Contacts of the helix formed by residues 32 - 53 (chain O) in PDB entry 1VF5
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 TRP 32 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28N PRO* 2.9 19.7 - - + +
18O LEU* 5.3 0.2 - - - +
31O ALA* 1.3 82.5 - - + +
33O PRO* 1.3 80.6 - - - +
34O ASN 4.2 2.3 - - - +
35O ASP 3.6 9.5 + - - -
36O LEU* 3.2 56.4 + - + -
277P LYS* 3.2 42.8 - - + -
31T ARG* 4.0 20.4 - - + -
32T PRO* 4.9 2.2 - - + +
33T ASN* 3.6 20.9 - - - +
34T GLU* 5.2 0.6 - - - +
35T LEU* 4.5 26.9 - - + +
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Residues in contact with PRO 33 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24N LYS 5.9 0.4 - - - -
25N TYR* 3.2 18.2 - - - +
26N VAL* 3.4 20.0 - - - +
27N PRO* 3.1 28.9 - - + -
28N PRO* 3.3 5.3 - - - +
18O LEU* 6.2 1.3 - - + -
31O ALA* 4.3 1.1 - - - -
32O TRP* 1.3 99.0 - - - +
34O ASN* 1.3 72.0 + - + +
35O ASP* 5.8 0.4 - - - +
36O LEU* 4.3 4.3 + - - +
37O LEU* 5.0 1.0 - - - +
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Residues in contact with ASN 34 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24N LYS* 5.3 13.5 - - + +
25N TYR 3.7 6.5 + - - +
26N VAL* 6.2 0.9 - - - -
33O PRO* 1.3 84.6 - - + +
35O ASP* 1.3 91.6 + - - +
36O LEU* 2.6 16.5 + - - +
37O LEU* 3.1 35.8 + - - +
38O TYR* 4.0 11.0 - - - -
1307Q OPC 4.3 28.7 + - - -
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Residues in contact with ASP 35 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32O TRP* 3.6 16.0 + - - -
33O PRO* 3.8 1.0 - - - +
34O ASN* 1.3 94.0 + - - +
36O LEU* 1.3 58.0 + - - +
37O LEU 3.3 2.2 - - - +
38O TYR* 3.5 24.7 - - + +
39O VAL* 4.6 0.2 - - - +
276P LYS* 3.7 15.1 - - + -
277P LYS* 4.2 14.5 - - - +
1307Q OPC 3.2 23.8 + - - -
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Residues in contact with LEU 36 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28N PRO* 4.4 19.7 - - + -
31N ASN* 5.7 2.5 - - - +
303N HEM 4.4 18.4 - - + -
32O TRP* 3.2 38.6 - - + +
33O PRO 4.3 1.8 - - - +
34O ASN 2.6 8.3 + - - +
35O ASP* 1.3 68.0 - - - +
37O LEU* 1.3 58.1 + - + +
38O TYR 2.7 15.6 + - - -
39O VAL* 3.1 29.6 - - + +
40O PHE* 2.9 31.7 - - + -
31T ARG* 4.6 20.4 - - - +
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Residues in contact with LEU 37 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26N VAL* 6.5 1.8 - - + -
33O PRO 5.0 0.9 - - - +
34O ASN* 3.4 35.4 - - - +
36O LEU* 1.3 77.6 - - + +
38O TYR* 1.3 80.0 + - - +
40O PHE* 3.3 41.3 - - + -
41O PRO* 4.1 8.1 - - - +
1305Q PL9 3.9 44.4 - - + +
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Residues in contact with TYR 38 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34O ASN* 4.0 10.5 - - - -
35O ASP* 3.5 20.9 - - + -
36O LEU 2.7 0.4 + - - -
37O LEU* 1.3 88.1 - - - +
39O VAL* 1.3 67.6 + - - +
40O PHE 3.7 0.2 - - - +
41O PRO* 3.6 21.3 - - + -
42O VAL* 4.4 2.6 - - - +
272P LEU* 3.8 15.5 - - + +
273P ILE* 5.0 1.0 + - - -
276P LYS* 3.0 49.7 - - + +
277P LYS* 5.3 0.2 - - - +
24Q PHE* 3.7 23.0 - + - -
1305Q PL9 3.3 41.7 - - + +
1307Q OPC 3.3 40.6 + - - +
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Residues in contact with VAL 39 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303N HEM 3.7 16.4 - - + -
