Contacts of the helix formed by residues 64 - 89 (chain J) in PDB entry 4PHZ
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 MET 64 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53J TRP* 3.3 23.6 - - + +
61J ASP* 3.0 11.2 + - - +
63J ARG* 1.3 92.9 - - + +
65J TRP* 1.3 58.5 + - - +
67J THR* 2.9 8.2 + - - -
68J VAL* 2.8 40.1 + - + +
204J MET* 3.0 29.4 - - - +
205J VAL* 3.5 23.1 - - - +
206J GLU* 3.7 6.3 - - - +
207J ARG 5.3 0.2 - - - +
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Residues in contact with TRP 65 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53J TRP* 3.7 28.6 + - + -
59J TRP 3.9 5.2 - - - +
60J LYS* 3.4 44.0 - - + +
61J ASP* 3.0 39.0 + - - +
64J MET* 1.3 74.5 - - - +
66J PRO* 1.3 65.5 - - + +
67J THR 2.8 10.4 + - - -
68J VAL* 4.7 0.9 - - - +
69J VAL* 3.2 41.1 + - + +
127J SER* 2.9 21.2 + - - -
161J PHE* 3.7 16.2 - + - -
162J TYR* 3.4 30.1 - + - -
165J ASN* 3.5 38.6 - - + -
169J ILE* 4.6 13.5 - - + -
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Residues in contact with PRO 66 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61J ASP 3.6 12.6 - - - +
62J ARG 3.3 27.6 - - - +
63J ARG 3.9 2.7 - - - +
65J TRP* 1.3 97.3 - - + +
67J THR* 1.3 57.7 + - - +
70J PRO* 3.4 8.9 - - - +
158J GLY 5.3 0.5 - - - +
161J PHE* 3.8 25.1 - - + +
162J TYR* 3.9 23.1 - - + -
218J VAL* 5.4 3.1 - - + -
221J ALA* 3.7 12.3 - - + +
222J ALA* 4.7 6.3 + - - +
225J SER* 3.3 20.1 + - - -
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Residues in contact with THR 67 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63J ARG* 2.8 18.4 + - - +
64J MET* 2.9 11.2 + - - -
65J TRP 2.8 2.2 + - - -
66J PRO* 1.3 77.1 - - - +
68J VAL* 1.3 71.3 + - + +
69J VAL 3.2 1.2 + - - -
70J PRO* 3.6 2.1 - - - +
71J ILE* 3.1 32.8 + - + +
221J ALA* 3.5 21.3 + - - +
224J PHE* 3.6 33.4 - - + -
225J SER* 4.0 3.7 - - - -
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Residues in contact with VAL 68 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50J ALA* 4.3 8.3 - - + -
53J TRP* 3.6 50.5 - - + -
64J MET* 2.8 29.8 + - + +
65J TRP 4.6 0.2 - - - +
67J THR* 1.3 78.9 - - + +
69J VAL* 1.3 68.6 + - + +
71J ILE* 4.7 4.0 - - - -
72J LEU* 2.8 44.0 + - + +
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Residues in contact with VAL 69 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46J PHE* 4.2 17.8 - - + -
50J ALA* 4.1 24.2 - - + +
53J TRP* 4.5 2.0 - - + -
54J ASP* 5.1 1.6 - - + +
65J TRP* 3.2 32.8 + - + +
68J VAL* 1.3 81.8 - - + +
70J PRO* 1.3 65.3 - - + +
72J LEU 3.2 0.2 + - - -
73J GLY* 2.6 35.3 + - - -
127J SER* 4.3 7.6 - - - +
129J LEU* 4.1 11.7 - - + -
157J TRP* 4.9 0.2 - - - -
161J PHE* 3.4 28.5 - - + -
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Residues in contact with PRO 70 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65J TRP 3.7 0.7 - - - +
66J PRO* 3.4 33.2 - - + +
67J THR 3.6 1.8 - - - +
69J VAL* 1.3 95.6 - - + +
71J ILE* 1.3 60.5 + - - +
