* 1.3 65.6 + - - +
73G ARG 3.1 0.2 - - - -
74G ALA* 3.0 6.9 + - + +
75G ILE* 3.0 24.3 + - - +
71J PRO* 3.6 19.0 - - + +
74J ALA 4.8 0.7 - - - -
75J ILE* 3.6 38.6 - - + +
107J TYR* 6.5 0.9 - - + -
111J PHE* 4.6 5.8 - - + -
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Residues in contact with ASN 72 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68G ILE* 3.5 15.9 - - + -
69G THR 3.3 14.3 + - - +
70G GLY 3.0 0.6 - - - -
71G PRO* 1.3 74.8 - - - +
73G ARG* 1.3 64.1 + - - +
75G ILE* 3.3 18.7 + - + +
76G TYR* 3.1 26.6 - - + -
72J ASN* 3.1 24.4 - - - +
75J ILE* 3.5 11.7 - - - +
111J PHE* 3.2 25.7 + - - +
112J ASN* 4.6 10.9 + - - +
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Residues in contact with ARG 73 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518 A 2.9 38.1 + - - +
60G SER* 2.7 45.3 + - - +
63G LEU* 3.5 16.9 - - + +
64G THR* 3.0 31.3 + - - +
68G ILE* 2.8 56.2 + - + +
69G THR* 3.8 8.1 - - - +
70G GLY 2.9 14.3 + - - +
72G ASN* 1.3 76.6 - - - +
74G ALA* 1.3 58.8 + - - +
76G TYR 3.1 3.5 + - - -
77G GLN* 2.8 32.2 + - - +
89I ARG 4.6 0.4 + - - -
90I ILE* 3.7 27.0 + - - +
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Residues in contact with ALA 74 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2997 A 4.1 25.6 - - + +
508 T 4.3 5.3 - - - +
518 A 3.8 37.4 + - + +
70G GLY 3.7 0.6 + - - -
71G PRO 3.0 13.0 + - - +
73G ARG* 1.3 79.9 - - - +
75G ILE* 1.3 61.4 + - - +
77G GLN* 3.6 8.9 - - - +
78G GLY* 2.9 20.4 + - - -
71J PRO* 4.8 3.8 - - + -
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Residues in contact with ILE 75 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2997 A 5.9 0.2 - - - -
71G PRO 3.0 14.1 + - - +
72G ASN* 3.4 23.3 - - + +
73G ARG 3.2 0.4 - - - -
74G ALA* 1.3 77.0 - - - +
76G TYR* 1.3 70.6 + - + +
78G GLY* 3.3 0.9 + - - -
79G PHE* 3.2 16.8 + - - +
107G TYR* 3.5 30.4 - - + -
111G PHE* 4.8 11.0 - - + +
113G ALA* 4.2 19.5 - - + -
71J PRO* 3.5 27.6 - - + -
72J ASN* 3.5 35.4 - - - +
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Residues in contact with TYR 76 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59G VAL* 4.3 5.5 - - - +
63G LEU* 3.6 32.8 - - + -
68G ILE* 4.0 19.2 - - + +
72G ASN* 3.1 26.2 - - + -
73G ARG 3.1 3.5 + - - +
75G ILE* 1.3 78.5 - - + +
77G GLN* 1.3 60.6 + - - +
79G PHE* 3.2 7.7 + - - +
80G GLY* 2.9 25.8 + - - -
112G ASN 5.2 0.2 + - - -
113G ALA* 4.0 8.0 - - + -
114G ASN* 2.9 38.3 + - - +
117G VAL* 3.7 27.6 - - + +
118G LEU* 3.6 31.9 - - + -
121G VAL* 4.4 8.6 - - + +
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Residues in contact with GLN 77 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508 T 3.2 33.0 + - + +
518 A 3.2 20.1 + - - +
55G VAL* 4.8 0.5 - - - +
56G ASN* 3.1 41.4 + - - +
59G VAL* 3.3 23.9 - - - +
60G SER* 3.4 12.3 - - - +
63G LEU* 4.0 3.3 - - + +
73G ARG 2.8 22.9 + - - +
74G ALA* 3.6 7.6 - - - +
75G ILE 3.3 0.2 - - - -
76G TYR* 1.3 76.3 - - - +
78G GLY* 1.3 56.1 + - - +
80G GLY* 3.2 1.2 + - - -
81G LEU* 2.9 36.9 + - + +
