Contacts of the helix formed by residues 81 - 104 (chain A) in PDB entry 4K2S
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 81 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ARG* 1.3 78.9 - - - +
82A PRO* 1.4 72.4 - - - +
83A VAL 3.4 2.0 - - - -
84A THR 4.0 1.8 - - - -
85A MET* 2.8 31.4 + - - +
268A ASN* 2.9 16.7 + - - -
80B ARG 4.9 0.2 - - - -
81B GLY* 3.7 16.1 - - - -
82B PRO* 4.1 1.6 - - - -
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Residues in contact with PRO 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 4.0 17.1 - - + +
81A GLY* 1.4 79.2 - - - +
83A VAL* 1.3 67.6 + - + +
86A THR* 2.7 32.0 + - - +
266A VAL 5.9 0.7 - - - +
268A ASN* 3.3 20.4 - - + +
291A HIS* 5.5 1.8 - - + +
48B TYR* 6.1 0.2 - - + -
78B TRP* 3.6 36.3 - - + +
79B ARG 4.1 2.2 - - - +
80B ARG 3.1 21.3 - - - +
81B GLY* 4.2 1.1 - - - -
84B THR* 3.6 18.2 - - - +
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Residues in contact with VAL 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 3.9 16.2 - - + -
44A ALA* 3.7 45.8 - - + +
45A VAL* 3.9 12.9 - - - +
48A TYR* 3.8 18.2 - - + -
81A GLY 3.4 0.4 - - - -
82A PRO* 1.3 78.9 - - + +
84A THR* 1.3 64.8 + - - +
86A THR* 3.9 1.9 - - - -
87A ALA* 3.1 22.5 + - - +
44B ALA* 4.7 0.2 - - + -
48B TYR* 4.1 12.3 - - + -
83B VAL* 4.0 28.0 - - + -
84B THR* 4.5 4.9 - - - +
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Residues in contact with THR 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A TYR* 3.5 35.5 + - - +
73A TYR* 5.7 0.9 - - + +
76A ALA* 4.8 2.9 - - + -
78A TRP 4.2 11.4 + - - +
79A ARG* 5.0 0.2 - - - -
80A ARG 3.1 35.1 + - - +
81A GLY 3.7 0.4 - - - -
83A VAL* 1.3 77.8 - - - +
85A MET* 1.3 62.9 + - - +
87A ALA* 3.3 6.1 + - - +
88A ILE* 3.1 40.4 + - + +
82B PRO* 3.5 18.5 - - - +
83B VAL* 4.5 2.3 - - - +
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Residues in contact with MET 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A TRP* 3.9 28.5 - - + -
73A TYR* 3.8 26.5 - - + -
80A ARG* 3.8 14.6 - - + -
81A GLY 2.8 29.8 + - - +
84A THR* 1.3 72.5 - - - +
86A THR* 1.3 60.7 + - - +
88A ILE* 3.8 13.0 - - + +
89A ALA* 2.8 29.1 + - - +
268A ASN* 3.5 30.1 - - + +
269A SER* 5.1 4.9 - - - -
291A HIS 3.6 19.7 - - - +
292A GLY 4.9 0.7 - - - +
293A GLY* 3.7 16.4 - - - +
297A ALA* 5.3 1.8 - - + -
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Residues in contact with THR 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ASP 4.2 0.3 - - - +
36A ALA* 3.3 37.2 - - - +
37A THR 4.1 5.4 - - - +
38A LEU* 4.0 3.3 - - + +
45A VAL* 4.0 10.8 - - + -
82A PRO 2.7 23.9 + - - -
83A VAL 3.9 2.7 - - - -
85A MET* 1.3 74.7 - - - +
87A ALA* 1.3 66.1 + - - +
89A ALA* 3.2 1.2 + - - +
90A ALA* 3.0 22.7 + - - +
290A THR* 3.3 20.9 + - + +
291A HIS* 3.3 23.9 - - - +
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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
----------------------------------------------------------
45A VAL* 3.9 10.4 - - + +
48A TYR* 3.4 36.1 - - + -
49A LEU* 3.7 23.8 - - + +
53A VAL* 4.7 2.7 - - + -
83A VAL 3.1 11.8 + - - +
84A THR 3.6 6.5 - - - +
86A THR* 1.3 74.5 - - - +
88A ILE* 1.3 63.3 + - + +
90A ALA* 3.3 4.3 + - - +
91A VAL* 3.3 26.0 + - - +
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Residues in contact with ILE 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A TYR* 5.5 4.3 - - + +
53A VAL* 6.3 0.9 - - + -
69A TRP* 3.4 44.6 - - + +
72A LEU* 3.9 24.7 - - + +
73A TYR* 3.6 32.3 - - + +
84A THR* 3.1 25.9 + - + +
85A MET* 3.8 23.1 - - + +
86A THR 3.2 0.2 - - - -
