Contacts of the helix formed by residues 33 - 46 (chain H) in PDB entry 3BID
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 SER 33 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13H TYR* 3.3 16.8 - - - +
31H TYR* 3.8 9.4 - - - +
32H THR* 1.3 82.7 - - - +
34H LYS* 1.3 61.5 + - - +
35H GLN* 3.4 9.1 + - - +
36H ASN* 3.1 31.6 + - - +
37H CYS 3.8 11.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 34 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55G GLU* 3.4 27.6 + - + +
57G LEU* 5.3 5.9 - - - +
5H ILE* 4.6 17.9 - - + +
13H TYR* 3.2 39.2 - - + +
33H SER* 1.3 74.2 - - - +
35H GLN* 1.3 67.2 + - - +
37H CYS* 3.4 2.6 + - - +
38H GLN* 3.2 34.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 35 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H SER* 3.3 9.5 + - - +
34H LYS* 1.3 79.5 - - - +
36H ASN* 1.3 68.9 + - - +
38H GLN* 3.3 16.5 + - - +
39H HIS* 3.2 23.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 36 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H TYR* 4.4 19.0 - - + -
32H THR* 3.6 22.6 - - + +
33H SER* 3.1 24.2 + - - +
35H GLN* 1.3 82.0 - - - +
37H CYS* 1.3 62.5 + - - +
39H HIS* 3.4 7.2 + - - +
40H ALA* 3.2 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 37 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H ILE* 4.1 19.3 - - + -
13H TYR* 4.2 7.9 - - + -
14H ARG* 3.8 31.4 - - - -
15H TRP* 4.1 6.1 - - - -
31H TYR* 3.6 33.1 - - + -
33H SER 3.8 11.1 + - - +
34H LYS* 3.4 8.0 + - - +
35H GLN 3.2 0.6 - - - -
36H ASN* 1.3 80.5 - - - +
38H GLN* 1.3 61.5 + - - +
40H ALA* 3.3 4.3 + - - +
41H VAL* 3.2 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 38 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G VAL* 5.8 4.0 - - + -
55G GLU* 4.9 9.0 - - - +
5H ILE* 3.9 22.3 - - + +
34H LYS* 3.2 26.7 + - - +
35H GLN* 3.7 15.7 + - - +
37H CYS* 1.3 80.1 - - - +
39H HIS* 1.3 62.7 + - - +
41H VAL* 3.4 4.2 + - + +
42H ASP* 3.0 39.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 39 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G ILE* 6.2 0.2 - - + -
35H GLN* 3.2 16.1 + - + +
36H ASN* 3.7 11.4 - - - +
37H CYS 3.2 0.2 - - - -
38H GLN* 1.3 75.0 - - - +
40H ALA* 1.3 64.9 + - - +
42H ASP* 3.3 11.4 + - + +
43H LEU* 3.1 53.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 40 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G ILE* 3.9 23.5 - - + +
26G ALA* 5.5 2.7 - - + -
15H TRP* 5.4 3.6 - - + +
31H TYR* 3.2 31.0 - - + +
36H ASN 3.2 10.1 + - - +
37H CYS 3.5 9.2 - - - +
39H HIS* 1.3 80.6 - - - +
41H VAL* 1.3 62.9 + - + +
43H LEU* 3.3 4.6 + - - +
44H LEU* 3.1 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 41 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G VAL* 4.1 16.8 - - + -
3H PHE* 3.6 40.1 - - + -
5H ILE* 4.2 14.1 - - + -
15H TRP* 3.9 33.9 - - + -
37H CYS 3.2 15.1 + - - +
38H GLN* 3.7 8.3 - - + +
39H HIS 3.3 0.2 - - - -
40H ALA* 1.3 77.6 - - - +
42H ASP* 1.3 61.7 + - - +
44H LEU* 3.3 8.7 + - - +
45H LYS* 3.0 26.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 42 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G VAL* 5.3 2.9 - - - +
38H GLN* 3.0 31.7 + - - +
39H HIS* 3.3 13.1 + - - +
41H VAL* 1.3 76.8 - - - +
43H LEU* 1.3 63.1 + - + +
45H LYS* 3.1 24.8 + - + +
46H SER* 3.1 23.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 43 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G MSE 3.8 24.7 - - - +
17G LEU* 5.0 1.3 - - + -
25G ILE* 3.7 38.1 - - + -
39H HIS* 3.1 48.4 + - + +
40H ALA 3.6 6.3 - - - +
42H ASP* 1.3 74.6 - - + +
44H LEU* 1.3 65.5 + - - +
46H SER* 2.8 25.2 + - - +
47H THR* 3.5 9.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 44 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3G PHE* 4.1 18.4 - - + -
17G LEU* 3.6 24.4 - - + +
25G ILE* 5.9 0.2 - - + -
26G ALA* 4.1 17.0 - - + -
44G LEU* 4.1 31.8 - - + +
47G THR* 5.1 0.6 - - - +
3H PHE* 4.6 14.8 - - + -
15H TRP* 3.9 36.3 - - + +
40H ALA* 3.1 18.1 + - + +
41H VAL* 3.3 11.2 + - - +
43H LEU* 1.3 76.3 - - - +
45H LYS* 1.3 58.1 + - - +
47H THR* 3.0 28.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 45 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47G THR* 3.3 41.0 - - + +
48G THR* 3.5 23.8 - - - +
49G ALA* 3.9 19.7 + - - +
51G THR* 2.7 30.6 + - - -
52G PRO* 4.9 0.2 - - - +
53G VAL* 3.4 15.3 - - + +
3H PHE* 4.3 3.5 - - + -
41H VAL* 3.0 29.7 + - + +
42H ASP* 3.1 32.1 + - - +
44H LEU* 1.3 72.2 - - - +
46H SER* 1.3 59.0 + - - +
47H THR 3.0 7.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 46 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G MSE 3.8 13.3 - - - +
49G ALA* 6.1 2.7 - - - +
42H ASP 3.1 15.8 + - - -
43H LEU* 2.8 24.4 + - - +
45H LYS* 1.3 74.9 - - - +
47H THR* 1.3 62.6 + - - +
48H THR* 4.0 2.1 + - - -
----------------------------------------------------------
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