Contacts of the helix formed by residues 37 - 55 (chain A) in PDB entry 5YHN
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 37 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A CYS* 3.2 44.0 - - - +
21A THR 3.9 3.4 + - - -
23A GLU 5.0 0.2 + - - -
24A SER* 2.6 37.0 + - - -
33A ARG 2.8 16.5 - - - +
34A MET* 2.5 21.4 + - - +
36A GLY* 1.3 82.8 - - - +
38A LYS* 1.3 63.7 + - - +
39A CYS* 3.0 3.6 - - - -
40A ALA* 2.9 12.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A GLU* 5.8 4.7 - - - +
5A PHE* 3.6 46.6 - - + -
9A TYR* 3.6 26.0 - - + +
20A CYS* 4.5 0.2 - - - +
23A GLU 4.3 4.3 - - - +
24A SER* 4.2 0.2 - - - -
25A ASP* 3.0 52.1 + - - +
27A VAL* 4.7 8.3 - - - +
33A ARG 3.8 5.4 - - - -
34A MET* 3.3 10.0 - - + +
37A ASN* 1.3 77.5 - - - +
39A CYS* 1.3 57.5 + - - +
41A LEU* 2.8 56.5 + - + +
42A CYS* 3.1 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A TYR* 4.4 1.9 - - - -
18A LEU* 3.3 25.6 - - + +
19A PHE* 6.4 0.2 - - - -
20A CYS* 2.0 65.7 - - - +
37A ASN* 3.3 8.7 - - - -
38A LYS* 1.3 79.1 - - - +
40A ALA* 1.3 62.5 + - - +
42A CYS 3.2 0.3 + - - -
43A ALA* 2.6 39.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ASP* 3.3 34.9 - - + +
33A ARG 3.6 5.8 - - - +
35A HIS 5.6 0.2 - - - +
36A GLY* 5.0 6.1 - - - +
37A ASN 2.9 19.9 + - - +
39A CYS* 1.3 84.2 - - - +
41A LEU* 1.3 57.6 + - - +
43A ALA* 3.7 5.7 - - - +
44A GLU* 2.7 29.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
2A GLU* 3.9 24.5 - - + +
5A PHE* 5.5 0.9 - - + -
6A CYS* 4.5 7.6 - - + -
9A TYR* 6.3 0.2 - - + -
33A ARG* 2.8 68.7 + - + +
38A LYS* 2.8 40.1 + - + +
40A ALA* 1.3 74.9 - - - +
42A CYS* 1.3 74.9 + - + +
44A GLU* 3.1 20.5 - - - +
45A ILE* 3.1 23.2 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
6A CYS* 2.0 65.1 - - + -
9A TYR* 4.0 4.7 - - + -
10A GLU* 4.7 0.4 - - - -
18A LEU* 3.1 40.4 - - + -
38A LYS 3.1 6.3 + - - +
39A CYS* 3.8 0.4 - - - +
41A LEU* 1.3 84.5 - - + +
43A ALA* 1.3 57.5 + - - +
45A ILE* 2.9 21.3 + - - +
46A PHE* 3.0 22.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 3.3 18.3 - - + +
39A CYS 2.6 23.5 + - - +
40A ALA* 3.9 5.6 - - - +
42A CYS* 1.3 73.5 - - - +
44A GLU* 1.3 51.4 + - - +
46A PHE* 3.0 5.1 + - - +
47A LYS* 2.6 62.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
30A PRO* 3.3 47.1 - - + +
31A ASP* 3.7 16.6 - - + +
40A ALA 2.7 20.2 + - - +
41A LEU* 3.1 12.8 - - - +
43A ALA* 1.3 76.4 - - - +
45A ILE* 1.3 74.5 + - - +
47A LYS* 3.7 10.2 - - + +
48A ARG* 3.0 46.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LYS* 5.6 17.9 - - + -
6A CYS* 4.8 10.1 - - + -
33A ARG* 5.6 5.8 - - - +
41A LEU* 3.1 24.4 + - + +
