Contacts of the helix formed by residues 28 - 46 (chain A) in PDB entry 2AR0
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 28 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A VAL* 4.0 10.8 - - + -
25A SER* 3.2 23.9 + - - +
27A GLN* 1.3 101.7 + - - +
29A TYR* 1.3 63.7 + - - +
30A VAL 3.4 2.5 - - - -
31A ASN* 3.2 20.8 + - + +
32A GLU* 3.0 30.3 + - - +
98A THR* 3.9 27.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A TRP* 5.7 0.2 - - - -
16A CYS* 3.4 29.6 - - + -
19A LEU* 3.6 19.5 - - + +
20A ARG* 2.9 51.8 + - - +
24A VAL* 3.7 11.4 + - + -
25A SER 2.9 23.8 - - - -
26A TYR* 3.5 47.6 - + - +
27A GLN 3.5 1.8 - - - -
28A ASN* 1.3 78.5 - - - +
30A VAL* 1.3 67.5 + - + +
32A GLU* 3.1 2.9 + - - +
33A LEU* 3.0 27.3 + - - +
502A LEU* 5.8 0.2 - - + -
506A MSE 3.2 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A TYR 6.1 0.4 - - - +
27A GLN 5.0 2.8 + - - +
28A ASN 3.4 0.2 - - - -
29A TYR* 1.3 77.7 - - + +
31A ASN* 1.3 60.1 + - - +
33A LEU* 3.2 9.6 + - - +
34A ALA* 2.7 38.7 + - + +
499A LEU* 3.8 29.6 - - + +
502A LEU* 4.4 12.6 - - + +
503A ASP* 3.5 53.6 - - + +
506A MSE 5.9 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLN 4.3 6.7 + - - +
28A ASN* 3.2 29.9 + - + +
30A VAL* 1.3 87.1 - - - +
32A GLU* 1.3 64.7 + - + +
34A ALA* 3.5 6.0 + - - +
35A SER* 3.1 26.9 + - - -
95A VAL* 5.6 4.1 - - + +
503A ASP* 4.6 5.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 3.5 19.3 - - + -
24A VAL* 3.6 21.8 - - + -
28A ASN* 3.0 22.1 + - - +
29A TYR 3.4 5.8 - - - +
31A ASN* 1.3 79.6 - - - +
33A LEU* 1.3 63.9 + - - +
35A SER* 3.6 5.1 + - - -
36A LEU* 3.5 28.2 + - + +
73A TYR* 4.0 7.3 + - - -
96A SER 3.8 5.1 - - - +
97A THR* 2.7 34.4 + - - -
98A THR* 2.9 32.0 + - - +
99A ILE* 4.0 6.8 - - - +
108A LEU* 5.6 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 3.9 15.9 - - + +
15A LEU* 4.1 17.7 - - + -
16A CYS* 3.5 26.0 - - - -
19A LEU* 4.0 15.0 - - + -
29A TYR 3.0 16.7 + - - +
30A VAL 3.6 5.2 - - - +
32A GLU* 1.3 76.4 - - - +
34A ALA* 1.3 55.9 + - - +
35A SER 3.3 0.2 + - - -
36A LEU* 3.3 2.4 + - - +
37A LEU* 2.8 43.9 + - + +
108A LEU* 4.4 4.7 - - + -
112A MSE 3.6 27.6 - - + -
499A LEU* 4.2 14.6 - - + -
502A LEU* 4.0 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A VAL* 2.7 25.5 + - + +
31A ASN* 3.8 7.0 - - - +
32A GLU 3.4 0.2 - - - -
33A LEU* 1.3 72.8 - - - +
35A SER* 1.3 56.7 + - - +
37A LEU* 3.4 2.2 + - - +
38A PHE* 2.9 32.4 + - - +
492A MSE 5.8 0.5 - - - +
499A LEU* 4.2 20.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ASN 3.1 13.8 + - - -
32A GLU* 3.7 5.2 - - - -
33A LEU 3.2 0.2 - - - -
34A ALA* 1.3 81.1 - - - +
36A LEU* 1.3 63.5 + - - +
38A PHE* 3.1 10.0 + - - +
39A LEU* 3.2 20.3 + - - +
73A TYR* 3.6 21.3 + - - -
77A LEU* 4.9 3.3 - - - +
91A VAL* 6.3 0.9 - - - -
92A PHE* 4.0 22.8 - - - -
95A VAL* 4.1 20.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A GLU* 3.5 16.6 + - + +
33A LEU* 3.3 4.6 + - - +
35A SER* 1.3 80.7 - - - +
37A LEU* 1.3 63.7 + - - +
38A PHE 3.3 0.2 + - - -
39A LEU* 3.3 3.3 + - + -
40A LYS* 3.0 18.7 + - - +
58A TRP* 3.4 12.9 - - + -
61A LEU* 3.8 21.1 - - + -
73A TYR* 3.6 35.9 - - + +
99A ILE* 5.7 2.7 - - + -
105A ILE* 6.0 2.2 - - + -
108A LEU* 3.9 29.2 - - + -
109A VAL* 4.5 16.2 - - + -
112A MSE 3.5 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 4.1 22.4 - - + -