74J VAL* 3.0 13.5 + - - +
157J TRP* 2.8 43.0 + - + +
158J GLY* 4.3 2.5 - - - -
161J PHE* 3.9 26.7 - - + -
225J SER* 3.7 20.2 - - - +
229J SER* 3.6 4.0 + - - +
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Residues in contact with ILE 71 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67J THR* 3.1 39.2 + - + +
68J VAL* 4.1 4.0 - - - +
69J VAL 3.2 0.6 - - - -
70J PRO* 1.3 76.0 - - - +
72J LEU* 1.3 66.9 + - + +
74J VAL* 3.5 16.5 - - - +
75J THR* 4.2 0.5 - - - +
224J PHE* 4.2 6.3 - - + -
225J SER* 3.8 17.0 - - - +
228J VAL* 3.9 26.7 - - + -
229J SER* 3.5 17.3 - - - +
232J VAL* 3.9 31.1 - - + +
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Residues in contact with LEU 72 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42J TYR* 4.5 0.5 - - - -
45J HIS* 3.8 24.4 + - + +
46J PHE* 4.4 6.5 - - + -
49J THR* 3.1 46.2 - - + +
50J ALA* 3.8 19.5 - - + +
53J TRP* 6.0 0.2 - - + -
68J VAL* 2.8 35.0 + - + +
71J ILE* 1.3 78.8 - - + +
73J GLY* 1.3 60.0 + - - +
75J THR* 2.8 27.6 + - + +
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Residues in contact with GLY 73 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42J TYR* 2.7 29.9 + - - -
46J PHE* 4.2 12.1 - - - -
69J VAL 2.6 23.3 + - - -
70J PRO 3.7 0.9 - - - -
72J LEU* 1.3 71.7 - - - +
74J VAL* 1.3 58.7 + - - +
75J THR* 2.8 15.4 + - - -
76J PHE 3.7 1.0 + - - -
77J CYS* 4.1 1.2 + - - -
129J LEU* 5.4 3.1 - - - -
157J TRP* 3.5 10.3 - - - -
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Residues in contact with VAL 74 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70J PRO 3.0 13.4 + - - +
71J ILE 3.5 15.0 - - - +
73J GLY* 1.3 73.6 - - - +
75J THR* 1.3 67.6 + - - +
77J CYS* 3.1 3.6 + - - +
78J ALA* 2.8 23.0 + - - +
136J LEU* 4.2 19.5 - - + -
154J SER* 4.7 3.8 - - - -
157J TRP* 3.2 29.7 - - + +
229J SER* 4.1 15.5 - - - +
232J VAL* 3.7 22.9 - - + -
233J TYR* 4.2 22.2 - - + +
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Residues in contact with THR 75 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42J TYR* 4.2 1.2 - - - -
45J HIS* 3.6 16.7 + - + +
71J ILE 4.2 4.0 - - - +
72J LEU* 2.8 25.4 + - + +
73J GLY 2.8 1.8 + - - -
74J VAL* 1.3 80.6 - - - +
76J PHE* 1.3 72.6 + - - -
78J ALA 3.1 10.0 + - - -
79J ALA 3.2 9.4 + - - -
232J VAL* 3.7 14.8 - - + -
236J TRP* 3.4 58.7 - - + +
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Residues in contact with PHE 76 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38J VAL* 4.1 7.4 - - + -
41J GLY* 3.4 18.6 - - - -
42J TYR* 3.3 56.3 - + + -
45J HIS* 3.8 16.8 - + + -
73J GLY 3.7 1.6 + - - -
74J VAL 3.5 0.4 - - - -
75J THR* 1.3 86.0 + - - +
77J CYS* 1.3 60.4 + - - +
79J ALA* 3.9 6.3 - - - +
80J SER* 2.9 31.2 + - - -
97J ALA* 3.7 4.6 - - + +
236J TRP* 3.4 30.5 - + - -
227K MET* 4.0 22.4 - - + -
229K LEU* 3.9 32.8 - - + -
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Residues in contact with CYS 77 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42J TYR* 3.8 13.7 - - - -