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Residues in contact with GLY 78 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2997 A 5.6 1.3 - - - -
3007 T 3.7 30.6 + - - +
508 T 5.3 0.2 + - - -
74G ALA 2.9 13.9 + - - -
75G ILE 3.8 3.8 - - - -
76G TYR 3.2 0.2 - - - -
77G GLN* 1.3 76.7 - - - +
79G PHE* 1.3 61.9 + - - +
81G LEU* 3.3 5.9 + - - +
82G LYS* 3.0 23.2 + - - +
107G TYR* 3.5 11.5 + - - -
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Residues in contact with PHE 79 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75G ILE 3.2 12.4 + - - +
76G TYR 3.2 7.4 + - - +
78G GLY* 1.3 75.3 - - - +
80G GLY* 1.3 64.3 + - - +
82G LYS* 3.2 6.4 + - - +
83G VAL* 3.1 30.2 + - + +
100G ILE* 5.0 0.9 - - + -
103G LEU* 3.6 31.2 - - + -
104G LYS* 3.8 28.9 - - + -
107G TYR* 3.5 26.9 + + + -
118G LEU* 3.3 51.4 - - + -
121G VAL* 3.8 16.4 - - + -
122G VAL* 3.6 24.9 - - + -
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Residues in contact with GLY 80 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55G VAL* 4.1 6.7 - - - -
59G VAL* 4.7 2.0 - - - -
76G TYR 2.9 11.8 + - - -
77G GLN 3.2 2.9 + - - -
79G PHE* 1.3 77.0 - - - +
81G LEU* 1.3 62.6 + - - +
83G VAL* 3.1 3.1 + - - -
84G ALA* 3.1 19.6 + - - +
121G VAL* 3.6 14.4 - - - -
125G ILE* 3.2 29.8 - - - +
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Residues in contact with LEU 81 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3007 T 3.6 23.3 - - + +
3017 A 3.4 31.5 - - - +
498 A 4.9 7.2 - - + +
508 T 5.2 2.2 - - - +
52G PHE* 3.7 37.8 - - + +
55G VAL* 4.3 6.0 - - + +
56G ASN* 3.3 30.7 - - - +
77G GLN* 2.9 26.4 + - + +
78G GLY* 3.6 4.7 - - - +
80G GLY* 1.3 76.0 - - - +
82G LYS* 1.3 57.5 + - - +
84G ALA* 3.3 7.0 + - - +
85G ARG* 2.9 27.9 + - - +
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Residues in contact with LYS 82 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3007 T 4.0 13.8 + - - +
3017 A 2.9 31.1 + - - +
408 T 5.6 1.6 - - - -
418 A 3.8 13.8 + - - -
78G GLY 3.0 13.4 + - - +
79G PHE* 3.2 10.5 + - - +
81G LEU* 1.3 74.5 - - - +
83G VAL* 1.3 64.8 + - - +
85G ARG* 3.2 11.7 + - - +
86G ALA* 3.1 24.1 + - + +
99G MET* 4.7 16.8 - - + -
103G LEU* 3.5 29.8 - - + +
106G TYR* 5.5 4.6 - - - -
107G TYR* 5.2 1.1 - - + -
106H TYR* 2.7 38.6 + - - -
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Residues in contact with VAL 83 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79G PHE* 3.1 35.7 + - + +
80G GLY* 3.1 8.9 + - - +
82G LYS* 1.3 77.3 - - - +
84G ALA* 1.3 62.4 + - - +
86G ALA* 3.4 6.3 + - - +
87G LEU* 3.0 20.9 + - + +
96G LEU* 4.3 4.6 - - + +
99G MET* 6.3 0.7 - - - -
100G ILE* 4.3 19.3 - - + -
103G LEU* 3.6 18.2 - - + -
122G VAL* 4.5 8.5 - - + -
125G ILE* 3.7 26.7 - - + -
126G THR* 4.3 15.0 - - + -
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Residues in contact with ALA 84 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51G LYS 5.5 0.7 - - - +
52G PHE* 3.6 20.6 - - + -
55G VAL* 4.0 21.1 - - + -
80G GLY 3.1 7.9 + - - +
81G LEU* 3.5 8.7 - - - +
83G VAL* 1.3 79.8 - - - +
85G ARG* 1.3 64.0 + - - +
