Contacts of the helix formed by residues 5 - 21 (chain W) in PDB entry 5FLX
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 ASN 5 (chain W).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6831 G 5.5 1.0 + - - -
11581 G 3.9 24.1 + - - +
4W MET* 1.3 78.6 - - + +
6W VAL* 1.3 64.7 + - - +
7W LEU* 3.0 5.0 + - - +
8W ALA* 3.0 37.2 + - + +
9W ASP 3.1 8.0 + - - -
74W VAL* 3.6 20.0 - - - +
76W SER* 3.9 24.9 + - - +
78W ARG* 4.6 14.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 6 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6841 G 4.1 19.1 - - - +
6851 A 3.9 12.8 - - - +
3W ARG* 4.1 26.5 - - + -
4W MET* 4.3 4.5 - - - -
5W ASN* 1.3 76.2 - - - +
7W LEU* 1.3 59.7 - - - +
9W ASP* 3.2 9.8 + - - +
10W ALA* 2.9 28.2 + - - +
29W PRO* 3.6 25.9 - - + +
31W SER* 3.5 25.6 - - - +
34W ILE* 3.7 10.8 - - + +
78W ARG* 5.9 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 7 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5W ASN* 3.0 6.4 + - - +
6W VAL* 1.3 82.4 - - + +
8W ALA* 1.3 56.7 + - - +
10W ALA* 3.1 4.0 + - + +
11W LEU* 2.9 39.5 + - + +
33W VAL* 4.5 7.0 - - + -
34W ILE* 3.8 30.3 - - + +
37W PHE* 4.1 33.2 - - + -
74W VAL* 3.7 22.2 - - + -
78W ARG* 4.7 10.0 - - - +
126W LEU* 4.0 38.8 - - + +
127W GLY* 5.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 8 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11581 G 4.3 20.6 - - - +
5W ASN* 3.0 32.6 + - - +
7W LEU* 1.3 71.5 - - - +
9W ASP* 1.3 60.2 + - - +
11W LEU* 4.4 1.3 - - - +
12W LYS* 2.9 44.5 + - - +
74W VAL* 3.6 24.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 9 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10931 A 3.1 41.8 + - - +
3W ARG* 3.5 17.9 + - - +
4W MET 5.2 3.1 - - - +
5W ASN 3.1 7.0 + - - +
6W VAL* 3.2 19.5 + - + +
8W ALA* 1.3 76.4 - - - +
10W ALA* 1.3 60.6 + - - +
12W LYS* 4.3 7.4 - - - +
13W SER* 3.4 20.3 + - - -
28W ARG* 4.2 4.5 - - - +
29W PRO* 3.2 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 10 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6W VAL 2.9 12.6 + - - +
7W LEU* 3.1 8.7 + - + +
9W ASP* 1.3 76.3 + - - +
11W LEU* 1.3 65.0 + - + +
12W LYS 3.2 0.2 - - - -
13W SER* 3.0 9.2 + - - -
14W ILE* 2.9 29.0 + - - +
27W ILE* 3.6 41.6 - - + +
34W ILE* 4.5 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 11 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7W LEU* 2.9 23.0 + - + +
8W ALA* 4.3 2.2 - - - +
10W ALA* 1.3 75.5 - - + +
12W LYS* 1.3 61.4 + - + +
14W ILE* 3.7 22.2 - - + -
15W ASN* 2.9 27.9 + - - +
37W PHE* 3.4 45.3 - - + -
38W LEU* 5.2 4.3 - - + -
41W MET* 5.0 4.5 - - + -
72W CYS* 3.4 26.0 - - + +
73W GLY* 4.1 13.5 - - - +
74W VAL* 3.5 28.0 - - + -
128W PHE 5.4 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 12 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10921 G 4.7 4.1 - - - +
10931 A 4.6 24.4 - - + +
10941 C 5.4 0.9 - - - -
11521 U 5.1 9.2 - - + +
11531 C 6.1 0.9 - - - -
11581 G 3.0 72.6 + - - -
8W ALA* 2.9 26.9 + - - +
9W ASP* 4.3 6.3 - - - +
11W LEU* 1.3 76.8 - - + +
13W SER* 1.3 59.1 + - - +
15W ASN* 3.8 4.8 - - - +
16W ASN* 2.8 41.8 + - - +
72W CYS 5.8 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 13 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10931 A 3.9 3.3 + - - -
10941 C 3.4 38.3 + - - -
9W ASP 3.4 12.7 + - - -
10W ALA* 3.0 10.8 + - - -
12W LYS* 1.3 76.3 - - - +
14W ILE* 1.3 64.7 + - - +
16W ASN* 3.9 0.9 - - - +