32O TRP* 4.5 1.3 - - + -
35O ASP 4.6 0.2 - - - +
36O LEU* 3.1 44.6 - - + +
38O TYR* 1.3 78.0 - - - +
40O PHE* 1.3 70.5 + - - +
41O PRO 3.3 1.1 - - - -
42O VAL* 2.9 29.0 + - + +
43O VAL* 2.9 15.1 + - + +
273P ILE* 5.5 6.3 - - + -
277P LYS* 3.6 33.2 - - + -
28T GLN* 4.0 4.7 + - + +
31T ARG* 5.2 12.6 - - + -
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Residues in contact with PHE 40 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303N HEM 3.3 83.0 - + + -
36O LEU* 2.9 46.0 - - + +
37O LEU* 3.3 34.3 - - + -
39O VAL* 1.3 83.9 - - + +
41O PRO* 1.3 65.7 - - + +
43O VAL* 2.6 29.6 + - - +
44O ILE* 2.8 20.2 + - + +
1305Q PL9 4.6 16.4 - + + -
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Residues in contact with PRO 41 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37O LEU 4.1 3.4 - - - +
38O TYR* 3.6 26.5 - - + +
39O VAL 3.5 3.6 - - - +
40O PHE* 1.3 93.2 - - + +
42O VAL* 1.3 56.9 + - - +
44O ILE* 3.8 12.5 - - + +
45O MET* 2.9 40.0 + - + +
272P LEU* 3.6 28.3 - - + -
27Q VAL* 5.6 6.5 - - + -
1305Q PL9 4.6 23.1 - - + -
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Residues in contact with VAL 42 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38O TYR 4.4 0.2 - - - +
39O VAL* 2.9 29.7 + - + +
41O PRO* 1.3 78.2 - - - +
43O VAL* 1.3 53.7 + - - +
46O GLY* 2.8 24.8 + - - -
269P GLN* 3.0 37.7 + - + +
272P LEU* 3.7 30.7 - - + -
273P ILE* 4.1 14.6 - - + -
24T ALA* 4.6 1.2 - - - +
27T GLN* 4.1 21.1 - - + -
28T GLN* 3.4 16.8 + - - +
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Residues in contact with VAL 43 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39N ILE* 3.2 33.7 - - + -
303N HEM 3.2 53.2 - - + -
39O VAL 2.9 11.1 + - - +
40O PHE* 2.6 13.2 + - - +
42O VAL* 1.3 68.6 - - - +
44O ILE* 1.3 53.9 + - - +
46O GLY* 3.1 1.6 + - - -
47O THR* 2.7 38.3 + - - -
1101R BCR 4.1 14.0 - - + +
28T GLN* 3.2 25.1 - - + +
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Residues in contact with ILE 44 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42N THR* 4.1 19.2 - - + +
303N HEM 3.3 47.8 - - + -
40O PHE 2.8 18.4 + - - +
41O PRO* 3.8 12.8 - - + +
43O VAL* 1.3 68.5 - - - +
45O MET* 1.3 68.7 + - + +
47O THR* 3.1 8.4 + - - +
48O PHE* 2.9 25.9 + - + +
1305Q PL9 4.7 13.0 - - + -
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Residues in contact with MET 45 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41O PRO* 2.9 30.0 + - + +
44O ILE* 1.3 79.9 - - + +
46O GLY* 1.3 57.1 + - - +
48O PHE* 3.7 5.6 - - - +
49O ALA* 2.9 32.7 + - - +
265P VAL* 3.9 14.3 - - + +
268P ALA* 3.9 11.9 - - + -
269P GLN* 3.8 29.8 - - - +
272P LEU* 4.6 9.0 - - - -
27Q VAL* 3.9 26.0 - - + +
30Q VAL* 3.5 42.4 - - + -
31Q ALA 5.3 0.2 - - - +
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Residues in contact with GLY 46 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42O VAL 2.8 15.1 + - - -
43O VAL 3.1 4.2 + - - -
45O MET* 1.3 78.4 - - - +
47O THR* 1.3 61.2 + - - +
49O ALA* 3.9 4.0 - - - +
50O CYS* 3.4 28.6 + - - -
269P GLN* 3.5 3.3 - - - +
1101R BCR 3.8 7.6 - - - +
24T ALA* 3.3 26.6 - - - +
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Residues in contact with THR 47 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39N ILE* 3.3 29.4 - - + +
