Contacts of the helix formed by residues 75 - 104 (chain P) in PDB entry 1PP9
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 TYR 75 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73P VAL 3.1 2.0 + - - -
74P ASN* 1.3 77.7 - - + +
76P GLY* 1.3 64.4 + - - +
77P TRP* 3.2 25.3 - + - +
78P ILE* 3.2 29.3 + - + +
79P ILE* 3.3 11.6 + - + +
200Q HIS* 3.8 31.0 - + - -
204Q MET* 4.9 2.9 - - - -
3006Q PEE 4.6 4.8 + - - -
57R GLN* 3.5 60.1 - - + +
60R SER* 3.9 19.1 - - - -
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Residues in contact with GLY 76 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69P ILE* 3.2 33.8 - - - +
73P VAL* 2.8 18.9 + - - -
74P ASN 3.0 3.4 + - - -
75P TYR* 1.3 77.6 - - - +
77P TRP* 1.3 61.6 + - - +
79P ILE* 3.4 9.2 + - - +
80P ARG* 3.0 24.3 + - - +
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Residues in contact with TRP 77 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69P ILE 3.7 4.0 + - - -
70P CYS* 3.6 30.5 + - + +
73P VAL 5.2 1.8 - - - -
75P TYR* 4.1 22.3 - + - +
76P GLY* 1.3 77.3 - - - +
78P ILE* 1.3 93.7 + - + +
80P ARG* 3.4 0.5 + - - +
81P TYR* 3.0 44.6 + + + -
243P VAL* 5.0 5.2 - - + -
244P LEU* 4.3 3.4 - - + -
197Q GLU* 3.5 41.8 - - + +
200Q HIS* 4.0 30.9 + + + -
201Q ARG* 3.5 38.8 - - + -
204Q MET* 3.8 22.0 - - + -
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Residues in contact with ILE 78 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75P TYR* 3.2 22.2 + - + +
77P TRP* 1.3 102.3 - - + +
79P ILE* 1.3 67.5 + - + +
81P TYR 3.9 0.2 - - - -
82P MET* 2.9 47.7 + - - +
240P MET* 4.0 16.2 - - + -
243P VAL* 4.0 14.1 - - + +
244P LEU* 4.2 3.6 - - + -
204Q MET* 3.0 38.1 - - + -
3006Q PEE 4.4 2.5 - - + -
57R GLN* 3.9 22.4 - - + +
58R PHE* 5.7 2.0 - - + -
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Residues in contact with ILE 79 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47P THR* 3.6 35.3 - - - +
50P PHE* 4.3 11.7 - - + -
51P LEU* 3.8 13.7 - - + +
73P VAL* 6.0 0.2 - - + -
75P TYR* 3.3 13.3 + - + +
76P GLY* 3.8 8.5 - - - +
77P TRP 3.3 0.2 - - - -
78P ILE* 1.3 81.3 - - + +
80P ARG* 1.3 57.7 + - - +
82P MET* 3.4 8.1 + - - +
83P HIS* 3.0 26.7 + - - +
57R GLN 4.8 1.6 - - - +
58R PHE* 4.0 37.7 - - + -
61R SER* 3.7 32.1 - - - +
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Residues in contact with ARG 80 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51P LEU* 3.8 17.7 - - + +
66P VAL* 3.7 15.5 - - + +
69P ILE* 4.3 2.7 - - + -
70P CYS* 3.5 29.6 - - - -
76P GLY 3.0 17.8 + - - +
77P TRP 3.7 3.4 - - - +
79P ILE* 1.3 77.1 - - - +
81P TYR* 1.3 95.1 + - - +
83P HIS* 3.0 4.9 + - - +
84P ALA* 2.8 25.8 + - - +
134P PRO* 4.5 3.2 - - - +
255P ASN* 5.8 0.4 - - - +
256P TYR* 4.6 2.5 + - - -
501P HEM 2.9 52.1 + - + +
3014P AZI 3.3 42.6 + - - -
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Residues in contact with TYR 81 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70P CYS* 4.1 17.2 - - + +
77P TRP* 3.0 35.5 + + + +
78P ILE* 5.0 0.2 - - - -
80P ARG* 1.3 102.2 + - - +
82P MET* 1.3 60.3 + - - +
84P ALA* 3.8 7.6 - - + -
85P ASN* 2.9 38.1 + - - +
243P VAL* 3.5 20.7 - - + +
247P PRO* 3.9 31.4 - - + -
248P ASP* 3.9 5.6 - - - -
256P TYR* 2.7 30.5 + - - -
115Q TYR* 5.7 0.7 - - - -
118Q ARG* 3.2 21.5 + - - -
197Q GLU* 3.6 21.5 - - + -
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Residues in contact with MET 82 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43P LEU* 4.7 4.9 - - + +
