Contacts of the helix formed by residues 42 - 55 (chain A) in PDB entry 1WY9
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 42 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ASP* 2.6 16.2 + - - +
41A GLU* 1.3 98.1 - - - +
43A LEU* 1.3 64.0 + - - +
44A PRO* 3.2 3.8 - - - -
45A SER* 2.9 15.1 + - - +
46A LYS* 2.8 41.9 + - + +
114A ARG* 5.6 3.3 - - - +
117A ILE* 5.4 6.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PHE* 3.8 11.9 - - + +
32A LEU* 3.5 22.7 - - + -
37A TYR* 3.6 35.9 - - + +
38A SER* 4.8 2.5 - - - +
40A ASP* 3.1 29.9 + - + +
42A ASP* 1.3 76.0 - - - +
44A PRO* 1.3 69.0 - - + +
46A LYS* 3.6 4.2 - - - +
47A LEU* 2.9 56.1 + - + +
111A LEU* 3.9 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 4.2 22.0 - - + -
40A ASP 4.1 5.4 - - - +
41A GLU 4.2 6.1 - - - +
42A ASP* 3.2 6.7 - - - -
43A LEU* 1.3 97.1 - - + +
45A SER* 1.3 62.2 + - - +
47A LEU* 3.6 4.5 + - + +
48A GLU* 3.3 25.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ASP* 2.9 17.4 + - - -
44A PRO* 1.3 76.4 - - - +
46A LYS* 1.3 67.2 + - - +
48A GLU* 3.3 8.2 + - - +
49A ALA* 3.2 21.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
40A ASP* 2.6 32.6 + - - +
42A ASP* 2.8 35.7 + - + +
43A LEU* 3.6 4.3 - - - +
45A SER* 1.3 73.5 - - - +
47A LEU* 1.3 57.8 + - - +
49A ALA* 3.1 4.2 + - - +
50A PHE* 2.8 47.5 + - + -
111A LEU* 4.2 17.1 - - + +
112A GLY 4.2 13.9 + - - +
114A ARG* 4.2 16.4 - - - +
116A ALA* 6.1 0.2 - - - +
117A ILE* 3.7 30.7 - - + +
120A MET* 4.0 23.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ASN* 3.3 32.8 + - + +
31A PHE* 4.3 7.2 - - + -
32A LEU* 3.3 46.7 - - + -
43A LEU* 2.9 42.6 + - + +
44A PRO* 3.8 4.3 - - + +
46A LYS* 1.3 76.9 - - - +
48A GLU* 1.3 61.2 + - - +
50A PHE* 4.5 2.5 - - - +
51A LYS* 3.0 25.5 + - - +
103A TYR* 3.3 5.8 + - - -
107A LEU* 3.9 25.4 - - + -
111A LEU* 4.3 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLU* 4.6 4.0 - - - +
28A ASN* 4.3 4.9 + - - +
44A PRO 3.3 14.8 + - - +
45A SER* 3.7 9.6 - - - +
46A LYS 3.2 0.6 - - - -
47A LEU* 1.3 78.2 - - + +
49A ALA* 1.3 62.7 + - - +
51A LYS* 2.7 39.3 + - - +
52A VAL* 3.2 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A SER 3.2 9.5 + - - +
46A LYS 3.1 7.4 + - - +
48A GLU* 1.3 78.1 - - - +
50A PHE* 1.3 66.0 + - - +
52A VAL* 3.4 9.4 + - - +
53A LYS* 3.2 21.1 + - - +
120A MET* 3.8 19.1 - - + -
123A MET* 4.2 11.1 - - + +
----------------------------------------------------------
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 LYS* 2.8 46.3 + - + +
47A LEU 4.1 1.8 - - - +
49A ALA* 1.3 69.4 - - - +
51A LYS* 1.3 60.6 + - - +
53A LYS* 3.5 2.2 + - - -
54A TYR* 2.9 32.2 + - - +
103A TYR* 4.1 2.0 - - - -
106A PHE* 3.7 21.4 - + + -
107A LEU* 3.8 30.1 - - + -
110A MET* 3.4 46.2 - - + -
111A LEU* 4.1 13.2 - - + -
116A ALA 6.0 0.4 - - - -
120A MET* 3.7 32.8 - - + -
123A MET* 4.1 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLU* 3.8 25.7 + - + +
24A LEU* 3.7 22.8 - - + +
25A GLU* 3.3 42.4 + - + +
28A ASN* 3.9 8.5 - - - +
47A LEU 3.0 18.0 + - - +
48A GLU* 2.7 36.1 + - - +
50A PHE* 1.3 79.3 - - - +
52A VAL* 1.3 67.7 + - - +
54A TYR* 3.4 2.4 + - - +
55A MET* 2.9 34.0 + - + +
103A TYR* 3.5 15.9 + - - +
----------------------------------------------------------
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 GLU* 3.2 16.1 + - + +
49A ALA* 3.6 9.9 - - - +
50A PHE 3.3 0.2 - - - -
51A LYS* 1.3 84.5 - - - +
53A LYS* 1.3 64.0 + - - +
55A MET* 3.2 23.2 - - - +
56A GLU* 3.6 17.8 + - + +
----------------------------------------------------------
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 ALA 3.2 6.9 + - - +
50A PHE* 3.8 4.0 - - - +
51A LYS 3.3 0.2 - - - -
52A VAL* 1.3 77.9 - - - +
54A TYR* 1.3 61.0 - - - +
56A GLU* 2.8 56.8 + - - +
57A PHE* 3.9 35.4 + - + -
106A PHE* 4.4 9.0 - - + -
122A LEU 5.6 0.6 + - - -
123A MET* 3.6 52.4 + - + +
125A GLU* 5.5 3.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 4.1 13.9 - - + -
50A PHE 2.9 18.5 + - - +
51A LYS 3.7 3.8 - - - +
53A LYS* 1.3 76.6 - - - +
55A MET* 1.3 57.8 + - - +
56A GLU 3.0 4.9 + - - -
57A PHE* 3.1 31.7 + + - +
59A LEU* 3.7 22.2 - - + +
63A GLY 3.1 27.8 + - - -
64A ASP* 3.3 7.8 - - - -
65A ILE* 3.4 21.1 + - + -
101A PHE 3.1 18.4 + - - -
102A SER 4.0 5.4 - - - -
103A TYR* 3.3 49.5 + + + -
106A PHE* 3.8 25.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LYS 4.1 17.7 - - - +
20A GLN* 4.3 11.0 - - - -
21A GLU* 3.7 45.1 - - + +
24A LEU* 3.7 20.6 - - + -
51A LYS* 2.9 26.4 + - + +
52A VAL* 3.2 15.3 - - - +
53A LYS 3.1 0.4 - - - -
54A TYR* 1.3 75.9 - - - +
56A GLU* 1.3 59.3 + - + +
57A PHE 3.4 4.9 + - - +
59A LEU* 4.9 8.9 - - - +
----------------------------------------------------------
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