Contacts of the helix formed by residues 21 - 47 (chain K) 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 LEU 21 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25J THR* 4.7 18.8 - - + +
29J MET* 4.2 18.6 - - + -
19K VAL* 4.8 6.5 - - + -
20K ASP* 1.3 82.9 - - - +
22K ARG* 1.3 66.3 + - - +
23K GLY 3.2 3.1 - - - -
24K MET* 3.1 23.4 + - + +
25K TRP* 3.1 46.6 + - + +
105K VAL* 4.7 4.9 - - + -
109K GLN* 3.3 40.2 + - + +
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Residues in contact with ARG 22 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20K ASP* 3.0 44.7 + - - +
21K LEU* 1.3 78.1 - - - +
23K GLY* 1.3 57.9 + - - +
25K TRP* 3.3 37.5 + - - +
26K ILE* 2.9 43.1 + - + +
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Residues in contact with GLY 23 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20K ASP* 5.2 1.2 + - - +
21K LEU 3.2 0.8 - - - -
22K ARG* 1.3 75.0 - - - +
24K MET* 1.3 64.5 + - - +
26K ILE* 3.4 13.9 + - - +
27K GLY 3.0 18.2 + - - -
109K GLN* 4.3 1.8 + - - -
302K PGT 3.6 36.6 + - - +
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Residues in contact with MET 24 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29J MET* 4.1 24.5 - - + -
21K LEU* 3.1 19.8 + - + +
23K GLY* 1.3 74.4 - - - +
25K TRP* 1.3 92.0 + - + +
27K GLY* 2.9 5.0 + - - -
28K LEU* 2.7 50.2 + - + +
109K GLN* 3.6 33.6 + - + +
112K VAL* 4.0 24.0 - - + -
113K VAL* 4.2 2.6 - - + +
302K PGT 3.6 15.1 - - - +
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Residues in contact with TRP 25 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21K LEU* 3.1 38.3 + - + +
22K ARG* 3.3 38.1 - - - +
24K MET* 1.3 102.0 - - + +
26K ILE* 1.3 66.8 + - - +
28K LEU* 4.1 20.4 - - + -
29K VAL* 2.9 36.1 + - + +
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Residues in contact with ILE 26 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22K ARG* 2.9 38.8 + - + +
23K GLY* 3.5 11.0 - - - +
24K MET 3.2 0.2 - - - -
25K TRP* 1.3 72.9 - - + +
27K GLY* 1.3 59.0 + - - +
29K VAL* 3.8 3.5 - - - +
30K LEU* 2.8 56.7 + - + +
302K PGT 6.1 1.8 - - + -
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Residues in contact with GLY 27 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23K GLY 3.0 10.0 + - - -
24K MET 2.9 11.4 + - - -
26K ILE* 1.3 70.9 - - - +
28K LEU* 1.3 64.3 + - - -
30K LEU* 3.3 4.0 + - - +
31K LEU* 3.0 27.1 + - - +
113K VAL* 4.3 9.2 - - - -
302K PGT 3.6 32.5 - - - +
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Residues in contact with LEU 28 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24K MET* 2.7 34.0 + - + +
25K TRP* 3.8 29.8 - - + +
27K GLY* 1.3 70.7 - - - +
29K VAL* 1.3 63.7 + - + +
31K LEU* 3.2 2.5 + - + +
32K ASN* 2.9 41.4 + - - +
112K VAL* 4.4 11.2 - - + -
113K VAL* 3.8 21.1 - - + +
116K ILE* 4.2 37.7 - - + -
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Residues in contact with VAL 29 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25K TRP* 2.9 30.2 + - + +
26K ILE* 3.8 3.1 - - - +
28K LEU* 1.3 74.0 - - + +
30K LEU* 1.3 61.0 + - + +
31K LEU 2.8 6.8 + - - -
32K ASN* 4.8 2.5 - - - +
33K VAL* 3.0 42.7 + - + +
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Residues in contact with LEU 30 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26K ILE* 2.8 46.0 + - + +
27K GLY* 3.7 6.7 - - - +
29K VAL* 1.3 73.8 - - + +
31K LEU* 1.3 59.6 + - - +
33K VAL* 4.8 4.0 - - - -
