Contacts of the helix formed by residues 9 - 35 (chain T) 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 LEU 9 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41P LEU* 3.4 27.8 - - + -
44P THR* 6.2 2.5 - - + -
10T VAL* 1.3 82.0 + - + +
11T LEU* 3.4 26.2 - - + +
12T GLY* 3.2 16.6 + - - +
13T LEU* 3.6 8.0 + - - +
8U TRP* 5.5 4.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 10 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41P LEU* 4.8 13.7 - - + -
252P PRO* 4.9 15.5 - - + +
255P VAL* 4.3 23.6 - - + -
256P LYS* 5.9 0.4 - - - +
259P ILE* 5.4 2.0 - - + -
9T LEU* 1.3 96.5 - - + +
11T LEU* 1.3 58.1 + - + +
13T LEU* 3.1 20.7 + - + +
14T VAL* 2.8 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 11 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38P GLN* 5.1 2.7 - - - +
39P SER* 3.9 33.2 - - - +
41P LEU* 3.4 33.9 - - + +
250P GLN* 4.0 22.9 - - + -
255P VAL* 5.4 3.6 - - + -
9T LEU* 3.4 39.0 - - + +
10T VAL* 1.3 78.0 - - + +
12T GLY* 1.3 63.6 + - - +
14T VAL* 2.8 37.3 - - + +
15T PHE* 3.3 7.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 12 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9T LEU 3.2 15.6 + - - +
10T VAL 3.1 1.2 - - - -
11T LEU* 1.3 80.3 - - - +
13T LEU* 1.3 62.3 + - - +
15T PHE* 3.5 4.2 + - - +
16T ALA* 3.0 21.4 + - - +
4U ASP* 5.3 8.1 - - - +
8U TRP* 5.4 5.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 13 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259P ILE* 4.0 22.0 - - + -
9T LEU 3.6 6.9 + - - +
10T VAL* 3.1 18.0 + - + +
12T GLY* 1.3 75.5 - - - +
14T VAL* 1.3 50.5 + - - +
16T ALA* 2.6 11.6 + - + +
17T THR* 2.6 41.4 + - - +
8U TRP* 4.0 47.5 - - + +
12U LEU* 4.0 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 14 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57O LEU* 3.1 31.6 - - + +
250P GLN* 6.5 0.2 - - + -
255P VAL* 3.2 34.1 - - + -
258P MET* 3.5 10.1 - - - +
259P ILE* 4.3 0.4 - - - +
10T VAL 2.8 20.0 - - - +
11T LEU* 2.8 24.7 - - + +
13T LEU* 1.3 72.2 - - - +
15T PHE* 1.3 89.5 + - + +
17T THR* 2.7 30.4 + - - -
18T LEU 3.0 4.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 15 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54O LEU* 6.0 1.6 - - + -
57O LEU* 3.3 38.8 - - + -
58O ASP* 5.3 5.2 - - + -
38P GLN* 2.6 46.9 - - + -
39P SER* 4.8 0.2 - - - -
7S TYR* 5.8 5.8 - - - -
11T LEU* 3.3 9.3 + - + -
12T GLY* 4.1 4.5 - - - +
13T LEU 3.2 0.2 - - - -
14T VAL* 1.3 98.7 - - + +
16T ALA* 1.3 52.9 + - - +
17T THR 2.7 6.3 + - - -
18T LEU* 2.6 13.7 + - + +
19T GLY* 2.6 35.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 16 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12T GLY 3.0 14.6 + - - +
13T LEU* 2.6 23.5 + - + +
15T PHE* 1.3 73.2 - - - +
17T THR* 1.3 56.1 + - - +
19T GLY* 5.0 0.9 - - - -
20T GLY* 2.9 26.2 + - - +
4U ASP 4.5 3.4 - - - +
5U VAL* 4.9 4.7 - - - +
8U TRP* 4.2 23.8 - - + -
9U VAL* 4.2 17.1 - - + +
12U LEU* 3.7 11.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 17 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53O ALA* 4.8 0.6 - - - +
258P MET* 3.9 17.3 - - + -
259P ILE* 3.6 20.9 - - + +
262P ILE* 3.9 31.6 - - + +
13T LEU* 2.6 29.3 + - - +
14T VAL* 2.7 16.7 + - - -
15T PHE 2.7 0.8 - - - -
16T ALA* 1.3 79.8 - - - +
18T LEU* 1.3 49.9 + - - -
21T LEU* 2.5 39.6 + - - +
12U LEU* 4.2 10.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 18 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50O CYS* 4.4 23.3 - - + +
53O ALA* 3.9 18.6 - - + -
54O LEU* 3.5 33.4 - - + -
57O LEU* 3.6 28.7 - - + -
14T VAL 3.0 4.4 + - - +
15T PHE* 2.6 22.0 + - + +
