Contacts of the helix formed by residues 19 - 40 (chain P) in PDB entry 6CP3
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 19 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18O GLY* 3.6 23.6 - - - +
61O THR* 3.8 30.5 - - - +
62O GLY* 4.7 1.1 - - - +
64O PHE* 5.2 5.4 - - + -
65O CYS* 4.3 17.3 - - + +
68O VAL* 6.2 1.8 - - + -
16P THR* 3.3 22.3 + - - +
17P ILE 3.2 0.2 - - - -
18P GLY* 1.3 73.9 - - - +
20P LEU* 1.3 52.8 + - - +
21P GLY 3.2 0.9 - - - -
22P ALA* 3.1 6.3 + - + +
23P GLY* 2.7 34.1 + - - +
62P GLY* 3.8 36.3 - - - +
65P CYS* 3.6 7.9 - - - -
66P LEU* 4.7 13.5 - - + -
19Q LEU* 4.4 0.7 - - - -
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Residues in contact with LEU 20 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17O ILE* 3.3 30.5 - - + +
18O GLY* 3.8 13.4 + - - +
20O LEU* 3.7 12.6 - - + -
21O GLY* 3.3 30.5 - - - +
22O ALA 4.6 0.4 + - - +
17P ILE* 3.3 20.0 + - + +
18P GLY 3.1 0.2 - - - -
19P LEU* 1.3 76.5 - - - +
21P GLY* 1.3 57.6 + - - +
23P GLY* 3.3 1.8 + - - +
24P ILE* 2.9 39.6 + - + +
20Q LEU* 3.7 26.0 - - + -
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Residues in contact with GLY 21 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18P GLY 3.5 3.8 + - - -
19P LEU 3.2 0.6 - - - -
20P LEU* 1.3 76.5 - - - +
22P ALA* 1.3 60.0 + - - +
24P ILE* 3.5 2.1 + - - +
25P GLY* 2.9 26.5 + - - -
20Q LEU* 3.4 37.7 - - - +
23Q GLY* 3.9 14.0 - - - -
24Q ILE* 3.8 8.7 - - - +
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Residues in contact with ALA 22 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61O THR* 5.7 4.0 - - - +
18P GLY 4.5 1.0 + - - -
19P LEU* 3.1 14.0 + - + +
21P GLY* 1.3 75.7 - - - +
23P GLY* 1.3 57.4 + - - +
25P GLY* 3.0 2.8 + - - -
26P ILE* 3.0 43.1 + - + +
58P SER* 4.1 7.2 - - - +
59P GLU* 4.2 10.3 - - + -
61P THR* 3.8 22.7 + - - +
62P GLY* 4.0 16.6 - - - +
19Q LEU* 5.4 0.8 + - - +
23Q GLY* 4.8 2.2 - - - -
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Residues in contact with GLY 23 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18O GLY 5.3 1.6 - - - -
22O ALA* 3.4 33.9 - - - +
25O GLY* 4.5 3.8 - - - -
26O ILE* 4.9 3.3 + - - +
58O SER* 5.0 3.5 - - - +
61O THR* 3.9 19.9 + - - -
62O GLY 5.3 1.1 - - - -
19P LEU* 2.7 19.4 + - - +
20P LEU* 3.3 2.9 + - - -
22P ALA* 1.3 72.1 - - - +
24P ILE* 1.3 59.9 + - - +
26P ILE* 4.8 3.2 - - - +
27P ALA* 4.8 5.7 - - - +
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Residues in contact with ILE 24 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21O GLY* 3.3 36.1 - - - +
24O ILE* 5.1 12.1 - - + -
25O GLY* 4.2 6.4 - - - -
28O ILE* 6.1 0.7 - - + -
20P LEU* 2.9 29.4 + - + +
21P GLY* 3.7 3.4 - - - +
23P GLY* 1.3 78.6 - - - +
25P GLY* 1.3 69.8 + - - +
26P ILE 3.4 0.4 - - - -
27P ALA* 3.3 12.5 + - - +
28P ILE* 3.3 34.1 + - + +
20Q LEU* 5.0 0.4 - - + -
24Q ILE* 4.0 31.2 - - + -
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Residues in contact with GLY 25 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21P GLY 2.9 19.4 + - - -
24P ILE* 1.3 74.3 - - - +
26P ILE* 1.3 66.4 + - - +
27P ALA 3.1 2.9 + - - -
28P ILE* 3.4 12.2 - - - +
29P VAL* 3.4 13.5 - - - +
58P SER* 5.3 1.7 - - - -
23Q GLY 4.3 2.9 - - - -
24Q ILE* 5.2 1.3 - - - -
27Q ALA* 3.3 33.6 - - - +