34K PHE* 3.5 20.5 - - - +
302K PGT 5.0 20.0 - - + +
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Residues in contact with LEU 31 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27K GLY 3.0 15.0 + - - +
28K LEU* 3.7 4.5 - - + +
29K VAL 2.8 2.2 + - - -
30K LEU* 1.3 78.6 - - - +
32K ASN* 1.3 68.5 + - - +
33K VAL 3.1 0.7 - - - -
34K PHE* 2.9 19.7 + - + +
35K TYR* 2.9 33.8 + - + +
113K VAL* 4.4 15.9 - - + +
116K ILE* 3.5 28.0 - - + -
117K ALA* 4.0 22.2 - - + +
156K ILE* 4.2 23.1 - - + -
160K ILE* 4.6 1.3 - - + -
302K PGT 3.9 24.2 - - + -
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Residues in contact with ASN 32 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28K LEU* 2.9 36.1 + - - +
29K VAL* 4.4 2.6 - - - +
31K LEU* 1.3 74.1 - - - +
33K VAL* 1.3 63.7 + - + +
35K TYR* 3.5 1.6 + - - +
36K LEU* 3.0 33.7 + - + +
116K ILE* 3.8 13.3 - - - +
120K TRP* 3.3 34.2 + - + +
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Residues in contact with VAL 33 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29K VAL* 3.0 37.2 + - + +
30K LEU* 4.8 2.9 - - - -
32K ASN* 1.3 76.4 - - + +
34K PHE* 1.3 66.0 + - - +
36K LEU* 3.1 7.8 + - - +
37K ILE* 2.9 39.7 + - + +
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Residues in contact with PHE 34 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30K LEU 3.5 16.7 + - - +
31K LEU* 2.9 16.7 + - + +
33K VAL* 1.3 76.0 - - - +
35K TYR* 1.3 73.0 + + - +
37K ILE* 3.3 20.8 - - + +
38K VAL* 3.0 48.2 + - + +
152K MET* 3.9 28.5 - - + -
156K ILE* 4.1 13.9 - - + -
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Residues in contact with TYR 35 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31K LEU* 2.9 33.8 + - + +
32K ASN 4.0 0.2 - - - +
34K PHE* 1.3 87.5 - + - +
36K LEU* 1.3 56.0 + - - +
38K VAL* 3.0 3.2 + - + +
39K ARG* 2.6 38.1 + - - +
117K ALA* 5.0 4.0 + - - -
120K TRP* 3.1 70.5 - + + +
125K PHE* 3.6 16.8 - + + -
152K MET* 3.2 31.6 - - + -
153K SER* 3.3 25.9 + - - -
156K ILE* 3.5 23.2 - - + +
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Residues in contact with LEU 36 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32K ASN* 3.0 26.7 + - + +
33K VAL* 3.3 8.3 - - - +
35K TYR* 1.3 73.1 - - - +
37K ILE* 1.3 66.3 + - - +
39K ARG* 3.8 5.6 - - + +
40K ILE* 2.9 52.8 + - + +
120K TRP* 4.7 13.2 - - + -
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Residues in contact with ILE 37 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33K VAL* 2.9 38.9 + - + +
34K PHE* 3.3 18.2 - - + +
36K LEU* 1.3 76.9 - - - +
38K VAL* 1.3 57.7 + - + +
40K ILE* 3.5 8.7 - - + +
41K TYR* 2.6 44.7 + - + +
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Residues in contact with VAL 38 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34K PHE* 3.0 50.5 + - + +
35K TYR* 3.0 11.9 + - - +
37K ILE* 1.3 77.6 - - + +
39K ARG* 1.3 58.8 + - - +
41K TYR* 3.3 10.1 + - + +
42K GLU* 2.9 29.0 + - - +
62K TRP* 5.4 0.4 - - + -
125K PHE* 4.4 6.1 - - + -
148K ILE* 3.8 44.4 - - + -
152K MET* 4.1 8.1 - - + -
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Residues in contact with ARG 39 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111J VAL* 2.9 34.0 + - + +
112J ASN* 3.0 16.5 + - - -
115J GLY* 3.8 1.0 - - - -
116J TRP* 3.2 26.5 - - - +
35K TYR 2.6 19.7 + - - +
36K LEU* 3.8 6.1 - - + +
38K VAL* 1.3 75.4 - - - +
40K ILE* 1.3 63.8 + - + +
