Contacts of the helix formed by residues 33 - 54 (chain A) in PDB entry 6ACQ
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 LYS 33 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ASP* 3.2 2.4 + - - +
32A ILE* 1.3 91.2 - - + +
34A ASP* 1.3 67.6 + - - +
35A GLU* 4.0 24.3 + - + +
36A PHE* 3.1 47.2 + - + +
37A VAL* 3.1 15.8 + - - +
73A VAL* 3.6 9.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LYS* 1.3 71.3 - - - +
35A GLU* 1.3 68.1 + - - +
37A VAL* 3.0 6.8 + - - +
38A ASP* 2.9 39.9 + - - +
72A THR* 5.6 1.4 - - - -
73A VAL* 3.8 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LYS* 4.0 23.3 + - + +
34A ASP* 1.3 81.2 - - - +
36A PHE* 1.3 86.0 + - + +
38A ASP* 3.8 4.9 - - - +
39A ARG* 3.1 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ALA* 3.2 12.6 - - + +
31A ASP* 3.7 33.4 - - - +
32A ILE* 3.9 19.7 - - + -
33A LYS* 3.1 35.5 + - + +
35A GLU* 1.3 103.7 - - + +
37A VAL* 1.3 66.7 + - - +
39A ARG* 3.7 15.4 + - - +
40A GLY 3.2 15.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ALA* 4.0 6.3 - - + -
29A LEU* 4.0 11.6 - - + +
31A ASP* 3.6 18.8 - - + +
33A LYS 3.1 16.6 - - - +
34A ASP* 3.0 11.1 + - - +
36A PHE* 1.3 76.5 - - - +
38A ASP* 1.3 62.5 + - - +
40A GLY* 3.3 1.9 + - - -
41A LEU* 2.9 37.7 + - + +
71A GLY* 3.6 31.4 - - - -
72A THR 3.5 25.8 - - - +
73A VAL* 4.5 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASP* 2.9 31.8 + - - +
35A GLU* 3.8 4.7 + - - +
37A VAL* 1.3 77.7 - - - +
39A ARG* 1.3 56.9 + - - +
41A LEU* 3.0 16.6 + - - +
42A ASP* 2.7 48.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ALA 5.1 4.7 + - - +
10A GLY* 5.1 13.5 - - - -
11A THR* 5.1 6.9 + - - -
35A GLU* 3.1 24.5 + - - +
36A PHE* 3.7 16.5 - - - +
38A ASP* 1.3 78.8 - - - +
40A GLY* 1.3 57.5 + - - +
42A ASP* 3.4 10.7 + - - +
43A PHE* 2.9 28.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ALA* 3.3 27.8 - - - -
14A SER* 3.6 8.9 - - - -
29A LEU* 4.8 1.8 - - - -
36A PHE 3.2 9.4 + - - -
37A VAL 3.7 2.9 - - - -
38A ASP 3.2 0.8 - - - -
39A ARG* 1.3 77.2 - - - +
41A LEU* 1.3 64.7 + - - +
43A PHE* 3.4 5.3 + - - +
44A ILE* 3.1 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 4.2 11.9 - - + -
37A VAL* 2.9 31.5 + - + +
38A ASP* 3.0 19.3 + - - +
40A GLY* 1.3 74.6 - - - +
42A ASP* 1.3 61.0 + - - +
44A ILE* 3.3 9.8 + - + +
45A ASN* 3.0 27.0 + - - +
66A LEU* 4.8 12.3 - - + +
69A ILE* 3.7 34.5 - - + +
71A GLY* 4.7 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ASP* 2.7 33.3 + - - +
39A ARG* 3.5 9.2 + - - +
41A LEU* 1.3 70.9 - - - +
43A PHE* 1.3 66.3 + - - +
45A ASN* 2.9 9.0 + - - +
46A LYS* 2.9 29.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLY 5.2 0.7 - - - -
11A THR* 4.0 39.9 - - + -
14A SER* 3.8 19.7 - - - +
15A GLY* 4.7 7.0 - - - -
39A ARG* 2.9 18.6 + - + +
40A GLY* 3.5 7.2 - - - +
41A LEU 3.3 0.2 - - - -
42A ASP* 1.3 76.2 - - - +
44A ILE* 1.3 64.4 + - + +
46A LYS* 3.5 7.9 + - + +
47A ASN* 3.1 54.9 + - - +
142A PRO* 6.5 0.4 - - + -