17T THR* 1.3 70.3 - - - +
19T GLY* 1.3 67.7 + - - +
21T LEU* 3.0 2.7 + - + +
22T PHE* 3.0 26.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 19 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11S LEU* 6.4 1.6 - - - -
15S LEU* 3.4 19.1 - - - +
15T PHE 2.6 17.2 + - - -
16T ALA* 4.7 0.9 - - - -
18T LEU* 1.3 76.1 - - - +
20T GLY* 1.3 56.2 + - - -
22T PHE* 3.6 6.7 - - - +
26T TYR* 3.0 23.4 + - - -
9U VAL* 4.2 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 20 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266P MET* 4.1 7.4 - - - +
16T ALA 2.9 25.8 + - - -
17T THR* 3.8 1.1 - - - -
19T GLY* 1.3 79.0 - - - +
21T LEU* 1.3 56.2 + - - +
22T PHE 3.4 0.2 - - - -
23T TYR* 3.3 21.2 - - - +
26T TYR* 4.5 1.1 - - - -
9U VAL* 3.7 15.6 - - - +
12U LEU* 5.2 7.6 - - - +
13U VAL* 4.3 13.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 21 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46O GLY 4.5 0.9 - - - +
49O ALA* 3.5 17.0 - - + +
50O CYS* 3.1 51.1 - - - +
53O ALA* 5.1 2.5 - - + -
262P ILE* 3.6 27.8 - - + +
265P VAL* 5.0 2.9 - - + -
266P MET* 4.0 28.0 - - + -
269P GLN* 5.4 0.2 - - - +
17T THR 2.5 23.5 + - - +
18T LEU* 3.0 4.2 + - - +
20T GLY* 1.3 72.3 - - - +
22T PHE* 1.3 54.7 + - - +
23T TYR* 2.6 17.6 + - - -
24T ALA* 3.0 14.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 22 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50O CYS* 4.1 11.7 - - - -
10R VAL* 5.2 7.6 - - + -
1101R BCR 3.5 45.3 - - + -
12S SER* 4.1 19.5 - - - -
15S LEU* 3.9 20.9 - - + -
16S ILE* 3.9 28.5 - - + -
18T LEU* 3.0 14.2 + - + +
19T GLY* 3.6 8.3 - - - +
20T GLY 3.4 0.4 - - - -
21T LEU* 1.3 76.4 - - - +
23T TYR* 1.3 49.4 + - - +
24T ALA* 2.9 2.7 - - - -
25T ALA* 2.9 24.0 + - + +
26T TYR* 2.6 38.3 - + - +
29T TYR* 4.5 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 23 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266P MET* 3.5 48.7 + - + -
269P GLN* 4.3 4.3 - - + -
270P LEU* 4.8 8.0 - - - +
22S LEU* 5.6 2.5 - - + -
20T GLY 3.3 18.6 - - - +
21T LEU 2.6 2.1 - - - +
22T PHE* 1.3 71.2 - - - +
24T ALA* 1.3 70.6 - - - +
25T ALA 3.0 2.2 - - - -
26T TYR* 2.7 54.9 + + + +
27T GLN* 3.3 41.7 + - + -
13U VAL* 5.3 9.4 - - + -
16U THR* 4.2 27.5 + - + -
17U TRP* 5.1 9.9 - + + -
20U ALA* 4.6 9.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 24 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42O VAL* 4.6 1.1 - - - +
46O GLY* 3.3 38.4 - - - +
50O CYS* 5.0 0.4 - - - -
269P GLN* 4.1 19.5 - - - +
1101R BCR 3.7 9.4 - - + -
21T LEU* 3.0 16.8 + - + +
22T PHE* 4.2 2.2 - - - +
23T TYR* 1.3 80.4 - - - +
25T ALA* 1.3 62.7 + - - +
27T GLN* 3.0 16.8 + - - +
28T GLN* 3.0 12.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 25 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1101R BCR 3.6 18.4 - - + -
22T PHE* 2.9 20.1 + - + +
24T ALA* 1.3 80.3 - - - +
26T TYR* 1.3 48.0 + - - +
27T GLN 2.6 12.5 + - - -
28T GLN* 3.0 12.5 - - - +
29T TYR* 2.6 64.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 26 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15S LEU* 3.0 36.3 - - + +
18S VAL* 4.9 4.7 - - + -
19S GLY* 3.5 25.8 - - - +
22S LEU* 3.9 24.0 - - + +
23S GLY* 3.9 10.0 + - - -
26S LEU* 6.0 0.9 - - - +
19T GLY 3.0 12.3 + - - -
20T GLY 4.5 3.8 - - - -
22T PHE* 2.6 32.3 - + + +
23T TYR* 2.7 47.8 + + + +
25T ALA* 1.3 69.3 - - + +
27T GLN* 1.3 64.6 + - - +
29T TYR* 2.9 37.5 - + + +
30T LYS* 3.8 5.4 + - - +
13U VAL* 5.0 10.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 27 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42O VAL* 4.1 20.4 - - + -
269P GLN* 4.7 6.2 - - + +