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Residues in contact with ILE 26 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57O LEU 3.8 4.9 - - - +
58O SER* 3.9 11.8 + - - +
61O THR* 3.8 32.8 - - + +
22P ALA* 3.0 23.3 + - + +
23P GLY* 4.8 1.8 - - - -
25P GLY* 1.3 78.0 - - - +
27P ALA* 1.3 59.8 + - + +
29P VAL* 4.5 3.5 + - - +
30P PHE* 3.3 23.7 - - - -
55P PHE* 3.4 40.8 - - + +
58P SER* 3.7 14.1 - - - -
59P GLU* 3.5 39.5 - - + +
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Residues in contact with ALA 27 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25O GLY 4.3 10.8 - - - -
26O ILE* 4.3 3.8 - - + +
29O VAL* 3.3 24.0 - - + +
54O GLY 4.2 5.1 - - - +
58O SER* 3.3 28.7 - - - +
23P GLY 4.8 2.5 - - - +
24P ILE 3.3 10.5 + - - +
25P GLY 3.1 0.6 - - - -
26P ILE* 1.3 79.1 - - - +
28P ILE* 1.3 59.1 + - - +
29P VAL 3.2 2.7 - - - -
30P PHE* 3.1 10.9 + - - +
31P ALA 3.1 18.7 + - - -
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Residues in contact with ILE 28 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25O GLY* 4.4 5.6 - - - +
28O ILE* 3.7 35.0 - - + -
29O VAL* 4.3 0.2 - - - -
24P ILE* 3.3 29.6 - - + +
25P GLY* 3.4 17.3 - - - +
27P ALA* 1.3 73.8 - - - +
29P VAL* 1.3 63.3 + - + +
31P ALA* 3.2 10.7 + - + +
32P ALA* 2.9 26.5 + - - +
24Q ILE* 5.1 3.8 - - + +
27Q ALA* 3.9 25.6 - - + +
28Q ILE* 4.7 13.0 - - + -
31Q ALA* 4.7 6.6 - - + +
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Residues in contact with VAL 29 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25P GLY 3.4 17.0 - - - +
26P ILE* 4.7 6.7 - - - +
27P ALA 3.2 0.4 - - - -
28P ILE* 1.3 75.6 - - - +
30P PHE* 1.3 60.4 + - + +
32P ALA* 3.2 9.0 + - - +
33P LEU 2.9 20.6 + - - -
51P ALA* 4.2 23.6 - - + +
54P GLY* 5.2 8.1 - - - -
55P PHE 5.5 1.3 - - - +
58P SER* 5.4 0.9 - - - +
27Q ALA* 3.6 32.3 - - + +
30Q PHE* 3.7 25.8 - - + -
31Q ALA* 5.0 0.9 - - - +
34Q ILE* 3.4 19.4 - - + +
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Residues in contact with PHE 30 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29O VAL* 5.1 2.7 - - + -
50O MET* 5.2 7.4 - - + -
51O ALA* 5.7 4.7 - - - -
53O LEU* 5.8 5.8 - - + -
54O GLY* 4.6 26.0 - - - -
26P ILE 3.3 17.9 - - - -
27P ALA* 3.1 7.4 + - - +
29P VAL* 1.3 76.0 - - + +
31P ALA* 1.3 60.4 + - - +
33P LEU* 3.1 22.0 + - + +
34P ILE* 2.9 33.2 + - - +
48P PHE* 3.6 28.0 - + - -
51P ALA* 3.6 30.5 - - + -
52P ILE* 4.1 5.6 - - + -
55P PHE* 3.5 40.2 - + + -
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Residues in contact with ALA 31 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28O ILE* 4.6 4.7 - - + +
29O VAL* 3.8 19.4 - - + +
32O ALA* 3.7 19.2 - - + +
27P ALA 3.1 5.5 + - - -
28P ILE* 3.2 22.2 + - + +
30P PHE* 1.3 77.6 - - - +
32P ALA* 1.3 57.8 + - - +
34P ILE* 3.3 15.3 + - - +
35P ASN* 3.0 34.1 + - - +
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Residues in contact with ALA 32 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28P ILE 2.9 11.1 + - - +
29P VAL 3.3 8.7 - - - +
31P ALA* 1.3 75.2 - - - +
33P LEU* 1.3 58.0 + - - +
35P ASN* 3.3 8.8 + - - +
36P GLY* 2.8 23.2 + - - -
31Q ALA* 3.6 39.9 - - + +
34Q ILE* 3.3 14.9 - - + +
35Q ASN* 3.7 13.8 - - - +
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Residues in contact with LEU 33 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50O MET* 3.8 29.2 - - + -
29P VAL 2.9 12.7 + - - +
30P PHE* 3.1 29.1 + - + +