144A PRO* 6.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A SER* 3.5 39.5 - - - +
17A ALA* 4.3 11.0 - - + -
18A GLN* 3.5 28.0 - - + +
29A LEU* 4.5 8.1 - - + -
40A GLY 3.1 19.6 + - - +
41A LEU* 3.7 12.3 - - + +
42A ASP 3.2 0.2 - - - -
43A PHE* 1.3 75.4 - - + +
45A ASN* 1.3 66.9 + - - +
47A ASN* 3.4 2.5 + - - +
48A LEU* 3.1 37.3 + - + +
66A LEU* 4.3 11.2 - - + -
69A ILE* 4.5 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU 3.0 13.8 + - - +
42A ASP* 2.9 12.5 + - - +
44A ILE* 1.3 78.4 - - - +
46A LYS* 1.3 59.0 + - + +
48A LEU* 3.1 5.4 + - - +
49A SER* 2.8 33.7 + - - -
62A LYS* 3.2 21.9 + - - +
66A LEU* 2.9 40.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ASP* 2.9 16.3 + - + +
43A PHE* 3.7 11.0 - - + +
45A ASN* 1.3 78.4 - - + +
47A ASN* 1.3 64.3 + - - +
49A SER* 3.0 11.8 + - - +
50A LYS* 2.9 37.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLN* 3.2 33.2 + - - +
43A PHE* 3.1 52.1 + - - +
44A ILE 3.7 1.1 - - - +
45A ASN 3.3 0.2 - - - -
46A LYS* 1.3 77.0 - - - +
48A LEU* 1.3 61.5 + - - +
50A LYS* 3.4 21.8 + - - +
51A LEU* 3.2 27.2 + - + +
144A PRO* 4.8 7.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLN* 3.8 26.5 - - + +
22A ALA* 5.6 1.6 - - + -
44A ILE* 3.1 29.4 + - + +
45A ASN 3.1 3.3 + - - +
47A ASN* 1.3 74.6 - - - +
49A SER* 1.3 63.3 + - - +
51A LEU* 3.5 14.9 + - + -
52A VAL* 3.3 21.5 + - - +
57A ILE* 3.7 12.2 - - + +
62A LYS* 3.9 24.3 - - + +
65A ILE* 3.6 42.0 - - + -
66A LEU* 4.0 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ASN* 2.8 13.9 + - - -
46A LYS* 3.3 17.8 - - - +
48A LEU* 1.3 75.6 - - - +
50A LYS* 1.3 65.1 + - - +
52A VAL* 3.0 12.7 - - - +
53A LYS* 2.9 25.0 + - - +
62A LYS* 2.7 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LYS* 2.9 26.5 + - - +
47A ASN* 3.6 24.7 + - - +
48A LEU 3.4 0.2 - - - -
49A SER* 1.3 75.9 - - - +
51A LEU* 1.3 62.4 + - + +
53A LYS* 3.4 10.9 + - + +
54A LYS* 3.1 46.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLN* 4.5 9.6 - - - +
47A ASN* 3.2 16.8 + - + +
48A LEU* 3.8 24.2 - - + +
49A SER 3.1 0.8 - - - -
50A LYS* 1.3 80.1 - - + +
52A VAL* 1.3 61.9 + - - +
54A LYS* 3.7 7.7 - - + +
55A GLY 3.4 1.4 + - - -
56A LYS* 2.8 47.7 + - + +
57A ILE* 3.3 27.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU 3.3 10.3 + - - +
49A SER* 3.0 23.3 - - - +
51A LEU* 1.3 76.6 - - - +
53A LYS* 1.3 61.8 + - - +
55A GLY* 2.9 18.9 + - - -
57A ILE* 2.8 34.0 - - + +
58A GLU 3.3 5.6 - - - +
59A GLU* 3.3 50.5 - - + +
62A LYS* 4.5 4.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A SER 2.9 17.3 + - - +
50A LYS* 3.6 11.2 - - + +
52A VAL* 1.3 79.6 - - - +
54A LYS* 1.3 58.8 + - + +
55A GLY 3.4 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LYS* 3.1 30.6 + - + +
51A LEU* 3.7 9.0 - - + +
52A VAL 3.2 0.2 - - - -
53A LYS* 1.3 77.9 - - + +
55A GLY* 1.3 58.4 + - - +
56A LYS* 2.8 13.3 + - + +
----------------------------------------------------------
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