270P LEU* 4.6 14.0 + - - +
273P ILE* 4.4 30.3 - - + +
26S LEU* 5.7 5.1 - - - +
23T TYR* 3.4 46.0 + - + +
24T ALA* 3.2 15.5 - - - +
25T ALA 2.6 6.1 + - - -
26T TYR* 1.3 81.2 + - - +
28T GLN* 1.3 60.8 + - - +
29T TYR 3.1 0.4 - - - -
30T LYS* 3.1 18.4 + - - +
31T ARG* 2.9 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 28 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32N ILE* 6.1 0.3 - - - +
35N CYS* 5.6 1.6 - - - -
303N HEM 4.4 12.8 - - + -
39O VAL* 4.0 4.5 + - + +
42O VAL* 3.4 28.7 + - - +
43O VAL* 3.2 38.5 - - + +
1101R BCR 3.7 14.3 - - + +
24T ALA 3.0 10.9 + - - +
25T ALA* 3.0 19.9 - - - +
27T GLN* 1.3 70.0 - - - +
29T TYR* 1.3 60.5 + - + +
30T LYS 2.3 8.8 + - - -
31T ARG* 2.2 51.8 + - + +
32T PRO* 3.3 5.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 29 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32N ILE* 6.1 4.7 - - + +
1101R BCR 4.0 28.3 - - + +
16S ILE* 4.0 31.4 - - + +
19S GLY* 3.0 30.5 - - - +
20S TRP* 3.2 19.8 - + + +
23S GLY* 3.7 15.4 - - - -
24S VAL* 4.3 1.7 + - - +
27S LEU* 4.8 2.9 - - - +
22T PHE* 4.5 3.6 - - - -
25T ALA* 2.6 44.5 + - + +
26T TYR* 2.9 45.0 - + - +
28T GLN* 1.3 82.7 - - + +
30T LYS* 1.3 55.3 + - - +
32T PRO* 4.4 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 30 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273P ILE* 4.6 20.6 - - + +
274P LEU* 6.3 0.4 - - - +
277P LYS* 5.4 0.3 + - - -
278P GLN* 4.4 12.8 - - - +
23S GLY* 4.1 9.2 - - - -
26S LEU* 3.3 49.3 - - + +
27S LEU* 3.1 32.1 - - + +
30S GLN* 4.0 19.4 - - - +
26T TYR 4.1 8.5 - - - +
27T GLN* 3.1 18.3 + - - +
28T GLN 2.3 14.4 + - - -
29T TYR* 1.3 71.0 - - - +
31T ARG* 1.3 63.7 + - - +
32T PRO* 2.9 6.9 - - - +
33T ASN* 5.6 0.2 - - - +
20U ALA* 5.8 3.2 - - - +
24U TRP* 6.3 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 31 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31N ASN* 4.5 11.7 - - - +
32N ILE* 3.1 46.4 - - - +
303N HEM 3.2 35.0 - - - +
32O TRP* 4.0 16.5 - - + -
36O LEU* 4.6 18.8 - - - +
39O VAL* 5.2 11.2 - - + -
273P ILE* 6.3 2.5 - - + -
277P LYS* 2.8 41.1 + - + +
27T GLN 2.9 8.0 + - - +
28T GLN* 2.2 45.6 + - + +
30T LYS* 1.3 65.5 - - - +
32T PRO* 1.3 74.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 32 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32N ILE* 5.3 13.2 - - + -
32O TRP* 4.9 4.7 - - + +
27S LEU* 3.3 40.1 - - + +
28T GLN 3.3 8.7 - - - +
29T TYR 4.4 5.2 - - - +
30T LYS* 2.9 5.6 - - - +
31T ARG* 1.3 103.7 - - + +
33T ASN* 1.3 61.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 33 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32O TRP* 3.6 18.8 - - - +
277P LYS* 2.8 35.7 + - - +
278P GLN* 3.4 10.0 - - - +
280P GLU* 3.1 33.0 + - - +
27S LEU* 5.2 1.6 - - + -
30S GLN* 5.3 8.5 - - - +
33S GLU* 4.9 13.9 + - - +
30T LYS 5.6 0.2 - - - +
32T PRO* 1.3 76.6 - - - +
34T GLU* 1.3 82.9 + - + +
35T LEU* 5.5 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 34 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32O TRP* 5.2 0.4 - - - +
280P GLU* 4.1 4.5 - - - +
33S GLU* 5.4 11.2 - - - +
34S LYS* 5.9 1.0 + - - -
33T ASN* 1.3 91.2 - - + +
35T LEU* 1.3 83.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 35 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18O LEU* 2.8 43.2 - - - +
31O ALA* 4.3 10.3 - - - -
32O TRP* 4.5 26.2 - - + +
280P GLU* 3.6 44.9 - - + +
283P GLN* 5.8 3.1 - - + -
284P ALA* 3.8 28.5 - - + +
33T ASN* 4.8 1.6 - - - +
34T GLU* 1.3 88.9 - - + +
----------------------------------------------------------
Back to top of page
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