42K GLU* 3.0 26.1 - - - +
43K GLN* 3.0 50.3 + - - +
120K TRP* 5.3 2.5 - - + -
124K PHE* 3.8 20.6 - - + -
125K PHE* 4.7 1.5 - - + -
128K GLN* 3.7 6.7 - - - +
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Residues in contact with ILE 40 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36K LEU* 2.9 43.4 + - + +
37K ILE* 3.5 6.7 - - + +
39K ARG* 1.3 76.4 - - + +
41K TYR* 1.3 68.0 + - + +
43K GLN* 3.2 18.4 + - + +
44K VAL* 3.2 19.8 + - + +
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Residues in contact with TYR 41 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37K ILE* 2.6 28.0 + - + +
38K VAL* 3.6 10.1 - - + +
40K ILE* 1.3 77.8 - - + +
42K GLU* 1.3 59.6 + - - +
44K VAL* 3.2 6.9 + - - +
45K PHE* 2.8 55.9 + + + -
60K THR 5.0 0.2 + - - -
61K TYR* 2.6 40.6 + + - +
62K TRP* 3.8 22.0 - + - -
64K SER* 5.1 1.0 + - - -
65K ILE* 3.7 23.5 - - + +
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Residues in contact with GLU 42 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116J TRP* 3.1 23.2 + - + -
38K VAL 2.9 16.2 + - - +
39K ARG* 3.0 34.0 + - - +
41K TYR* 1.3 73.6 - - - +
43K GLN* 1.3 60.0 + - - +
46K GLY* 2.7 30.3 + - - -
62K TRP* 3.4 27.5 - - + -
125K PHE* 3.4 12.9 - - - -
128K GLN* 2.6 41.4 + - - +
144K PRO 4.9 2.3 - - - +
145K SER* 5.1 0.5 - - - -
148K ILE* 3.7 20.6 - - + +
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Residues in contact with GLN 43 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115J GLY 3.2 20.0 + - - +
116J TRP* 3.6 19.1 + - - +
118J TYR* 3.5 17.2 + - - -
39K ARG* 3.0 40.4 + - - +
40K ILE* 3.2 14.6 - - + +
42K GLU* 1.3 79.7 - - - +
44K VAL* 1.3 66.0 + - + +
46K GLY 3.9 2.1 + - - -
47K TRP* 4.0 21.3 + - - +
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Residues in contact with VAL 44 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40K ILE* 3.2 15.7 + - + +
41K TYR* 3.2 10.3 + - - +
43K GLN* 1.3 85.9 - - + +
45K PHE* 1.3 88.1 + - + +
46K GLY 3.3 0.2 - - - -
47K TRP 3.1 19.9 - - - +
48K ARG 4.2 1.0 - - - +
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Residues in contact with PHE 45 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41K TYR* 2.8 52.2 + + + +
44K VAL* 1.3 93.4 - - + +
46K GLY* 1.3 58.6 + - - +
47K TRP 4.4 0.2 - - - -
48K ARG 4.3 1.6 - - - -
49K ALA* 3.0 25.1 - - + +
50K GLY 3.3 0.9 + - - -
61K TYR* 3.3 51.1 - + + -
62K TRP* 2.7 39.2 + - + +
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Residues in contact with GLY 46 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116J TRP* 4.2 12.8 - - - -
42K GLU 2.7 27.7 + - - -
44K VAL 3.3 0.4 - - - -
45K PHE* 1.3 71.0 - - - +
47K TRP* 1.3 57.4 + - - +
48K ARG 3.5 1.2 + - - -
50K GLY* 3.1 30.9 + - - -
51K LEU* 4.0 1.2 - - - +
62K TRP* 4.1 9.0 - - - -
132K TRP* 3.7 15.3 - - - -
144K PRO* 5.1 0.7 - - - -
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Residues in contact with TRP 47 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90I PRO* 3.8 19.0 + - + +
128I ARG* 3.6 31.8 - - - +
132I TRP* 3.6 27.8 - + + -
116J TRP* 2.2 72.9 - + - -
117J THR* 3.1 30.1 - - + -
118J TYR* 4.5 0.2 - + - -
43K GLN* 4.0 17.7 + - - +
44K VAL 3.1 14.0 - - - +
46K GLY* 1.3 70.2 - - - +
48K ARG* 1.3 80.9 + - + +
51K LEU* 4.2 14.1 - - + -
132K TRP* 4.5 7.0 - + - -
135K THR* 4.3 10.5 - - + +
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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