Contacts of the helix formed by residues 86 - 110 (chain A) in PDB entry 4H9Q
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 SER 86 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A PHE 3.4 1.4 + - - -
85A GLN* 1.3 70.3 - - - +
87A ALA* 1.3 57.6 + - - +
89A ILE* 3.0 25.8 + - - +
90A GLY* 3.1 9.9 + - - -
205C LEU 3.3 27.0 + - - -
206C GLN* 3.6 5.8 + - - +
208C LYS 3.0 9.3 + - - -
210C LEU* 3.6 20.6 - - - +
221C ALA 3.8 1.2 + - - -
222C TYR* 3.2 36.5 + - - -
225C ALA* 4.8 3.1 - - - +
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Residues in contact with ALA 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A GLN* 3.1 1.1 - - - +
86A SER* 1.3 76.0 - - - +
88A ALA* 1.3 57.7 + - - +
90A GLY* 3.4 3.6 + - - +
91A ALA* 3.0 27.9 + - - +
83B ALA* 4.0 8.8 - - + +
206C GLN* 3.1 31.1 + - + +
337C GLY* 6.1 0.5 - - - -
338C CYS* 3.7 30.5 - - - -
340C LEU* 3.9 10.3 - - + -
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Residues in contact with ALA 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A PHE* 4.6 9.2 - - + -
85A GLN* 2.9 14.9 + - - +
87A ALA* 1.3 76.1 - - - +
89A ILE* 1.3 58.3 + - - +
91A ALA* 3.4 3.3 + - - +
92A LEU* 2.9 36.0 + - - +
81B VAL 3.8 9.9 - - - +
82B THR 3.7 10.3 - - - +
83B ALA* 3.7 29.5 - - - +
86B VAL* 3.8 12.9 - - + +
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Residues in contact with ILE 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A PHE* 3.6 17.5 - - + -
68A GLN* 4.3 9.0 - - + -
71A VAL* 3.7 31.9 - - + -
84A PHE* 3.9 17.9 - - + -
85A GLN 3.8 9.2 - - - +
86A SER* 3.0 14.8 + - - +
88A ALA* 1.3 77.4 - - - +
90A GLY* 1.3 57.1 + - - +
92A LEU* 3.4 7.6 + - + +
93A GLN* 2.9 24.8 + - - +
210C LEU* 5.0 3.8 - - + -
215C LEU* 3.8 23.1 - - + -
222C TYR* 3.6 32.8 - - + -
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Residues in contact with GLY 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 5.4 1.9 - - - +
86A SER 3.1 11.6 + - - -
87A ALA* 3.4 4.7 + - - -
88A ALA 3.3 0.4 - - - -
89A ILE* 1.3 78.3 - - - +
91A ALA* 1.3 60.6 + - - +
93A GLN* 3.2 2.4 + - - +
94A GLU* 3.0 25.3 + - - +
222C TYR* 3.5 21.4 - - - -
229C LYS* 5.8 5.6 - - - -
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Residues in contact with ALA 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ALA 3.0 17.2 + - - +
88A ALA* 3.4 6.0 + - - +
90A GLY* 1.3 70.7 - - - +
92A LEU* 1.3 66.9 + - - +
94A GLU* 3.4 1.0 + - - -
95A ALA* 3.0 26.5 + - - +
83B ALA* 5.2 7.6 - - + +
86B VAL* 4.0 17.0 - - + -
87B VAL* 5.5 1.8 - - + -
336C PHE* 3.6 32.3 - - + -
337C GLY* 5.3 8.7 - - - +
341C THR* 6.1 0.9 - - + -
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Residues in contact with LEU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A PHE* 3.7 10.3 - - + -
71A VAL* 4.0 27.4 - - + -
84A PHE* 4.5 9.6 - - + -
88A ALA 2.9 22.5 + - - +
89A ILE* 3.5 9.9 - - + +
91A ALA* 1.3 77.5 - - - +
93A GLN* 1.3 56.8 + - - +
95A ALA* 3.8 4.1 - - - +
96A ALA* 2.9 31.7 + - - +
61B PHE* 5.0 0.7 - - + -
62B LEU* 4.2 12.4 - - + +
65B VAL* 3.5 37.7 - - + -
66B ILE* 4.2 20.9 - - + -
86B VAL* 3.9 16.5 - - + +
90B LEU* 5.2 0.9 - - + -
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Residues in contact with GLN 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 3.9 19.0 - - + +
62A ILE* 2.8 33.7 + - - +
64A LYS* 3.7 10.8 - - - +
67A PHE* 3.3 45.9 - - + +
89A ILE 2.9 8.5 + - - +
90A GLY 3.2 2.2 + - - +
92A LEU* 1.3 73.8 - - - +
94A GLU* 1.3 67.3 + - - +
96A ALA* 4.0 0.2 - - - +
97A GLU* 2.9 45.6 + - + +
222C TYR* 2.6 33.7 + - - +
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Residues in contact with GLU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LYS* 3.1 45.0 + - - +
57A SER* 5.0 0.9 + - - -
60A LEU* 4.0 25.2 - - + +
90A GLY 3.0 15.3 + - - +