87A ALA* 1.3 78.0 - - + +
89A ALA* 1.3 57.7 + - - +
91A VAL* 3.3 7.7 + - - +
92A ASP* 2.9 26.3 + - - +
293A GLY* 4.5 2.7 - - - +
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Residues in contact with ALA 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ASP 4.7 0.2 - - - +
85A MET 2.8 14.9 + - - +
86A THR 3.5 1.8 - - - +
88A ILE* 1.3 77.1 - - - +
90A ALA* 1.3 56.6 + - - +
92A ASP* 3.7 0.9 - - - +
93A MET* 2.9 36.4 + - + +
289A LEU 3.4 6.5 - - - +
290A THR* 3.1 31.2 - - - +
293A GLY* 3.7 1.8 - - - -
294A GLY* 3.3 29.3 - - - +
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Residues in contact with ALA 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 3.8 20.0 - - + +
34A GLY* 3.4 13.5 - - - +
35A ASP 3.3 23.8 + - - +
36A ALA* 3.6 22.0 - - + -
49A LEU* 4.2 3.4 - - + -
86A THR 3.0 7.7 + - - +
87A ALA 3.3 9.4 + - - +
89A ALA* 1.3 76.7 - - - +
91A VAL* 1.3 62.0 + - - +
94A ALA* 3.1 21.3 + - - +
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Residues in contact with VAL 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 3.5 22.9 - - + -
24A ILE* 4.2 5.8 - - + +
49A LEU* 4.2 0.9 - - + -
53A VAL* 3.9 16.6 - - + -
57A LEU* 4.1 11.0 - - + -
68A THR* 3.8 29.6 - - + -
72A LEU* 3.8 20.4 - - + -
87A ALA 3.3 12.7 + - - +
88A ILE 3.3 6.7 + - - +
90A ALA* 1.3 75.8 - - - +
92A ASP* 1.3 65.0 + - - +
94A ALA* 3.2 3.8 + - - +
95A LEU* 2.9 32.9 + - + +
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Residues in contact with ASP 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ILE* 3.4 13.5 - - - +
69A TRP* 3.6 13.4 - - + +
88A ILE 2.9 17.2 + - - +
89A ALA 3.7 3.4 - - - +
91A VAL* 1.3 78.2 - - - +
93A MET* 1.3 56.9 + - - +
95A LEU* 3.2 6.9 + - - +
96A TRP* 2.9 43.6 + - - -
293A GLY 4.0 9.6 - - - +
294A GLY* 4.2 1.1 - - - -
295A ILE 2.9 12.7 + - - -
296A THR* 2.6 51.7 + - - -
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Residues in contact with MET 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ILE 3.6 4.1 - - - +
34A GLY* 3.6 11.9 - - - -
35A ASP 3.6 28.9 - - - +
89A ALA* 2.9 21.7 + - + +
92A ASP* 1.3 76.5 + - - +
94A ALA* 1.3 57.5 + - - +
96A TRP* 3.4 6.6 + - - +
97A ASP* 3.0 28.6 + - - +
289A LEU* 4.0 9.9 - - + +
290A THR* 3.6 39.5 - - - +
294A GLY* 4.8 5.2 - - - -
295A ILE* 4.7 11.4 - - + -
323A VAL* 4.4 4.5 - - - +
324A CYS* 4.2 20.2 - - - -
327A ALA* 4.2 20.2 - - + -
373A HIS* 4.0 6.5 - - + -
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Residues in contact with ALA 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 4.4 3.4 - - + +
24A ILE* 3.8 20.9 - - + -
32A GLY* 3.5 14.7 - - - +
33A ILE* 3.4 26.6 + - - +
34A GLY 3.8 0.7 - - - +
90A ALA 3.1 16.7 + - - +
91A VAL* 3.7 3.8 - - - +
93A MET* 1.3 76.5 - - - +
95A LEU* 1.3 59.3 + - - +
97A ASP* 3.3 2.8 - - - +
98A ILE* 3.0 32.0 + - - +
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Residues in contact with LEU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ILE* 4.4 7.0 - - + -
24A ILE* 3.8 20.4 - - + -
62A ALA* 3.6 40.3 - - + +
65A ILE* 3.7 29.6 - - + +
68A THR* 3.8 37.9 - - + +
91A VAL* 2.9 26.6 + - + +
92A ASP* 3.2 4.9 + - - +
94A ALA* 1.3 75.0 - - - +
96A TRP* 1.3 59.5 + - - +
98A ILE* 3.2 10.2 + - + +
99A LYS* 2.8 28.8 + - - +
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Residues in contact with TRP 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ILE* 3.4 26.0 - - + +
92A ASP* 2.9 39.8 + - - +
93A MET 3.9 4.3 - - - +
95A LEU* 1.3 73.1 - - - +
97A ASP* 1.3 59.2 + - - +
99A LYS* 3.7 7.0 - - + +
100A ALA* 2.9 32.3 + - - +