44P GLN* 3.9 1.7 - - - +
47P THR* 4.1 20.4 - - + -
78P ILE* 2.9 40.7 + - - +
79P ILE* 3.6 8.5 - - - +
80P ARG 3.1 0.2 - - - -
81P TYR* 1.3 76.8 - - - +
83P HIS* 1.3 59.9 + - - +
86P GLY* 2.8 26.7 + - - -
239P LEU* 4.1 14.2 - - + +
240P MET* 4.2 17.0 - - + -
243P VAL* 3.8 19.5 - - + -
3006Q PEE 4.0 39.3 - - + -
57R GLN* 6.2 0.4 - - - -
58R PHE* 4.7 15.7 - - + -
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Residues in contact with HIS 83 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44P GLN* 3.0 48.8 + - - -
47P THR* 2.9 23.0 + - - +
48P GLY* 3.5 7.3 + - - -
51P LEU* 3.5 21.5 - - + -
79P ILE 3.0 9.6 + - - +
80P ARG 3.0 7.8 + - - +
82P MET* 1.3 75.1 - - - +
84P ALA* 1.3 64.2 + - - +
87P ALA* 3.2 8.5 + - - +
501P HEM 2.0 87.1 + + + +
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Residues in contact with ALA 84 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80P ARG* 2.8 17.2 + - - +
81P TYR* 4.0 14.6 - - + +
83P HIS* 1.3 76.5 - - - +
85P ASN* 1.3 65.4 + - - +
87P ALA* 3.3 10.6 + - - +
88P SER 3.5 0.2 + - - -
247P PRO 5.7 0.4 - - - +
501P HEM 3.9 34.3 - - + +
3009P GOL 3.0 32.0 - - - +
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Residues in contact with ASN 85 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81P TYR* 2.9 32.4 + - - +
84P ALA* 1.3 76.3 - - - +
86P GLY* 1.3 60.9 + - - +
88P SER* 3.1 7.1 + - - +
89P MET* 2.9 29.5 + - - +
239P LEU* 3.8 15.0 - - + -
242P LEU* 3.7 33.7 - - + +
243P VAL* 4.1 7.5 - - + +
246P ALA 4.6 0.5 - - - +
247P PRO* 3.2 36.5 + - - +
250P LEU* 4.4 14.6 + - - +
3009P GOL 4.3 4.7 + - - -
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Residues in contact with GLY 86 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40P CYS* 4.6 4.1 - - - +
43P LEU* 6.1 2.2 - - - -
44P GLN* 3.3 17.3 - - - +
82P MET 2.8 20.9 + - - -
84P ALA 3.2 0.4 - - - -
85P ASN* 1.3 74.3 - - - +
87P ALA* 1.3 60.3 + - - +
89P MET* 3.2 6.3 + - - +
90P PHE* 2.9 28.8 + - - +
239P LEU* 3.7 12.8 - - - +
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Residues in contact with ALA 87 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44P GLN* 3.6 10.7 - - - +
83P HIS 3.2 11.0 + - - +
84P ALA 3.4 10.5 - - - +
85P ASN 3.1 0.2 - - - -
86P GLY* 1.3 78.5 - - - +
88P SER* 1.3 60.2 + - - +
90P PHE* 3.3 13.1 - - - +
91P PHE* 3.1 25.1 - - + -
127P ALA* 5.3 0.7 - - + -
273P TYR* 4.5 5.2 - - + +
501P HEM 3.8 39.7 - - + -
3009P GOL 4.4 3.1 - - - -
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Residues in contact with SER 88 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84P ALA 3.5 1.8 + - - -
85P ASN* 3.1 12.6 + - - -
87P ALA* 1.3 77.6 - - - +
89P MET* 1.3 64.8 + - - +
91P PHE 3.1 2.6 + - - -
92P ILE* 3.0 27.4 + - - +
242P LEU* 5.2 1.6 - - - -
250P LEU* 3.6 25.1 - - - +
272P TRP* 2.8 32.7 + - - -
273P TYR* 4.0 3.7 - - - -
3009P GOL 3.4 21.8 + - - -
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Residues in contact with MET 89 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40P CYS* 4.0 13.9 - - - -
85P ASN 2.9 17.3 + - - +
86P GLY* 3.6 8.5 - - - +
88P SER* 1.3 76.3 - - - +
90P PHE* 1.3 62.3 + - - +
92P ILE* 3.3 15.7 + - + +
93P CYS* 2.9 30.2 + - - -
235P LEU* 3.7 24.0 - - + -
238P ALA* 3.8 17.0 - - + -
239P LEU* 3.9 25.1 - - + -
242P LEU* 3.9 23.6 - - + -
3003Q CDL 3.7 28.5 - - + -
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Residues in contact with PHE 90 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37P LEU* 3.7 26.0 - - + -