73J GLY 4.1 0.6 + - - -
74J VAL* 3.1 10.1 + - - +
76J PHE* 1.3 79.4 - - - +
78J ALA* 1.3 57.5 + - - +
80J SER* 3.9 1.1 - - - -
81J GLN* 3.0 35.7 + - - +
94J ALA* 3.3 37.7 - - + +
97J ALA* 4.1 5.4 - - - -
98J ALA* 4.2 10.3 - - - -
136J LEU* 3.9 11.9 - - + -
157J TRP* 3.7 30.1 - - - -
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Residues in contact with ALA 78 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74J VAL 2.8 11.5 + - - +
75J THR 3.4 8.7 - - - +
77J CYS* 1.3 75.7 - - - +
79J ALA* 1.3 58.4 + - - +
81J GLN* 3.3 4.2 + - - +
82J ALA* 2.9 27.7 + - - +
233J TYR* 3.5 46.1 - - + +
236J TRP* 3.7 18.6 - - + -
237J TRP* 3.8 7.0 - - - +
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Residues in contact with ALA 79 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75J THR 3.2 12.9 + - - +
76J PHE* 4.2 4.3 - - - +
78J ALA* 1.3 75.5 - - - +
80J SER* 1.3 63.3 + - - +
82J ALA* 3.2 5.2 + - - +
83J PHE* 3.1 16.5 + - - +
236J TRP* 3.4 28.5 + - + +
239J MET 5.0 0.7 - - - -
240J GLY* 3.8 14.7 - - - +
243J TYR* 5.8 0.4 - - + -
229K LEU* 3.8 26.7 - - + -
232K PHE* 3.8 10.2 - - + -
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Residues in contact with SER 80 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38J VAL* 5.3 4.7 - - - -
76J PHE* 2.9 20.6 + - - -
77J CYS 4.0 0.4 - - - -
79J ALA* 1.3 78.4 - - - +
81J GLN* 1.3 61.9 + - - +
83J PHE* 3.1 2.3 + - - -
84J TRP* 3.0 37.5 + - - -
93J GLY* 2.5 30.6 + - - -
96J PHE* 4.1 7.2 - - - +
97J ALA* 4.0 8.1 - - - -
229K LEU* 5.5 0.2 - - - +
232K PHE* 4.1 16.4 - - - -
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Residues in contact with GLN 81 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77J CYS 3.0 21.8 + - - +
78J ALA 3.3 3.8 + - - +
80J SER* 1.3 72.0 - - - +
82J ALA* 1.3 63.5 + - - +
83J PHE 2.8 6.7 + - - -
84J TRP 4.5 0.2 - - - +
85J TRP* 2.9 28.4 + - - +
93J GLY* 3.8 6.5 - - - -
94J ALA* 3.5 19.6 - - - +
136J LEU* 3.4 27.9 + - - +
137J ASP* 2.8 27.0 + - - +
140J LEU* 3.5 24.3 - - + +
149J THR* 3.8 1.9 - - - +
233J TYR* 2.8 32.1 + - - -
237J TRP* 3.8 5.2 - - + -
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Residues in contact with ALA 82 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78J ALA 2.9 12.3 + - - +
79J ALA 3.2 10.3 + - - +
81J GLN* 1.3 74.5 - - - +
83J PHE* 1.3 59.8 + - - +
86J VAL* 3.1 26.2 - - - +
87J ASN* 4.1 2.3 + - - -
237J TRP* 3.1 47.0 - - + +
240J GLY* 3.7 10.3 - - - -
241J ARG* 3.9 14.0 + - - +
244J SER* 4.9 2.2 + - - -
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Residues in contact with PHE 83 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34J LEU* 3.7 15.0 - - + -
79J ALA 3.1 5.5 + - - +
80J SER 3.1 6.8 + - - +
81J GLN 2.8 2.8 + - - -
82J ALA* 1.3 78.5 - - - +
84J TRP* 1.3 95.8 + + - +
85J TRP 3.3 0.7 + - - -
87J ASN* 3.0 32.9 + - - +
88J PHE* 3.5 28.3 - + - -
244J SER* 3.9 9.9 - - - +
