Contacts of the helix formed by residues 6 - 29 (chain P) in PDB entry 3FKS
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 VAL 6 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1P ALA* 3.6 30.7 - - + -
2P THR 3.5 16.2 - - - +
3P LEU 4.5 2.9 - - - +
4P LYS 2.9 1.2 - - - -
5P GLU* 1.3 83.1 - - + +
7P GLU* 1.3 58.2 + - - +
8P MET 3.5 0.2 - - - -
9P ARG* 4.2 3.3 - - - +
10P LEU* 2.9 30.6 + - - +
251P TYR* 4.4 11.1 - - + +
254P LEU* 4.0 16.4 - - + -
255P TYR* 3.6 42.2 - - + +
258P THR* 4.6 8.7 - - + +
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Residues in contact with GLU 7 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335J ASP* 6.1 0.7 - - - +
4P LYS* 2.9 49.4 + - + +
6P VAL* 1.3 77.9 - - - +
8P MET* 1.3 59.6 + - - +
10P LEU* 3.5 9.7 - - + +
11P LYS* 2.9 51.8 + - - +
255P TYR* 3.7 34.7 + - + -
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Residues in contact with MET 8 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357J GLU* 6.1 1.3 - - - +
386M ASP* 4.0 11.4 - - - +
4P LYS* 3.0 43.6 + - + +
5P GLU* 5.1 3.6 - - - -
7P GLU* 1.3 76.4 - - - +
9P ARG* 1.3 58.2 + - - +
11P LYS* 4.1 10.5 - - - +
12P SER* 3.2 24.3 + - - -
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Residues in contact with ARG 9 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386M ASP* 5.4 2.7 - - - -
390M ILE* 5.8 6.9 - - - +
386O ASP* 4.1 28.9 + - - +
5P GLU 3.3 22.5 + - - +
6P VAL* 4.2 3.1 - - - +
7P GLU 3.3 0.2 - - - -
8P MET* 1.3 76.0 - - - +
10P LEU* 1.3 63.0 + - - +
12P SER* 3.3 33.4 + - - -
13P ILE* 3.2 35.6 - - - +
16P ILE* 5.5 4.8 - - - +
247P MET* 5.3 4.9 - - - -
251P TYR* 3.6 32.8 + - + +
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Residues in contact with LEU 10 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6P VAL* 2.9 23.3 + - + +
7P GLU* 3.5 13.0 - - + +
8P MET 3.3 0.2 - - - -
9P ARG* 1.3 74.0 - - - +
11P LYS* 1.3 63.1 + - + +
12P SER 3.0 1.3 - - - -
13P ILE* 2.9 25.3 + - + +
14P LYS* 3.0 38.2 + - - +
248P ILE* 4.1 22.0 - - + +
251P TYR* 4.4 10.1 - - + +
252P SER* 4.2 21.1 - - - +
255P TYR* 4.5 23.6 - - + -
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Residues in contact with LYS 11 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4P LYS* 5.5 3.2 - - - +
7P GLU* 2.9 44.9 + - - +
8P MET* 4.3 11.2 - - - +
10P LEU* 1.3 72.9 - - + +
12P SER* 1.3 64.3 + - - +
14P LYS* 3.1 19.7 - - + +
15P ASN* 3.1 32.2 + - - +
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Residues in contact with SER 12 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386M ASP* 3.0 42.0 + - - +
387M ILE* 6.0 0.2 - - - +
8P MET 3.2 15.9 + - - -
9P ARG* 3.3 31.6 + - - -
10P LEU 3.0 0.2 - - - -
11P LYS* 1.3 79.1 - - - +
13P ILE* 1.3 61.4 + - - +
15P ASN* 3.4 8.0 + - - +
16P ILE* 3.3 26.2 + - - +
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Residues in contact with ILE 13 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390O ILE* 5.5 2.2 - - + -
9P ARG* 3.2 30.3 - - - +
10P LEU* 2.9 7.5 + - - +
12P SER* 1.3 72.8 - - - +
14P LYS* 1.3 65.6 + - - +
16P ILE* 3.4 10.7 + - + +
17P GLU* 3.2 18.4 + - - +
244P ALA* 3.9 12.1 - - + +
247P MET* 3.5 26.9 - - + +
248P ILE* 3.3 27.5 - - + +
251P TYR* 3.4 49.1 - - + -
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Residues in contact with LYS 14 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10P LEU* 3.0 36.6 + - + +