40P CYS* 3.8 16.5 - - + -
41P LEU* 3.9 31.2 - - + -
44P GLN* 4.0 19.1 - - + -
86P GLY 2.9 11.0 + - - +
87P ALA* 3.3 13.2 - - - +
89P MET* 1.3 77.1 - - - +
91P PHE* 1.3 61.3 + - + +
93P CYS* 3.4 2.3 + - - +
94P LEU* 2.8 33.6 + - + +
123P VAL* 4.0 23.3 - - + -
501P HEM 3.5 32.5 - - + -
502P HEM 4.0 19.7 - - + -
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Residues in contact with PHE 91 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87P ALA* 3.1 22.6 + - + -
88P SER 3.1 7.4 + - - +
90P PHE* 1.3 79.7 - - + +
92P ILE* 1.3 65.3 + - - +
94P LEU* 3.5 18.7 - - + +
95P TYR* 2.9 54.5 + + + -
120P LEU* 5.0 0.2 - - + -
123P VAL* 3.9 17.0 - - + -
124P MET* 3.9 30.5 - - + -
127P ALA* 3.7 25.8 - - + -
272P TRP* 4.2 2.0 - - + -
273P TYR* 3.5 55.2 - + + -
274P PHE* 4.3 1.8 - + - -
501P HEM 5.4 0.9 - - + -
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Residues in contact with ILE 92 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88P SER 3.0 19.6 + - - +
89P MET* 3.3 29.4 + - + +
91P PHE* 1.3 75.6 - - - +
93P CYS* 1.3 65.2 + - - +
95P TYR* 3.4 4.9 + - - +
96P MET* 3.0 38.8 + - + +
242P LEU* 5.7 0.9 - - + -
250P LEU* 5.3 8.7 - - + -
272P TRP* 3.7 23.3 - - + -
3003Q CDL 4.0 29.4 - - + -
3004T CDL 4.8 20.9 - - + -
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Residues in contact with CYS 93 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33P PHE* 3.9 31.3 - - + +
36P LEU* 4.0 12.8 - - - -
37P LEU* 3.7 19.1 - - + -
40P CYS* 4.2 6.3 - - - -
89P MET* 2.9 20.4 + - - +
90P PHE* 3.7 4.9 - - - +
92P ILE* 1.3 76.4 - - - +
94P LEU* 1.3 59.1 + - - +
96P MET* 3.2 1.7 + - - +
97P HIS* 2.8 31.7 + - - +
235P LEU* 4.0 25.1 - - - -
3003Q CDL 4.9 5.4 - - - -
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Residues in contact with LEU 94 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37P LEU* 3.7 19.3 - - + -
90P PHE* 2.8 24.2 + - + +
91P PHE* 3.1 22.0 + - + +
93P CYS* 1.3 75.7 - - - +
95P TYR* 1.3 61.2 + - + +
97P HIS* 3.4 3.6 - - + +
98P VAL* 2.9 34.9 + - - +
120P LEU* 4.0 25.1 - - + -
123P VAL* 3.7 31.6 - - + -
502P HEM 4.0 44.6 - - + -
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Residues in contact with TYR 95 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91P PHE* 2.9 37.7 + + + +
92P ILE* 3.9 4.9 - - - +
94P LEU* 1.3 76.3 - - + +
96P MET* 1.3 66.8 + - + +
98P VAL* 3.5 5.6 + - + +
99P GLY* 3.0 22.7 + - - -
120P LEU* 4.4 20.9 - - + -
124P MET* 3.8 10.0 - - + +
272P TRP* 4.4 8.3 - + - -
273P TYR* 2.6 43.1 + - + -
276P PHE* 3.5 12.4 - + - -
3007P PEE 3.7 78.8 - - + +
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Residues in contact with MET 96 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30P TRP* 3.8 24.0 - - + -
33P PHE* 3.7 38.4 - - + -
92P ILE* 3.0 35.7 + - + +
93P CYS 3.6 4.0 - - - +
95P TYR* 1.3 80.0 - - + +
97P HIS* 1.3 58.3 + - - +
99P GLY* 3.3 1.2 + - - -
100P ARG* 2.9 30.2 + - - +
3007P PEE 3.2 57.7 - - + +
3004T CDL 4.3 22.4 - - + -
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Residues in contact with HIS 97 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33P PHE* 3.8 9.3 - - + +
34P GLY* 3.5 21.2 + - - -
37P LEU* 3.4 10.5 - - + +
93P CYS 2.8 17.8 + - - +
94P LEU* 3.4 5.2 - - - +
96P MET* 1.3 77.7 - - - +
98P VAL* 1.3 62.1 + - - +
100P ARG* 3.1 34.0 + - - +
101P GLY* 3.2 17.2 + - - -
502P HEM 2.0 99.3 + + + +
