Contacts of the helix formed by residues 55 - 72 (chain A) in PDB entry 4XZC
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 55 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A THR* 1.3 90.3 + - - +
56A ASP* 1.3 60.3 + - - +
57A ARG* 3.0 46.3 - - - +
58A GLU* 3.2 28.1 + - - +
59A LYS* 3.2 13.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A THR 3.9 7.6 - - - +
55A ASP* 1.3 75.0 - - - +
57A ARG* 1.3 62.3 + - - +
59A LYS* 3.5 21.5 + - - +
60A ASP* 2.9 36.9 + - - +
441A GLY 4.8 1.9 - - - +
442A PHE* 4.1 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ASP* 3.0 38.0 + - - +
56A ASP* 1.3 79.3 - - - +
58A GLU* 1.3 62.7 + - - +
60A ASP* 3.5 10.4 + - - +
61A SER* 3.2 21.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LYS* 4.5 5.5 + - - +
52A LEU 4.4 3.6 - - - +
53A ALA* 3.3 30.7 - - + +
54A THR* 3.6 15.4 + - - -
55A ASP* 3.2 23.9 + - - +
57A ARG* 1.3 77.9 - - - +
59A LYS* 1.3 55.5 + - - +
61A SER* 3.3 7.7 + - - -
62A ILE* 3.0 45.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A MET* 3.4 29.4 + - - +
53A ALA* 3.7 28.1 + - + -
54A THR 3.4 23.0 + - - -
55A ASP 3.2 12.3 + - - +
56A ASP* 3.6 20.3 + - - +
57A ARG 3.2 0.4 - - - -
58A GLU* 1.3 73.2 - - - +
60A ASP* 1.3 64.6 + - - +
62A ILE* 3.3 2.6 + - - -
63A TYR* 3.1 20.1 + - - +
440A ALA 4.7 3.2 + - - -
441A GLY* 3.1 39.9 + - - +
442A PHE* 4.0 11.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ASP* 2.9 28.4 + - - +
57A ARG* 3.8 10.5 - - - +
58A GLU 3.2 0.2 - - - -
59A LYS* 1.3 76.7 - - - +
61A SER* 1.3 58.7 + - - +
63A TYR* 3.4 6.7 + - - +
64A ALA* 3.0 29.9 + - - +
442A PHE* 3.4 23.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ARG 3.2 11.7 + - - -
58A GLU* 3.4 11.7 - - - -
60A ASP* 1.3 79.9 - - - +
62A ILE* 1.3 56.9 + - - +
64A ALA* 3.4 6.9 + - - +
65A CYS* 3.0 36.6 + - - -
339A PRO* 4.2 18.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PHE* 3.8 35.1 - - + +
49A LYS* 3.7 45.3 - - + +
50A MET* 3.8 22.9 - - + +
53A ALA* 3.9 16.8 - - + -
58A GLU* 3.0 31.1 + - + +
59A LYS* 3.5 6.5 - - - +
60A ASP 3.3 0.2 - - - -
61A SER* 1.3 74.7 - - - +
63A TYR* 1.3 65.3 + - - +
65A CYS* 3.1 9.6 + - - +
66A ALA* 3.1 20.3 + - - +
437A ILE* 4.7 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A MET* 4.0 10.9 - - + +
59A LYS 3.1 13.9 + - - +
60A ASP* 3.8 6.5 - - - +
62A ILE* 1.3 76.7 - - - +
64A ALA* 1.3 69.5 + - - +
66A ALA* 3.1 4.7 + - + +
67A MET* 3.0 52.4 + - + +
434A LEU* 4.0 28.1 - - + +
437A ILE* 4.4 15.5 - - + -
438A GLN* 3.7 38.4 + - + -
442A PHE* 4.9 6.5 - + + -
451A ALA* 3.1 24.2 - - + +
452A SER* 4.4 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ASP 3.0 17.9 + - - +
61A SER* 3.6 7.2 - - - +
62A ILE 3.3 0.2 - - - -
63A TYR* 1.3 80.0 - - + +
65A CYS* 1.3 61.8 + - - +
67A MET* 3.3 7.5 + - - +
68A VAL* 3.1 29.5 + - + +