11P LYS* 3.1 22.9 - - + +
12P SER 3.1 0.2 - - - -
13P ILE* 1.3 79.1 - - - +
15P ASN* 1.3 67.0 + - - +
17P GLU* 3.3 4.7 + - - +
18P LYS* 3.3 22.4 + - - +
248P ILE* 3.5 36.6 - - + +
252P SER* 5.3 4.6 + - - -
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Residues in contact with ASN 15 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383M SER 4.7 4.8 + - - -
387M ILE* 4.0 31.9 - - + +
11P LYS* 3.1 21.4 + - - +
12P SER* 3.8 8.7 + - - +
13P ILE 3.4 0.2 - - - -
14P LYS* 1.3 78.4 - - - +
16P ILE* 1.3 55.1 + - - +
18P LYS* 3.0 8.8 + - - +
19P ILE* 2.8 43.4 + - + +
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Residues in contact with ILE 16 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386M ASP 4.1 11.7 - - - +
387M ILE* 5.6 4.3 - - + -
390M ILE* 3.6 41.1 - - + -
391M LEU* 6.4 1.3 - - + -
390O ILE* 3.9 30.5 - - + -
9P ARG* 5.5 4.3 - - - +
12P SER* 3.3 19.0 + - - +
13P ILE* 3.7 12.6 - - + +
14P LYS 3.2 0.8 - - - -
15P ASN* 1.3 78.1 - - + +
17P GLU* 1.3 52.2 + - - +
19P ILE* 4.0 10.8 - - + -
20P THR* 2.6 49.9 + - + +
244P ALA* 4.2 11.9 - - + -
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Residues in contact with GLU 17 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13P ILE 3.2 13.1 + - - +
14P LYS* 3.9 8.2 - - - +
15P ASN 3.3 0.2 - - - -
16P ILE* 1.3 76.2 - - - +
18P LYS* 1.3 62.7 + - - +
20P THR* 3.0 13.7 + - - -
21P LYS* 3.2 20.7 + - - +
241P SER* 3.2 29.6 - - - +
244P ALA* 4.3 9.6 - - + -
245P GLY* 3.7 23.5 - - - +
248P ILE* 4.5 11.9 - - + +
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Residues in contact with LYS 18 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401J GLU 5.8 5.6 - - - +
404J ALA* 5.5 4.9 - - + -
14P LYS 3.3 11.4 + - - +
15P ASN* 3.0 11.0 + - - +
17P GLU* 1.3 80.3 + - - +
19P ILE* 1.3 57.3 + - + +
20P THR 3.0 4.5 - - - -
21P LYS* 2.8 19.1 + - + +
22P THR* 2.7 40.7 + - - +
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Residues in contact with ILE 19 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404J ALA* 4.4 17.3 - - + -
387M ILE* 5.0 16.2 - - + -
391M LEU* 3.7 34.3 - - + -
15P ASN* 2.8 32.4 + - + +
16P ILE* 3.8 11.0 - - + +
18P LYS* 1.3 76.2 - - + +
20P THR* 1.3 74.0 + - + +
22P THR* 3.5 11.4 - - + +
23P MET* 3.0 37.0 + - + +
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Residues in contact with THR 20 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391M LEU* 5.7 3.4 - - + -
390O ILE* 5.7 0.4 - - + -
391O LEU* 6.0 3.1 - - + -
16P ILE* 2.6 36.1 + - + +
17P GLU 3.0 11.8 + - - -
19P ILE* 1.3 90.3 - - + +
21P LYS* 1.3 62.8 + - - +
22P THR 3.0 1.6 - - - -
23P MET* 3.2 8.0 + - - +
24P LYS* 3.0 21.8 + - - +
237P MET* 3.9 22.2 - - + +
240P ALA* 4.0 18.3 - - + -
241P SER* 3.2 24.5 - - - -
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Residues in contact with LYS 21 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386N ASP* 4.1 23.3 - - - -
17P GLU* 3.2 17.0 + - - +
18P LYS* 2.8 17.9 + - + +
20P THR* 1.3 81.2 + - - +
22P THR* 1.3 58.8 + - - +
24P LYS* 3.5 22.7 + - - +
25P ILE* 3.2 25.6 - - + +
241P SER* 3.8 12.1 - - - +
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Residues in contact with THR 22 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404J ALA* 3.4 40.4 - - + +
405J PHE* 4.3 19.4 - - + -
18P LYS* 2.7 16.7 + - - +
19P ILE* 3.5 15.0 - - + +