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Residues in contact with VAL 98 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94P LEU 2.9 21.4 + - - +
95P TYR* 4.0 6.7 - - + +
97P HIS* 1.3 70.9 - - - +
99P GLY* 1.3 65.8 + - - +
101P GLY* 3.1 3.6 + - - +
102P LEU* 3.0 26.0 + - + +
113P TRP* 4.3 6.9 - - + -
120P LEU* 4.7 12.3 - - + -
301P LEU* 4.0 26.2 - - + -
502P HEM 3.7 41.7 - - + -
3007P PEE 3.7 24.9 - - + -
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Residues in contact with GLY 99 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95P TYR 3.0 16.4 + - - -
96P MET 3.3 2.9 + - - -
98P VAL* 1.3 78.3 - - - +
100P ARG* 1.3 61.4 + - - +
102P LEU* 3.3 4.1 + - - -
103P TYR* 3.0 26.7 + - - +
325P PHE* 3.7 6.4 - - - -
3007P PEE 3.7 34.5 - - - +
----------------------------------------------------------
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Residues in contact with ARG 100 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30P TRP* 3.5 37.0 - - + +
31P TRP* 3.2 41.1 - - + +
96P MET 2.9 17.0 + - - +
97P HIS* 3.1 42.7 + - - +
99P GLY* 1.3 75.0 - - - +
101P GLY* 1.3 73.2 + - - +
104P TYR* 3.0 38.7 + - + +
106P SER* 3.9 10.8 - - - -
502P HEM 2.9 52.5 + - - +
3007P PEE 3.6 10.4 - - + +
----------------------------------------------------------
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Residues in contact with GLY 101 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97P HIS 3.2 7.2 + - - -
98P VAL 3.1 8.0 + - - -
100P ARG* 1.3 85.0 - - - +
102P LEU* 1.3 61.0 + - - +
105P GLY 3.1 2.9 + - - -
106P SER* 2.9 44.8 + - - -
107P TYR* 3.5 4.5 - - - -
113P TRP* 4.1 15.9 - - - -
502P HEM 5.5 2.0 - - - -
----------------------------------------------------------
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Residues in contact with LEU 102 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98P VAL* 3.0 23.5 + - + +
99P GLY* 3.8 4.7 - - - +
101P GLY* 1.3 75.9 - - - +
103P TYR* 1.3 65.1 + - - +
104P TYR 3.5 0.2 + - - -
105P GLY 3.5 1.9 + - - -
107P TYR* 3.4 19.4 + - - -
113P TRP* 3.6 23.1 - - + -
301P LEU* 4.4 7.2 - - + -
304P ILE* 3.8 36.3 - - + -
315P MET* 3.9 15.0 - - + +
325P PHE* 4.3 11.2 - - + -
328P LEU* 5.0 13.0 - - + -
366P MET* 6.5 0.4 - - + -
3007P PEE 3.8 30.3 - - + -
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Residues in contact with TYR 103 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99P GLY 3.0 17.2 + - - +
100P ARG 3.9 2.9 - - - +
102P LEU* 1.3 78.7 - - - +
104P TYR* 1.3 91.5 + + + +
105P GLY 3.7 0.2 + - - -
313P ARG 4.8 0.3 - - - +
314P SER 3.9 0.2 - - - -
315P MET* 3.0 54.1 + - + +
316P MET 4.1 3.8 - - - -
322P GLN* 3.2 37.7 + - + -
325P PHE* 3.6 37.4 - + + -
326P TRP* 4.3 6.6 + - - -
3007P PEE 2.6 60.3 + - + -
----------------------------------------------------------
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Residues in contact with TYR 104 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28P SER* 4.9 1.6 + - - -
30P TRP* 4.1 9.9 - + - -
31P TRP* 3.5 30.7 - + + -
100P ARG* 3.0 33.4 + - + +
103P TYR* 1.3 97.0 - + - +
105P GLY* 1.3 58.3 + - - +
106P SER* 3.2 3.4 - - - +
206P ASN* 2.8 32.7 + - - +
207P ASN 4.6 0.2 - - - +
208P PRO* 3.3 37.1 - - + +
313P ARG* 3.6 14.3 - - - +
314P SER* 3.4 13.8 - - - -
3007P PEE 2.6 60.3 + - + +
3004T CDL 4.9 2.1 - - - -
----------------------------------------------------------
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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