42N THR* 3.7 27.0 - - + +
43N CYS* 4.3 12.6 - - - -
46N ILE* 4.4 0.9 - - + -
43O VAL 2.7 18.8 + - - -
44O ILE* 3.4 7.7 - - - -
46O GLY* 1.3 73.4 - - - +
48O PHE* 1.3 71.9 + - - +
50O CYS* 3.3 2.9 + - - +
51O ILE* 3.3 36.5 + - + +
1101R BCR 4.0 12.3 - - - +
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Residues in contact with PHE 48 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42N THR* 6.1 0.7 - - + -
46N ILE* 3.9 33.8 - - + +
85N ILE* 4.6 15.5 - - + -
44O ILE* 2.9 17.7 + - + +
45O MET* 3.7 6.3 - - - +
47O THR* 1.3 78.9 - - - +
49O ALA* 1.3 63.7 + - - +
51O ILE* 2.9 8.2 + - + +
52O VAL* 2.8 46.1 + - + +
261P PHE* 3.8 33.0 - + - -
265P VAL* 5.9 0.2 - - + -
30Q VAL* 6.1 0.4 - - + -
34Q ALA* 4.0 18.4 - - + -
1305Q PL9 4.9 21.1 - - + -
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Residues in contact with ALA 49 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45O MET 2.9 21.6 + - - +
46O GLY* 3.9 2.9 - - - +
47O THR 3.4 0.2 - - - -
48O PHE* 1.3 75.6 - - - +
50O CYS* 1.3 57.9 + - - +
52O VAL* 3.1 9.8 + - - +
53O ALA* 2.8 29.5 + - - +
261P PHE* 4.9 2.2 - - - -
262P ILE* 4.1 10.8 - - + +
265P VAL* 4.1 16.2 - - + -
21T LEU* 3.5 30.7 - - + +
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Residues in contact with CYS 50 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46O GLY 3.4 15.9 + - - +
47O THR 3.3 4.6 + - - +
48O PHE 3.2 0.8 - - - -
49O ALA* 1.3 78.4 - - - +
51O ILE* 1.3 60.6 + - + +
53O ALA* 3.6 4.0 + - - +
54O LEU* 3.0 36.1 + - + +
1101R BCR 4.1 23.1 - - + -
18T LEU* 4.4 10.7 - - + +
21T LEU* 3.1 28.5 - - - -
22T PHE* 4.1 21.1 - - - -
24T ALA* 5.0 0.4 - - - -
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Residues in contact with ILE 51 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43N CYS* 4.1 10.3 - - - -
46N ILE* 3.7 18.4 - - + -
85N ILE* 4.1 13.5 - - + -
88N TRP* 4.1 6.9 - - + +
89N SER* 3.7 49.1 - - - +
92N MET* 4.3 18.4 - - + -
47O THR* 3.3 21.1 + - + +
48O PHE* 2.9 9.9 + - + +
50O CYS* 1.3 77.3 - - + +
52O VAL* 1.3 54.5 + - + +
54O LEU* 3.5 9.4 - - + +
55O SER* 2.4 40.9 + - - +
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Residues in contact with VAL 52 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81N LEU* 5.6 5.4 - - + -
85N ILE* 4.3 14.4 - - + -
48O PHE* 2.8 48.6 + - + +
49O ALA* 3.4 10.1 - - - +
51O ILE* 1.3 74.3 - - + +
53O ALA* 1.3 68.4 + - - +
54O LEU 3.1 1.9 + - - -
55O SER* 3.5 5.8 + - - -
56O VAL* 2.8 34.8 + - + +
258P MET* 4.7 7.2 - - + -
261P PHE* 4.2 12.1 - - + -
262P ILE* 4.2 14.1 - - + -
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Residues in contact with ALA 53 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49O ALA 2.8 18.8 + - - +
50O CYS* 3.8 7.6 - - - +
51O ILE 3.5 0.2 - - - -
52O VAL* 1.3 75.2 - - - +
54O LEU* 1.3 54.2 + - - +
56O VAL* 3.3 2.1 - - - +
57O LEU* 2.7 38.4 + - - +
258P MET* 3.9 26.2 - - + -
262P ILE* 4.5 6.3 - - + -
17T THR 4.8 1.8 - - - +
18T LEU* 3.9 28.3 - - + +
21T LEU* 5.1 0.9 - - + -
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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
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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