107A LEU* 4.3 20.3 - - + +
110A LEU* 3.6 39.0 - - + -
111A LEU* 4.9 4.9 - - + -
295A ILE* 3.5 33.3 - - + +
296A THR* 3.0 26.2 + - + -
299A ARG* 4.6 17.9 - - - -
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Residues in contact with ASP 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A HIS* 5.8 0.2 - - - -
32A GLY* 3.2 8.9 - - - -
33A ILE* 3.0 22.8 + - - +
93A MET 3.0 15.2 + - - +
94A ALA 3.3 10.8 - - - +
95A LEU 3.2 0.2 - - - -
96A TRP* 1.3 77.8 - - - +
98A ILE* 1.3 56.2 + - - +
100A ALA 3.4 0.2 + - - -
101A LYS* 3.0 49.7 + - - +
107A LEU* 6.0 0.2 - - - -
372A GLY* 3.2 9.7 - - - -
373A HIS* 2.9 55.6 + - + +
374A GLY 4.3 0.9 + - - -
375A VAL 4.2 1.7 - - - +
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Residues in contact with ILE 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LEU* 3.7 27.4 - - + -
24A ILE* 3.8 31.0 - - + +
26A THR* 4.1 19.1 - - + -
30A THR* 4.6 7.7 - - - +
31A HIS* 3.6 8.5 - - - +
32A GLY 3.3 25.4 - - - +
62A ALA* 4.4 7.0 - - + +
63A GLY* 6.3 0.2 - - - -
94A ALA 3.0 16.3 + - - +
95A LEU* 3.5 17.5 - - + +
97A ASP* 1.3 77.0 - - - +
99A LYS* 1.3 57.2 - - - +
101A LYS* 3.3 7.4 + - - +
102A ALA* 2.9 27.7 + - - +
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Residues in contact with LYS 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A LEU* 6.0 2.2 - - + +
62A ALA 5.2 0.4 - - - -
63A GLY* 2.8 40.7 + - - -
65A ILE* 3.8 20.2 - - + -
95A LEU 2.8 15.6 + - - +
96A TRP* 3.7 12.8 - - + +
97A ASP 3.3 0.2 - - - -
98A ILE* 1.3 77.7 - - - +
100A ALA* 1.3 57.7 + - - +
102A ALA* 3.2 9.5 + - + +
103A ALA* 2.9 28.6 + - + +
110A LEU* 3.6 21.1 - - + -
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Residues in contact with ALA 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A TRP 2.9 17.7 + - - +
99A LYS* 1.3 75.9 - - - +
101A LYS* 1.3 63.1 + - - +
103A ALA 3.2 1.6 + - - -
104A GLY 3.0 16.6 + - - -
105A MET 3.1 29.9 + - - +
107A LEU* 4.1 12.1 - - + -
110A LEU* 3.8 20.6 - - + +
372A GLY* 3.6 20.6 - - - +
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Residues in contact with LYS 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A THR* 5.5 10.8 - - + -
31A HIS* 2.8 57.0 + - - +
97A ASP* 3.0 38.2 + - - +
98A ILE* 3.6 5.6 - - - +
100A ALA* 1.3 78.0 - - - +
102A ALA* 1.3 61.9 + - - +
104A GLY* 3.0 13.5 + - - -
371A PRO* 3.8 30.9 - - + +
372A GLY* 3.8 0.9 - - - -
374A GLY 6.2 0.4 - - - +
375A VAL 5.3 4.4 + - - -
376A ASP* 5.3 1.6 + - - -
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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
----------------------------------------------------------
3A LEU* 4.6 22.4 - - + -
30A THR* 6.5 1.3 - - - -
98A ILE 2.9 16.7 + - - +
99A LYS* 3.2 11.2 + - + +
101A LYS* 1.3 76.6 - - - +
103A ALA* 1.3 61.5 + - - +
104A GLY* 3.1 1.1 + - - -
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Residues in contact with ALA 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A LYS* 2.9 17.8 + - + +
100A ALA 3.6 3.6 - - - +
101A LYS 3.1 0.2 - - - -
102A ALA* 1.3 75.8 - - - +
104A GLY* 1.3 62.1 + - - +
105A MET* 3.4 18.9 + - + +
110A LEU* 3.6 27.4 - - + -
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Residues in contact with GLY 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ALA 3.0 0.6 + - - -
101A LYS 3.0 17.1 + - - -
102A ALA 3.1 1.8 + - - -
103A ALA* 1.3 79.7 - - - +
105A MET* 1.3 60.4 + - - +
106A PRO* 4.6 1.6 - - - +
371A PRO* 3.9 20.8 - - - +
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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