17W ALA* 2.9 26.0 + - - +
25W VAL* 3.9 17.3 - - - +
26W LEU 4.3 9.6 + - - -
27W ILE* 4.9 1.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 14 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10W ALA 2.9 20.5 + - - +
11W LEU* 3.7 24.7 - - + +
12W LYS 3.3 0.2 - - - -
13W SER* 1.3 76.2 - - - +
15W ASN* 1.3 56.1 + - - +
17W ALA* 3.3 3.1 + - - +
18W GLU* 2.9 34.3 + - + +
25W VAL* 3.6 33.2 - - + +
27W ILE* 3.8 17.5 - - + -
38W LEU* 5.6 4.5 - - + -
41W MET* 5.7 1.3 - - + -
47W ILE* 5.5 2.7 - - + -
63W VAL* 4.5 15.7 - - + -
65W LEU* 4.6 7.9 - - + -
69W LEU* 3.9 27.8 - - + -
72W CYS* 4.1 9.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 15 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11521 U 4.3 12.9 + - - +
11531 C 4.7 1.4 + - - -
11W LEU 2.9 19.1 + - - +
12W LYS* 3.8 6.7 - - - +
13W SER 3.2 0.2 - - - -
14W ILE* 1.3 74.1 - - - +
16W ASN* 1.3 61.0 + - - +
18W GLU* 2.9 22.4 + - - +
19W LYS* 2.9 35.8 + - - +
70W ASN 4.4 6.9 - - - +
71W LYS* 3.2 39.9 - - - +
72W CYS* 3.7 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 16 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10941 C 3.0 43.8 + - - +
10951 C 3.6 16.6 + - - +
11511 G 4.1 4.8 - - - +
11521 U 2.9 46.4 + - - +
12W LYS* 2.8 24.1 + - - +
13W SER 4.1 0.2 - - - +
15W ASN* 1.3 76.7 - - - +
17W ALA* 1.3 57.5 + - - +
19W LYS* 4.1 8.9 - - - +
20W ARG* 2.9 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 17 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10941 C 5.1 0.4 + - - -
10951 C 5.7 1.8 - - - -
13W SER 2.9 20.0 + - - +
14W ILE 3.5 2.2 - - - +
15W ASN 3.1 0.2 - - - -
16W ASN* 1.3 76.5 - - - +
18W GLU* 1.3 55.7 + - - +
20W ARG* 4.3 4.7 - - - -
21W GLY* 2.6 28.8 + - - -
22W LYS* 3.1 29.6 + - + +
25W VAL* 3.5 28.3 - - + -
65W LEU* 4.0 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 18 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14W ILE 2.9 19.3 + - - +
15W ASN* 2.9 13.7 + - - +
17W ALA* 1.3 76.9 - - - +
19W LYS* 1.3 63.5 + - + +
21W GLY* 3.3 12.2 + - - -
65W LEU* 3.2 40.1 - - - +
66W THR 5.4 0.2 + - - -
67W GLY* 3.8 22.5 + - - +
69W LEU* 3.4 49.5 + - + +
70W ASN 5.4 2.5 - - - +
72W CYS* 5.7 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 19 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11391 C 5.2 1.7 - - - +
11401 G 4.3 17.6 + - - +
11521 U 3.0 49.9 + - - +
11531 C 4.1 6.1 + - - -
11551 U 5.3 6.3 - - - -
62V MET* 5.4 4.7 - - - +
15W ASN* 2.9 35.0 + - - +
16W ASN* 4.1 8.3 - - - +
18W GLU* 1.3 75.8 - - + +
20W ARG* 1.3 61.8 + - - +
70W ASN 5.2 8.1 - - - +
71W LYS* 5.5 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 20 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10951 C 3.5 25.8 + - - +
10961 G 2.4 50.7 + - - +
11391 C 3.7 29.4 + - - -
32A PHE* 5.6 5.5 - - - -
62V MET* 3.4 52.5 + - - +
16W ASN 2.9 21.2 + - - +
17W ALA* 4.0 4.9 - - - +
19W LYS* 1.3 77.5 - - - +
21W GLY* 1.3 59.6 + - - +
22W LYS* 4.0 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 21 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20V SER* 4.8 16.3 + - - -
59V ILE* 5.2 9.2 - - - +
62V MET* 5.4 2.7 - - - -
17W ALA 2.6 16.2 + - - -
18W GLU* 3.3 11.3 + - - -
19W LYS 4.6 0.2 - - - -
20W ARG* 1.3 76.1 - - - +
22W LYS* 1.3 63.6 + - - +
23W ARG* 3.9 0.3 + - - -
4b ALA 4.9 5.5 + - - -
----------------------------------------------------------
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