21P LYS* 1.3 74.5 - - - +
23P MET* 1.3 60.3 + - + +
24P LYS 3.0 5.0 + - - -
25P ILE* 3.2 3.8 + - - +
26P VAL* 2.9 50.5 + - + +
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Residues in contact with MET 23 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391M LEU* 5.3 4.3 - - - -
395M GLU* 3.6 29.8 - - - +
19P ILE* 3.0 29.6 + - + +
20P THR* 3.2 4.4 + - - +
22P THR* 1.3 79.4 - - + +
24P LYS* 1.3 58.4 + - - +
25P ILE 3.6 0.2 - - - -
26P VAL* 4.4 13.0 - - + -
27P ALA* 3.3 21.8 - - - +
30P ARG* 6.4 0.2 - - - +
81P LYS* 4.1 14.1 - - - +
83P LEU* 5.0 2.7 - - + -
233P ARG* 4.2 22.6 - - - +
237P MET* 3.5 43.8 - - + +
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Residues in contact with LYS 24 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386N ASP* 3.8 19.2 + - - -
20P THR 3.0 9.9 + - - +
21P LYS* 3.6 23.0 - - - +
22P THR 3.0 1.0 - - - -
23P MET* 1.3 78.9 - - - +
25P ILE* 1.3 80.3 + - - +
27P ALA* 3.8 4.1 - - - +
28P SER* 3.4 23.0 + - - -
234P ARG* 3.8 23.3 - - + +
237P MET* 4.4 3.6 - - - -
238P ASP* 3.2 43.9 + - + +
241P SER* 4.9 2.8 + - - +
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Residues in contact with ILE 25 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405J PHE* 4.0 24.0 - - + -
386N ASP* 3.5 50.3 - - + +
387N ILE* 6.3 0.4 - - + -
390N ILE* 3.5 32.0 - - + +
21P LYS* 3.2 20.6 - - + +
22P THR 3.2 5.1 + - - +
24P LYS* 1.3 86.7 - - - +
26P VAL* 1.3 61.5 + - - +
27P ALA 2.8 4.7 - - - -
28P SER* 2.8 24.0 + - - +
29P THR* 2.9 12.2 + - - -
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Residues in contact with VAL 26 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404J ALA 5.5 0.2 - - - +
405J PHE* 3.8 26.7 - - + -
410J SER 5.1 5.6 - - - +
411J ASP* 3.3 37.8 - - + +
22P THR* 2.9 42.8 + - + +
23P MET* 4.4 11.0 - - + -
25P ILE* 1.3 72.0 - - - +
27P ALA* 1.3 56.5 + - - +
29P THR* 3.0 21.9 - - - +
30P ARG* 4.1 8.0 + - - +
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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
----------------------------------------------------------
23P MET* 3.3 22.5 + - - +
24P LYS 3.8 2.0 - - - +
25P ILE 2.8 1.4 + - - -
26P VAL* 1.3 77.1 - - - +
28P SER* 1.3 55.8 + - - +
29P THR 3.0 4.0 - - - -
30P ARG* 2.9 31.0 + - - +
31P LEU* 4.4 0.3 - - - -
230P ILE* 3.9 18.1 - - + +
233P ARG* 4.7 10.8 - - + +
234P ARG* 3.8 32.3 - - + +
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Residues in contact with SER 28 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387N ILE* 5.2 13.4 - - - +
390N ILE* 4.7 2.9 - - - +
391N LEU* 4.2 16.0 - - - +
24P LYS 3.4 9.6 + - - -
25P ILE* 2.8 12.0 + - - -
27P ALA* 1.3 70.0 - - - +
29P THR* 1.3 60.1 + - - +
30P ARG 3.1 1.8 - - - -
31P LEU* 3.1 36.7 - - - +
32P SER 4.7 0.2 + - - -
234P ARG* 3.1 34.3 - - - +
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Residues in contact with THR 29 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411J ASP* 4.3 18.4 - - + +
412J LEU 5.2 2.3 + - - -
413J ASP* 4.6 12.4 - - - +
390N ILE* 3.9 27.4 - - - +
391N LEU* 6.0 0.5 - - - +
25P ILE* 2.9 11.1 + - - -
26P VAL* 3.0 33.0 - - - +
27P ALA 3.0 0.6 - - - -
28P SER* 1.3 79.2 - - - +
30P ARG* 1.3 71.6 + - + +
31P LEU 3.3 1.9 + - - -
32P SER 5.1 0.3 + - - -
33P LYS* 4.0 12.0 + - - +
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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