Contacts of the helix formed by residues 46 - 56 (chain A) in PDB entry 1WYN
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 THR 46 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 4.8 3.3 - - - +
41A GLY 3.7 7.0 + - - -
42A LEU 4.4 0.4 + - - -
44A ASP* 2.8 28.5 + - + +
45A GLY* 1.3 76.3 - - - +
47A ILE* 1.3 77.5 + - - +
49A CYS* 3.7 13.2 - - - +
50A THR* 3.8 7.3 + - - +
63A ILE* 3.8 15.7 - - + +
64A ASN 4.9 4.9 - - - +
65A ARG* 4.2 26.9 - - + -
75A ASN* 4.9 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ILE* 3.7 30.3 - - + -
27A GLU* 5.7 0.9 - - - -
30A THR* 3.7 17.7 - - + +
32A LEU* 3.8 20.4 - - + -
33A SER 3.1 31.6 - - - +
34A ILE* 3.4 30.1 - - + -
41A GLY 4.5 8.0 + - - +
42A LEU* 4.8 6.7 - - + +
46A THR* 1.3 82.8 + - - +
48A LEU* 1.3 55.4 + - - +
49A CYS 2.5 18.2 + - - -
50A THR* 2.7 23.7 + - - +
51A LEU 2.8 6.4 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
26A ILE* 5.1 2.0 - - + -
42A LEU* 4.0 27.3 - - + +
45A GLY* 4.6 7.0 - - - -
46A THR 4.4 0.4 - - - +
47A ILE* 1.3 78.1 - - - +
49A CYS* 1.3 63.0 + - - +
51A LEU* 3.6 18.4 - - + +
76A LEU* 3.3 33.9 - - + -
79A PHE* 3.3 39.0 - - + -
94A PHE* 4.0 12.6 - - + -
99A LEU* 3.4 21.8 - - + -
108A VAL* 5.1 2.0 - - + -
112A LEU* 3.9 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A GLY* 3.3 22.0 - - - -
46A THR 3.7 4.9 + - - +
47A ILE 2.5 4.9 + - - -
48A LEU* 1.3 74.3 - - - +
50A THR* 1.3 67.0 + - - +
52A MET* 3.0 16.5 + - - +
53A ASN* 3.3 15.3 + - - -
60A VAL* 4.1 20.9 - - + +
62A LYS 5.4 0.2 - - - -
63A ILE* 3.3 30.7 - - + -
75A ASN* 3.6 33.9 - - - -
78A ASN* 5.1 0.2 - - - -
79A PHE* 4.5 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A THR* 3.2 21.0 - - - +
32A LEU* 3.3 24.0 - - + +
46A THR 4.1 2.2 - - - +
47A ILE* 2.7 23.4 + - - -
49A CYS* 1.3 75.9 - - - +
51A LEU* 1.3 63.0 + - - -
53A ASN* 2.9 23.6 + - - +
54A LYS* 3.0 26.3 + - - +
63A ILE* 3.4 21.5 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
25A TRP* 4.0 15.5 - - + -
26A ILE* 3.5 48.9 - - + -
29A LEU* 3.3 35.7 - - + -
30A THR* 3.1 9.8 - - - +
47A ILE 2.8 9.7 + - - +
48A LEU* 3.6 17.3 - - + +
50A THR* 1.3 78.5 + - - +
52A MET* 1.3 65.1 + - - +
54A LYS* 3.3 16.1 - - - +
55A LEU* 3.5 8.1 + - + +
79A PHE* 4.6 2.5 - - + -
112A LEU* 4.3 14.6 - - + -
115A LEU* 4.3 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU 3.7 0.8 + - - -
49A CYS 3.0 10.9 + - - +
51A LEU* 1.3 75.1 - - - +
53A ASN* 1.3 58.7 + - - +
54A LYS 3.0 1.8 - - - -
55A LEU* 2.7 32.1 + - + +
56A GLN* 2.8 28.9 + - + +
59A SER* 3.2 22.2 + - - +
60A VAL* 4.8 2.5 - - + -
79A PHE* 3.6 30.3 - - + -
82A ALA* 4.0 12.6 - - + +
83A MET* 4.4 7.6 - - - -
86A TYR* 3.2 51.8 - - + -
115A LEU* 4.0 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A CYS 3.3 11.7 + - - -
50A THR* 2.9 17.1 + - + +
52A MET* 1.3 77.6 - - - +
54A LYS* 1.3 73.4 + - - +
56A GLN 2.6 21.1 - - - +
57A PRO* 3.8 8.8 - - - +
58A GLY* 5.2 0.2 - - - -
59A SER* 3.1 18.1 + - - -
60A VAL* 3.2 41.9 + - - +
63A ILE* 4.5 7.5 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
29A LEU* 3.7 34.1 - - + +
30A THR* 3.8 32.3 - - + +
50A THR* 3.0 32.4 + - - +
51A LEU 3.3 9.0 - - - +
52A MET 3.0 0.6 - - - -
53A ASN* 1.3 88.1 - - - +
55A LEU* 1.3 63.6 + - - +
56A GLN 4.9 0.2 - - - -
57A PRO* 5.2 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A TRP* 4.5 5.8 - - + +
29A LEU* 4.1 29.2 - - + -
51A LEU* 3.6 14.4 - - + +
52A MET* 2.7 17.4 + - + +
54A LYS* 1.3 75.1 - - - +
56A GLN* 1.3 57.7 + - - +
57A PRO* 3.9 6.2 - - - +
86A TYR* 3.7 18.6 - - + +
115A LEU* 4.0 33.0 - - + -
119A ALA* 3.5 34.1 - - + +
122A LYS* 3.4 26.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A MET* 2.8 22.7 + - + +
53A ASN* 2.6 20.8 - - - +
55A LEU* 1.3 74.3 - - - +
57A PRO* 1.3 65.9 - - + +
58A GLY* 2.9 37.8 + - - +
59A SER* 3.0 30.6 + - - +
82A ALA* 4.1 12.3 + - - +
85A SER* 3.8 22.9 + - - -
86A TYR* 4.4 12.9 - - + +
122A LYS* 5.4 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