32P ALA* 1.3 74.5 - - - +
34P ILE* 1.3 59.4 + - - +
37P VAL* 2.9 39.4 + - + +
44P LYS* 4.1 11.0 - - + +
47P VAL* 3.9 28.3 - - + -
48P PHE* 4.0 13.2 - - + +
51P ALA* 4.0 7.2 - - + -
34Q ILE* 3.8 18.8 - - + +
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Residues in contact with ILE 34 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29O VAL* 3.6 28.9 - - + +
32O ALA 3.3 22.7 - - - +
33O LEU* 3.8 19.1 - - + +
36O GLY* 4.2 9.2 - - - -
47O VAL* 4.9 10.1 - - + -
51O ALA* 3.7 32.5 - - + +
30P PHE 2.9 20.7 + - - +
31P ALA* 3.3 14.6 - - - +
33P LEU* 1.3 75.0 - - - +
35P ASN* 1.3 56.4 + - - +
37P VAL* 3.8 7.5 - - - +
38P SER* 2.8 34.8 + - - -
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Residues in contact with ASN 35 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32O ALA* 3.4 32.1 - - - +
35O ASN* 3.8 24.0 - - - +
31P ALA* 3.0 23.1 + - - +
32P ALA* 3.7 7.5 - - - +
34P ILE* 1.3 75.0 - - - +
36P GLY* 1.3 57.6 + - - +
38P SER* 3.2 14.2 + - - -
39P ARG* 3.2 25.2 - - - +
35Q ASN* 3.9 15.1 + - - +
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Residues in contact with GLY 36 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32P ALA 2.8 16.6 + - - -
33P LEU* 3.7 1.8 - - - -
34P ILE 3.1 0.4 - - - -
35P ASN* 1.3 77.2 - - - +
37P VAL* 1.3 60.0 + - - +
39P ARG* 3.5 2.3 + - - +
40P ASN* 3.0 22.9 + - - +
43P ILE 5.7 0.7 - - - -
34Q ILE* 4.5 6.7 - - - -
35Q ASN* 4.8 1.6 - - - -
38Q SER* 3.5 33.8 - - - -
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Residues in contact with VAL 37 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43O ILE* 3.7 5.1 - - - +
46O THR* 4.4 10.3 - - + -
47O VAL* 3.7 26.5 - - + -
33P LEU* 2.9 28.3 + - + +
34P ILE* 3.8 2.5 - - - +
36P GLY* 1.3 73.7 - - - +
38P SER* 1.3 66.9 + - - +
40P ASN 3.1 29.0 - - - +
41P PRO* 3.2 13.4 - - + +
43P ILE 4.3 2.5 - - - +
44P LYS* 3.7 44.4 - - + -
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Residues in contact with SER 38 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35O ASN 4.4 2.6 + - - -
36O GLY* 3.6 33.6 - - - -
39O ARG* 5.3 5.2 + - - -
40O ASN* 2.7 35.4 + - - +
43O ILE* 4.0 13.5 - - - -
47O VAL* 5.3 0.4 - - - -
34P ILE* 2.8 23.6 + - - -
35P ASN* 3.2 13.9 + - - -
37P VAL* 1.3 80.4 - - - +
39P ARG* 1.3 63.8 + - - +
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Residues in contact with ARG 39 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201G THR* 2.8 31.3 + - - +
202G ASP* 3.4 12.7 + - - -
39O ARG* 3.4 40.5 - - - +
40O ASN* 5.0 0.2 + - - -
35P ASN* 3.2 19.3 - - - +
36P GLY 3.5 6.4 + - - +
37P VAL 3.3 0.2 - - - -
38P SER* 1.3 86.3 + - - +
40P ASN* 1.3 60.1 + - + +
41P PRO* 3.3 9.9 - - - +
35Q ASN* 3.7 2.3 + - - +
38Q SER* 3.5 19.8 + - - +
39Q ARG* 3.1 58.9 - - - +
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Residues in contact with ASN 40 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36P GLY 3.0 12.2 + - - +
37P VAL* 3.1 20.7 - - - +
39P ARG* 1.3 77.0 - - + +
41P PRO* 1.3 62.8 - - - +
42P SER* 2.5 28.0 + - - -
43P ILE* 3.4 31.0 - - + +
38Q SER* 3.6 21.4 + - - +
41Q PRO* 3.5 23.8 - - - +
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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) + - + + + + + -
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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