87G LEU* 3.1 11.8 + - + +
88G ASN* 2.9 27.0 + - - +
125G ILE* 4.5 8.1 - - + -
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Residues in contact with ARG 85 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3017 A 3.0 36.1 + - - +
3027 T 3.1 34.4 + - - +
408 T 3.8 34.6 + - - +
418 A 3.9 20.7 + - - -
52G PHE* 3.6 10.5 - - - -
81G LEU 2.9 13.1 + - - +
82G LYS* 3.2 15.9 + - + +
84G ALA* 1.3 76.3 - - - +
86G ALA* 1.3 64.3 + - - +
88G ASN* 3.1 5.5 + - - +
89G ARG* 3.0 52.5 + - - +
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Residues in contact with ALA 86 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408 T 5.4 3.4 - - - +
82G LYS* 3.1 12.4 + - - +
83G VAL* 3.7 9.9 - - - +
85G ARG* 1.3 77.8 - - - +
87G LEU* 1.3 57.7 + - - +
89G ARG* 4.5 2.7 - - - +
90G ILE* 2.7 51.3 + - + +
96G LEU* 3.9 10.3 - - + -
99G MET* 3.8 32.8 - - + -
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Residues in contact with LEU 87 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83G VAL* 3.0 14.7 + - + +
84G ALA* 3.1 13.4 + - + +
86G ALA* 1.3 76.2 - - - +
88G ASN* 1.3 64.5 + - - +
91G GLY* 2.7 31.3 + - - +
92G SER* 3.6 32.8 - - - +
96G LEU* 3.8 23.7 - - + +
125G ILE* 4.8 22.4 - - + +
126G THR* 6.1 2.2 - - + -
57l GLU* 5.8 3.6 - - - +
58l ASN* 6.2 0.2 - - - +
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Residues in contact with ASN 88 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3027 T 5.9 0.9 - - - +
7F SER* 3.8 18.0 + - - +
48G ASN* 4.9 5.4 + - - -
51G LYS* 3.9 30.0 + - - +
52G PHE* 3.3 34.7 - - + -
84G ALA* 2.9 13.8 + - - +
85G ARG* 3.6 7.9 - - - +
87G LEU* 1.3 86.5 - - - +
89G ARG* 1.3 63.4 + - + +
90G ILE 5.0 0.3 - - - -
91G GLY 4.8 0.7 + - - -
57l GLU* 5.2 4.3 - - - +
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Residues in contact with ARG 89 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3027 T 3.8 18.3 + - - +
3037 A 4.3 14.8 + - - -
388 T 4.7 4.4 + - - -
398 A 3.6 25.9 + - - +
408 T 3.5 36.4 + - - +
60E SER* 4.7 2.1 + - - -
73E ARG* 4.6 4.0 + - - -
7F SER* 3.6 36.0 - - - +
8F ARG* 5.5 3.6 - - - +
85G ARG* 3.0 53.8 + - - +
86G ALA* 4.2 2.2 - - - +
88G ASN* 1.3 79.5 - - + +
90G ILE* 1.3 61.6 + - - +
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Residues in contact with ILE 90 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398 A 5.4 0.9 - - - +
408 T 4.4 11.4 - - - +
60E SER* 4.7 3.4 + - - -
64E THR* 2.6 36.5 + - + +
69E THR* 4.4 18.2 - - + -
70E GLY 5.5 0.4 - - - +
73E ARG* 3.7 19.1 + - - +
86G ALA* 2.7 27.8 + - + +
88G ASN 5.0 0.4 - - - -
89G ARG* 1.3 80.0 - - + +
91G GLY* 1.3 68.4 + - - +
95G ALA* 3.5 26.0 - - + +
96G LEU* 4.2 4.0 - - - +
99G MET* 3.7 30.7 - - + -
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Residues in contact with GLY 91 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E THR* 3.8 1.1 - - - +
86G ALA 3.6 0.4 + - - -
87G LEU* 2.7 30.5 + - - -
88G ASN 4.6 0.2 - - - -
90G ILE* 1.3 90.1 - - - +
92G SER* 1.3 68.0 + - - +
96G 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