Contacts of the helix formed by residues 17 - 33 (chain H) 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 ASP 17 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H LYS 3.2 5.8 + - - +
16H PRO* 1.3 74.6 - - - +
18H GLU* 1.3 69.6 + - + +
19H PHE* 3.1 31.2 - - - -
20H GLU* 3.1 34.2 + - - +
21H SER* 3.2 20.6 + - - -
48H ALA 4.8 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 18 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H ASP* 1.3 81.9 - - + +
19H PHE* 1.3 61.5 + - + +
21H SER* 3.3 4.5 + - - -
22H GLY* 2.9 23.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 19 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H ASP* 3.1 29.8 - - - -
18H GLU* 1.3 78.3 - - + +
20H GLU* 1.3 68.8 + - + +
22H GLY* 3.6 3.3 - - - +
23H ILE* 2.9 35.2 + - + +
48H ALA* 3.7 24.5 - - + -
49H LYS* 4.2 9.0 - - + -
50H GLU* 4.4 14.6 - - + +
60H ILE* 3.9 29.4 - - + -
87H PHE* 4.2 24.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 20 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H LYS 4.3 2.1 - - - +
16H PRO* 3.3 30.1 - - + +
17H ASP* 3.1 25.1 + - - +
19H PHE* 1.3 81.9 - - + +
21H SER* 1.3 57.2 + - - +
23H ILE* 3.4 8.4 + - - +
24H SER* 2.9 27.8 + - - -
45H ILE* 6.6 0.4 - - + -
46H THR 4.7 2.5 - - - +
47H ALA* 3.3 18.5 - - - +
48H ALA* 2.5 54.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 21 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H PRO* 5.0 9.9 - - - +
17H ASP 3.2 15.8 + - - -
18H GLU* 3.7 4.0 - - - -
20H GLU* 1.3 78.1 - - - +
22H GLY* 1.3 57.3 + - - +
24H SER* 3.6 7.8 - - - -
25H GLN* 2.9 35.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 22 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H GLU 2.9 14.5 + - - -
19H PHE* 3.2 5.6 + - - -
20H GLU 3.2 0.6 - - - -
21H SER* 1.3 75.6 - - - +
23H ILE* 1.3 60.0 + - - +
25H GLN* 3.2 19.5 + - - +
26H ALA* 2.9 27.7 + - - +
87H PHE* 5.9 8.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 23 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H PHE* 2.9 24.7 + - + +
20H GLU* 3.9 5.8 - - - +
22H GLY* 1.3 73.5 - - - +
24H SER* 1.3 59.8 + - - +
26H ALA* 3.2 7.2 + - - +
27H LEU* 2.9 35.4 + - + +
45H ILE* 4.9 8.5 - - + -
48H ALA* 5.2 2.0 - - + -
60H ILE* 4.0 31.9 - - + -
62H ILE* 4.6 18.2 - - + -
83H LEU* 4.3 23.6 - - + -
87H PHE* 4.1 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 24 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H GLU 2.9 18.0 + - - -
21H SER* 3.6 10.1 - - - -
22H GLY 3.2 0.2 - - - -
23H ILE* 1.3 76.5 - - - +
25H GLN* 1.3 57.3 + - - +
27H LEU* 2.9 28.8 + - - +
28H LEU* 2.9 27.0 + - - +
45H ILE* 5.5 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 25 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H SER* 2.9 30.0 + - - +
22H GLY* 3.2 19.3 + - - +
24H SER* 1.3 73.1 + - - +
26H ALA* 1.3 56.7 + - - +
28H LEU* 3.3 18.1 + - + +
29H GLU* 2.9 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 26 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H GLY 2.9 18.6 + - - +
23H ILE* 3.3 13.2 - - + +
24H SER 3.1 0.2 - - - -
25H GLN* 1.3 77.7 - - - +
27H LEU* 1.3 57.3 + - - +
29H GLU* 3.1 13.5 + - - +
30H LEU* 2.9 34.8 + - + +
83H LEU* 5.2 8.1 - - + -
86H LYS* 4.9 18.6 - - + +
87H PHE* 5.5 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 27 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23H ILE* 2.9 20.0 + - + +
24H SER* 2.9 11.7 + - - +
26H ALA* 1.3 73.8 - - - +
28H LEU* 1.3 67.4 + - + +
30H LEU* 3.3 13.6 + - + +
31H GLU* 3.3 20.1 + - - +
40H LEU* 3.5 27.7 - - + +
43H LEU* 3.3 22.9 - - + -
45H ILE* 3.2 35.4 - - + -
79H LEU* 4.6 10.3 - - + -
83H LEU* 4.0 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 28 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H SER* 2.9 37.8 + - - +
25H GLN* 3.5 16.6 - - + +
26H ALA 3.2 0.2 - - - -
27H LEU* 1.3 78.5 - - + +
29H GLU* 1.3 61.4 + - - +
31H GLU* 3.4 36.0 + - - +
32H MET* 4.1 9.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 29 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H GLN 2.9 13.1 + - - +
26H ALA* 3.1 15.1 + - - +
28H LEU* 1.3 73.7 - - - +
30H LEU* 1.3 61.3 + - + +
31H GLU 3.0 6.4 + - - -
32H MET* 3.2 41.2 - - + +
33H ASN* 4.0 3.1 + - - +
86H LYS* 4.6 28.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 30 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26H ALA* 2.9 20.3 + - + +
27H LEU* 3.3 28.0 + - + +
29H GLU* 1.3 77.1 - - + +
31H GLU* 1.3 60.3 + - - +
32H MET 3.4 0.4 - - - -
33H ASN 3.3 12.1 - - - +
34H SER* 3.2 24.3 - - - -
40H LEU* 3.3 16.1 - - + +
79H LEU* 4.7 9.9 - - + -
82H GLU* 3.9 42.4 - - + +
83H LEU* 4.5 11.4 - - + -
86H LYS* 4.4 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 31 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H LEU* 3.3 18.3 - - - +
28H LEU* 3.4 26.6 - - - +
29H GLU 3.0 1.0 - - - -
30H LEU* 1.3 79.1 - - - +
32H MET* 1.3 65.8 + - - +
34H SER* 3.9 9.8 + - - -
37H LYS* 5.2 10.9 - - + +
40H LEU* 2.9 44.0 - - + +
41H ARG* 4.7 2.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 32 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H LEU 4.1 6.6 + - - +
29H GLU* 3.2 43.2 + - + +
31H GLU* 1.3 81.8 - - - +
33H ASN* 1.3 71.0 + - + +
34H SER 3.9 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 33 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29H GLU 4.0 1.8 + - - +
30H LEU* 3.3 17.9 - - - +
32H MET* 1.3 84.3 - - + +
34H SER* 1.3 64.0 + - - +
35H ASP* 5.0 6.1 - - - +
172z A 4.4 14.6 + - - -
----------------------------------------------------------
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