42A CYS* 2.9 13.3 + - - +
44A GLU* 1.3 91.9 - - - +
46A PHE* 1.3 52.7 + - + +
48A ARG* 4.0 2.4 - - + +
49A ARG* 2.6 56.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A CYS* 4.4 2.0 - - - -
10A GLU* 3.2 39.0 - - + -
13A VAL* 5.0 8.5 - - + -
16A GLY 6.2 0.2 - - - -
18A LEU* 3.5 25.6 - - + -
42A CYS* 3.0 31.8 + - - -
43A ALA* 3.0 8.7 + - - +
45A ILE* 1.3 77.5 - - + +
47A LYS* 1.3 59.2 + - - +
49A ARG* 4.3 2.9 - - + -
50A PHE* 2.6 66.1 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ASP* 5.0 11.4 - - - -
43A ALA* 2.6 53.5 + - - +
44A GLU* 3.7 10.1 - - + +
46A PHE* 1.3 74.8 - - - +
48A ARG* 1.3 54.4 + - + +
50A PHE* 5.0 0.9 - - - -
51A SER* 2.5 44.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A GLU* 3.0 37.0 + - - +
45A ILE* 4.0 2.7 - - - +
47A LYS* 1.3 77.4 - - + +
49A ARG* 1.3 60.6 + - - +
51A SER* 4.9 7.9 - - - -
52A GLU* 2.9 72.5 + - - +
56A LYS* 5.7 5.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ILE* 2.6 37.6 + - + +
46A PHE* 4.2 3.6 - - + +
48A ARG* 1.3 72.2 + - - +
50A PHE* 1.3 53.7 + - + +
52A GLU* 3.8 26.1 + - - +
53A GLU* 2.6 71.8 + - + +
57A THR* 5.2 9.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PHE* 2.6 48.4 + + + +
47A LYS* 5.0 0.9 - - - -
49A ARG* 1.3 74.6 - - + +
51A SER* 1.3 53.0 + - - +
53A GLU* 4.5 9.4 - - + -
54A ASN* 2.6 66.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LYS* 2.5 29.2 + - - +
48A ARG* 4.2 11.0 - - - -
50A PHE* 1.3 76.2 - - - +
52A GLU* 1.3 52.4 + - - +
54A ASN* 4.7 1.3 - - - -
55A SER* 2.5 41.6 + - - +
56A LYS* 3.7 13.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ARG* 2.9 55.6 + - - +
49A ARG* 3.8 16.9 + - - +
51A SER* 1.3 73.8 - - - +
53A GLU* 1.3 53.4 + - - +
55A SER 2.4 23.2 - - - +
56A LYS* 4.8 12.9 - - + +
57A THR* 2.5 39.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ARG* 2.6 46.6 + - + +
50A PHE* 4.3 10.3 - - + +
52A GLU* 1.3 72.6 - - - +
54A ASN* 1.3 67.1 + - - +
55A SER 3.3 0.2 + - - -
57A THR* 3.9 6.1 - - + +
58A ASP* 2.5 66.4 - - - +
61A LEU* 5.5 6.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A PHE* 2.6 53.1 + - + +
51A SER* 4.5 1.6 - - - +
53A GLU* 1.3 81.9 + - - +
55A SER* 1.3 56.3 + - - +
58A ASP* 5.0 0.7 - - - -
60A ASN 2.5 36.4 - - - +
61A LEU* 3.9 20.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A SER* 2.5 24.5 + - - +
52A GLU 2.4 21.5 - - - +
53A GLU 3.1 0.4 - - - -
54A ASN* 1.3 81.6 + - - +
56A LYS* 1.3 82.7 + - - +
57A THR 3.3 0.7 - - - +
60A ASN* 4.1 19.0 + - - +
63A LYS* 6.2 0.2 - - - +
----------------------------------------------------------
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