232K PHE* 3.3 72.9 - + + -
235K VAL* 3.8 19.1 - - + -
236K LEU* 4.1 9.2 - - + -
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Residues in contact with TRP 84 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208I ILE* 4.0 24.0 - - + -
31J LEU* 4.6 4.0 - - + -
34J LEU* 3.2 36.3 - - + -
80J SER* 3.0 37.0 + - - +
81J GLN 4.5 0.2 - - - +
83J PHE* 1.3 93.0 - + - +
85J TRP* 1.3 59.2 + - - +
88J PHE* 3.0 37.5 + + - +
89J ARG 3.2 5.5 + - - -
90J LEU* 3.3 52.4 + - + +
92J PHE* 3.7 20.0 - + + -
93J GLY* 3.8 14.6 - - - +
96J PHE* 3.6 38.7 - + - -
232K PHE* 5.2 2.6 - + - -
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Residues in contact with TRP 85 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224I ILE* 4.5 7.6 - - + -
229I ARG* 5.7 1.6 - - - -
81J GLN* 2.9 16.7 + - - +
84J TRP* 1.3 77.5 - - - +
86J VAL* 1.3 70.5 + - + +
89J ARG* 2.7 94.9 + - + +
90J LEU 4.0 2.7 - - - +
91J PRO* 3.9 30.3 - - + -
140J LEU* 3.6 50.6 - - + +
141J LEU* 4.0 23.3 - - + -
144J GLY* 3.7 23.7 + - - -
237J TRP* 4.5 10.8 - + + -
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Residues in contact with VAL 86 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215I VAL* 3.6 7.1 - - - +
82J ALA 3.1 22.2 + - - +
85J TRP* 1.3 83.4 - - + +
87J ASN* 1.3 69.3 + - - +
89J ARG* 3.1 22.7 + - - +
237J TRP* 3.6 31.6 - - + -
241J ARG* 3.5 37.0 - - - +
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Residues in contact with ASN 87 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212I TYR* 3.7 18.0 - - + -
215I VAL* 3.5 19.5 - - - +
82J ALA 4.1 3.6 + - - -
83J PHE* 3.0 31.5 + - - +
85J TRP 3.4 0.4 - - - -
86J VAL* 1.3 85.9 - - - +
88J PHE* 1.3 76.6 + - + +
241J ARG* 5.2 3.4 + - - +
244J SER* 4.5 5.1 + - - -
236K LEU* 3.6 40.4 - - + +
----------------------------------------------------------
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Residues in contact with PHE 88 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208I ILE* 3.5 39.0 - - + -
211I SER* 3.3 23.4 - - - -
212I TYR* 3.8 9.9 - + + -
215I VAL* 3.7 7.4 - - - +
223I VAL* 3.5 3.3 - - - +
34J LEU* 5.7 0.7 - - + -
83J PHE* 3.5 40.4 - + - -
84J TRP* 3.0 26.7 + + - +
87J ASN* 1.3 92.1 - - + +
89J ARG* 1.3 70.5 + - - +
90J LEU* 3.0 20.3 + - + +
235K VAL* 4.9 1.1 - - + -
236K LEU* 4.1 6.3 - - + -
239K LEU* 3.5 33.0 - - + -
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Residues in contact with ARG 89 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215I VAL* 3.8 23.8 - - + +
220I ALA* 3.8 28.0 + - - +
223I VAL* 3.8 11.0 - - + +
224I ILE* 3.3 38.5 - - + +
84J TRP 3.2 0.2 + - - -
85J TRP* 2.7 72.2 + - + +
86J VAL* 3.1 24.5 + - - +
87J ASN 3.8 0.4 - - - -
88J PHE* 1.3 79.2 - - - +
90J LEU* 1.3 60.2 + - - +
91J PRO* 3.8 1.2 - - - +
144J GLY 5.3 2.0 + - - -
----------------------------------------------------------
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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