339A PRO* 4.3 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PHE* 3.7 18.2 - - + -
61A SER* 3.0 25.5 + - - -
62A ILE* 3.1 10.3 + - - +
64A ALA* 1.3 73.4 - - - +
66A ALA* 1.3 61.2 + - - +
68A VAL* 3.4 8.9 + - - +
69A GLU* 3.0 32.4 + - + +
339A PRO* 3.6 31.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU* 3.5 6.1 - - + +
46A PHE* 3.5 34.3 - - + -
62A ILE 3.1 9.2 + - - +
63A TYR* 3.1 10.3 + - - +
65A CYS* 1.3 74.9 - - - +
67A MET* 1.3 60.3 + - - +
69A GLU 3.3 0.3 + - - -
70A ALA* 3.0 30.0 + - - +
434A LEU* 4.2 8.3 - - + -
437A ILE* 3.6 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A TYR* 3.0 51.1 + - + +
64A ALA* 3.7 7.6 - - - +
66A ALA* 1.3 79.6 - - - +
68A VAL* 1.3 60.7 + - + +
70A ALA* 3.4 1.5 + - - +
71A THR* 2.8 35.2 + - - +
409A GLY 5.6 2.5 - - - +
410A HIS 5.2 0.2 - - - -
411A SER* 3.7 41.5 - - - +
414A LEU* 5.2 0.2 - - - -
434A LEU* 3.8 30.2 - - + +
451A ALA* 5.1 2.5 - - + -
455A LEU* 4.6 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ALA 3.1 17.5 + - - +
65A CYS* 3.7 9.6 - - - +
66A ALA 3.3 0.2 - - - -
67A MET* 1.3 77.2 - - + +
69A GLU* 1.3 66.7 + - - +
71A THR* 4.2 3.1 - - - -
72A LYS* 2.8 48.0 + - + +
336A GLY* 3.5 25.6 - - - +
337A GLN 4.5 2.5 - - - -
338A GLY* 4.1 34.1 - - - +
339A PRO* 5.2 1.1 - - + -
409A GLY* 4.2 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PRO* 3.5 17.8 - - + +
43A LEU* 3.8 14.8 - - + -
46A PHE* 3.7 19.5 - - + -
65A CYS* 3.0 18.8 + - + +
66A ALA 3.3 4.4 + - - +
68A VAL* 1.3 81.6 - - - +
70A ALA* 1.3 63.4 + - - +
71A THR 3.4 0.5 + - - -
72A LYS* 3.9 33.7 + - - +
73A PHE* 5.2 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PRO* 4.0 5.5 - - - +
43A LEU* 3.7 9.4 - - + +
66A ALA 3.0 16.7 + - - +
67A MET* 3.8 7.9 - - - +
68A VAL 3.3 0.2 - - - -
69A GLU* 1.3 77.5 - - - +
71A THR* 1.3 64.5 + - + +
73A PHE 5.2 0.6 + - - -
74A CYS* 3.8 0.7 + - - +
414A LEU* 4.6 3.8 - - + -
417A TYR* 2.7 33.1 + - - -
430A GLU* 3.4 24.9 - - - +
434A LEU* 4.6 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A MET* 2.8 24.3 + - - +
70A ALA* 1.3 87.9 - - + +
72A LYS* 1.3 65.2 + - - +
73A PHE 3.1 4.4 + - - -
74A CYS* 3.4 15.5 + - - -
75A ALA* 4.2 2.1 + - - +
408A SER 3.7 7.6 - - - +
409A GLY* 3.2 4.5 - - - -
410A HIS 3.2 39.1 + - - +
411A SER* 3.9 9.9 - - - +
413A SER* 4.0 9.0 + - - -
414A LEU* 3.8 28.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PHE* 5.5 1.7 - - - -
68A VAL* 2.8 31.8 + - + +
69A GLU* 3.9 30.9 + - - +
70A ALA 3.8 0.6 - - - -
71A THR* 1.3 76.9 + - - +
73A PHE* 1.3 86.6 + - + +
74A CYS 4.0 0.3 + - - -
75A ALA* 5.2 2.4 + - - +
336A GLY 5.1 0.9 - - - +
337A GLN* 5.0 11.6 + - - +
406A LEU 3.8 16.6 - - - -
407A GLY* 3.3 13.3 - - - -
408A SER* 3.2 39.7 + - - +
----------------------------------------------------------
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