91A ALA* 3.9 4.0 - - - +
93A GLN* 1.3 76.6 - - - +
95A ALA* 1.3 62.1 + - - +
97A GLU* 3.6 1.9 + - - +
98A ALA* 3.1 22.7 + - - +
332C LEU* 3.4 21.1 - - + +
335C ASN 3.3 15.1 - - - +
336C PHE* 3.6 15.2 - - + -
337C GLY 5.3 0.6 + - - +
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Residues in contact with ALA 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ALA 3.0 18.0 + - - +
92A LEU 3.9 1.8 - - - +
94A GLU* 1.3 76.6 - - - +
96A ALA* 1.3 59.8 + - - +
98A ALA* 3.2 2.8 + - - -
99A PHE* 2.9 26.0 + - - +
61B PHE* 4.1 2.7 - - + -
90B LEU* 3.6 35.9 - - + -
96B THR* 3.5 21.6 - - + +
97B LEU* 5.3 2.7 - - + -
332C LEU* 5.3 1.8 - - - -
336C PHE* 4.2 7.4 - - + -
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Residues in contact with ALA 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A PHE* 4.2 6.3 - - + -
92A LEU 2.9 19.6 + - - +
93A GLN 4.0 2.7 - - - +
95A ALA* 1.3 76.2 - - - +
97A GLU* 1.3 63.5 + - + +
99A PHE* 3.2 3.7 + - - +
100A LEU* 3.0 28.6 + - - +
58B LEU* 3.6 26.9 - - + -
61B PHE* 3.6 15.8 - - + -
62B LEU* 3.8 15.9 - - + -
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Residues in contact with GLU 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 3.6 17.5 - - + +
61A LEU* 2.7 31.6 + - - +
62A ILE* 2.8 44.9 + - + +
67A PHE* 5.9 0.2 - - + -
93A GLN* 2.9 41.0 + - + +
94A GLU 4.1 2.5 - - - +
96A ALA* 1.3 78.1 - - + +
98A ALA* 1.3 62.7 + - - +
100A LEU* 3.8 5.5 - - - +
101A VAL* 2.9 32.0 + - + +
37B LEU* 3.8 11.1 - - + +
40B ARG* 4.7 3.1 + - - -
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Residues in contact with ALA 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLU 3.1 15.7 + - - +
95A ALA 3.2 7.6 + - - +
97A GLU* 1.3 76.0 - - - +
99A PHE* 1.3 57.2 + - - +
101A VAL* 3.9 5.5 - - - +
102A ALA* 2.9 31.9 + - - +
96B THR* 4.1 5.8 - - + -
332C LEU* 3.6 30.3 - - + -
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Residues in contact with PHE 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ALA 2.9 13.4 + - - +
96A ALA 3.4 7.2 - - - +
98A ALA* 1.3 76.5 - - - +
100A LEU* 1.3 72.4 + - + +
102A ALA* 3.4 7.0 + - - +
103A LEU* 3.1 41.9 + - + +
128A ARG* 6.2 1.3 - - - -
133A GLU* 4.2 16.6 - - - -
57B VAL* 3.5 26.7 - - + -
58B LEU* 6.4 0.2 - - + -
61B PHE* 3.5 46.0 - + + -
93B GLN 5.6 2.5 - - - -
95B ARG* 5.1 2.0 + - - -
96B THR* 3.5 21.9 - - - +
372C LEU* 3.9 30.1 - - + -
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Residues in contact with LEU 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ILE* 4.4 7.6 - - + -
96A ALA 3.0 18.8 + - - +
97A GLU* 3.8 3.6 - - - +
99A PHE* 1.3 79.4 - - + +
101A VAL* 1.3 67.1 + - - +
103A LEU* 3.1 17.9 + - + +
104A PHE* 3.1 28.9 + - + -
37B LEU* 4.0 29.8 - - + -
54B THR* 4.1 21.5 - - + +
57B VAL* 4.0 27.6 - - + -
58B LEU* 4.0 37.7 - - + +
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Residues in contact with VAL 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A GLU* 2.9 24.1 + - + +
98A ALA* 3.9 5.6 - - - +
100A LEU* 1.3 77.4 - - - +
102A ALA* 1.3 58.3 + - - +
104A PHE* 3.0 6.0 + - - +
105A GLU* 2.8 44.6 + - - +
37B LEU* 3.8 36.3 - - + +
40B ARG* 4.0 19.3 - - + -
41B GLY* 4.0 12.8 - - - +
328C ARG* 3.7 15.5 - - - +
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Residues in contact with ALA 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ALA 2.9 18.9 + - - +
99A PHE* 3.8 5.6 - - - +
101A VAL* 1.3 72.2 - - - +
103A LEU* 1.3 66.8 + - - +
105A GLU* 3.6 19.5 - - - +
106A ASP* 2.9 29.5 + - - -
95B ARG* 3.4 26.0 - - - +
96B THR* 6.1 0.7 - - - +
325C GLN* 5.1 2.0 - - - +
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Residues in contact with LEU 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A PHE* 3.1 37.6 + - + +
100A LEU* 3.1 14.6 + - + +