15A LEU* 5.5 0.2 - - + -
33A LEU* 2.8 27.0 + - + +
34A ALA* 3.8 4.0 - - - +
36A LEU* 1.3 72.2 - - - +
38A PHE* 1.3 53.2 + - - +
40A LYS* 3.5 4.6 - - + +
41A MSE 2.8 52.4 + - + +
112A MSE 3.9 23.8 - - + -
115A LEU* 4.5 25.1 - - + -
492A MSE 5.4 3.1 - - + -
495A LEU* 4.7 18.4 - - + -
499A LEU* 3.9 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ALA 2.9 18.4 + - - +
35A SER* 3.1 6.3 + - - +
37A LEU* 1.3 75.9 - - - +
39A LEU* 1.3 60.4 + - + +
41A MSE 3.2 3.4 + - + +
42A CYS* 2.9 55.9 + - - -
51A TYR* 5.4 7.4 - + + -
52A LEU* 4.5 4.5 - - + -
88A VAL* 4.3 18.2 - - + -
91A VAL* 4.8 22.9 - - + -
92A PHE* 3.8 30.5 - + + -
492A MSE 3.2 36.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A SER 3.2 16.9 + - - +
36A LEU* 3.7 7.0 - - - +
38A PHE* 1.3 76.9 - - + +
40A LYS* 1.3 62.4 + - - +
42A CYS* 3.3 4.7 + - - +
43A LYS 3.3 15.8 + - - -
48A GLU* 5.0 0.2 - - - +
52A LEU* 3.9 36.0 - - + +
56A TYR 5.2 1.8 - - - +
58A TRP* 3.7 28.2 - - + +
61A LEU* 4.1 17.5 - - + -
73A TYR* 4.7 8.3 - - + -
76A MSE 4.0 26.7 - - + -
77A LEU* 5.9 1.1 - - + -
80A LEU* 4.1 10.8 - - + -
92A PHE* 4.0 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU 3.0 16.9 + - - +
37A LEU* 3.5 9.4 - - + +
39A LEU* 1.3 77.6 - - - +
41A MSE 1.3 76.2 + - + +
43A LYS* 3.3 4.4 + - + +
44A GLU* 3.1 53.7 + - - +
58A TRP* 3.4 44.4 - - + +
112A MSE 2.8 31.0 + - - +
113A ASP* 3.1 22.8 + - - -
115A LEU* 3.3 19.6 + - + +
117A TRP* 5.9 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 2.8 27.8 + - + +
38A PHE* 3.6 6.5 - - + +
40A LYS* 1.3 103.8 - - + +
42A CYS* 1.3 65.7 + - - +
44A GLU* 3.1 5.9 + - + +
45A THR* 2.9 25.7 + - - -
115A LEU* 4.6 14.1 - - + -
117A TRP* 3.9 32.8 - - + -
488A ALA* 4.3 17.3 - - + +
491A ALA* 4.7 1.6 - - - -
492A MSE 4.0 23.3 - - + -
495A LEU* 3.8 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A PHE* 2.9 59.1 + - - -
39A LEU 3.6 7.6 - - - +
40A LYS 3.3 0.2 - - - -
41A MSE 1.3 76.0 - - - +
43A LYS* 1.3 63.6 + - - +
45A THR* 3.3 19.7 - - - +
48A GLU* 3.4 21.1 + - + +
51A TYR* 4.3 23.1 - - + -
52A LEU* 3.9 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU 3.3 3.2 + - - -
40A LYS* 3.5 8.1 - - + +
41A MSE 3.1 0.4 - - - -
42A CYS* 1.3 80.1 - - - +
44A GLU* 1.3 66.0 + - - +
45A THR 2.9 0.2 - - - -
46A GLY* 2.7 29.5 + - - -
48A GLU* 3.3 33.8 + - - +
58A TRP* 3.5 33.7 - - + +
59A ASP* 3.8 24.7 + - - +
62A LYS* 4.8 10.1 - - - +
113A ASP* 5.1 3.8 + - - -
318A PHE* 5.6 8.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LYS* 3.1 42.9 + - - +
41A MSE 3.1 10.5 + - + +
43A LYS* 1.3 86.9 + - - +
45A THR* 1.3 62.6 + - - +
46A GLY* 3.2 1.1 + - - -
117A TRP* 3.3 42.9 - - + -
484A PRO* 3.9 15.2 - - - +
488A ALA* 4.0 8.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A MSE 2.9 10.4 + - - -
42A CYS* 3.3 12.0 - - - +
43A LYS 2.9 0.4 + - - -
44A GLU* 1.3 77.1 - - - +
46A GLY* 1.3 56.4 + - - +
47A GLN* 3.1 36.0 + - + +
51A TYR* 3.4 35.7 + - + +
484A PRO* 3.7 3.8 - - - +
485A ASP* 3.2 29.2 + - + +
488A ALA* 3.6 19.4 - - - +
489A ALA 5.0 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LYS 2.7 21.7 + - - -
44A GLU 3.2 1.5 - - - -
45A THR* 1.3 72.0 - - - +
47A GLN* 1.3 69.9 + - - +
48A GLU* 3.8 2.0 - - - -
484A PRO* 5.1 4.9 - - - -
----------------------------------------------------------
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