102A ALA* 1.3 75.2 - - - +
104A PHE* 1.3 62.3 + - + +
106A ASP* 3.5 5.5 + - + +
107A THR* 3.0 31.2 + - - -
124A ILE* 4.9 17.2 - - + +
127A ALA* 5.5 0.2 - - - +
128A ARG* 4.6 26.5 - - + +
133A GLU* 6.5 0.9 - - + -
57B VAL* 3.6 34.1 - - + -
95B ARG* 4.4 12.3 - - - +
376C ILE* 4.9 8.3 - - + -
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Residues in contact with PHE 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LEU* 3.1 29.3 + - + -
101A VAL 3.0 7.4 + - - +
103A LEU* 1.3 77.6 - - + +
105A GLU* 1.3 58.9 + - - +
107A THR* 3.3 2.5 + - - -
108A ASN* 2.9 31.2 + - - +
119A ILE* 5.4 0.4 - - + -
124A ILE* 4.2 20.2 - - + -
34B ILE* 5.0 3.1 - - + -
37B LEU* 4.1 8.5 - - + +
38B ALA* 3.6 55.9 - - + +
41B GLY* 3.8 5.8 - - - -
43B VAL* 3.5 17.0 - - + +
46B ILE* 4.3 4.9 - - + -
50B ILE* 4.0 18.8 - - + -
54B THR* 3.6 33.0 - - + -
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Residues in contact with GLU 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A VAL* 2.8 26.8 + - - +
102A ALA* 3.6 17.0 - - - +
104A PHE* 1.3 70.8 - - - +
106A ASP* 1.3 59.3 + - - +
108A ASN* 3.2 2.9 + - - +
109A LEU* 2.9 34.8 + - - +
41B GLY* 3.4 21.2 + - - -
283C PHE* 3.8 25.8 - - + -
325C GLN* 2.9 31.2 + - - +
328C ARG* 2.8 36.9 + - - +
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Residues in contact with ASP 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ALA 2.9 16.5 + - - +
103A LEU* 3.8 5.9 - - + +
105A GLU* 1.3 75.5 - - - +
107A THR* 1.3 64.9 + - - +
109A LEU 3.3 1.2 + - - -
110A CYS* 3.2 27.4 + - - -
127A ALA* 3.9 11.2 - - + +
128A ARG* 5.3 1.3 - - - +
131A ARG* 3.2 38.8 + - + +
132A GLY* 3.6 8.7 - - - -
95B ARG* 2.6 39.8 + - - -
325C GLN* 3.2 16.3 + - - -
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Residues in contact with THR 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LEU 3.0 15.6 + - - -
104A PHE* 3.6 7.9 - - - -
105A GLU 3.3 0.2 - - - -
106A ASP* 1.3 77.4 - - - +
108A ASN* 1.3 59.1 + - - +
110A CYS* 3.2 10.2 + - - +
111A THR* 2.8 27.1 + - - +
119A ILE* 3.8 37.9 - - + -
123A ASP* 4.0 20.9 - - + +
124A ILE* 3.3 27.7 + - - +
127A ALA* 3.5 10.6 - - - +
43B VAL* 4.6 2.7 - - + -
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Residues in contact with ASN 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A PHE 2.9 17.5 + - - +
105A GLU 3.3 4.0 - - - +
107A THR* 1.3 77.0 - - - +
109A LEU* 1.3 61.4 + - - +
111A THR* 3.0 26.1 + - - +
119A ILE* 6.2 0.7 - - - -
41B GLY 3.2 19.7 + - - +
42B GLY* 3.7 10.7 - - - +
43B VAL* 4.0 11.4 - - + +
283C PHE* 3.4 15.8 - - - -
284C PRO 3.0 24.2 + - - -
285C ASP* 3.3 23.7 - - - +
286C TYR 4.1 0.3 + - - -
317C PHE* 3.5 9.1 - - - -
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Residues in contact with LEU 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A GLU 2.9 20.0 + - - +
106A ASP 3.3 4.9 + - - +
108A ASN* 1.3 75.3 - - - +
110A CYS* 1.3 59.4 + - - +
111A THR 3.6 0.2 + - - -
112A ILE* 4.0 14.0 - - - +
131A ARG* 3.3 40.8 - - - +
283C PHE* 4.1 13.2 - - + -
317C PHE* 3.6 36.1 - - + +
318C ARG* 5.5 2.5 - - - +
321C GLY* 3.7 31.6 - - - -
322C ILE 4.9 0.2 - - - +
325C GLN* 3.6 17.7 - - - +
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Residues in contact with CYS 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ASP 3.2 18.5 + - - +
107A THR 3.2 5.1 + - - +
108A ASN 3.1 1.0 - - - -
109A LEU* 1.3 77.4 - - - +
111A THR* 1.3 60.3 + - - +
112A ILE* 3.7 8.0 + - - +
126A LEU* 6.4 0.2 - - + -
127A ALA* 3.8 22.7 - - + -
130A ILE* 4.0 26.9 - - + +
131A ARG* 3.5 26.9 - - - -
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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) + - + + + + + -
------------------------------------------------------------
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