Contacts of the strand formed by residues 40 - 48 (chain A) in PDB entry 1YCY
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 VAL 40 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PHE* 3.4 0.2 - - - -
37A ASP* 2.8 48.2 + - - +
39A GLU* 1.3 89.6 - - + +
41A ILE* 1.3 67.4 + - - +
58A LEU* 3.7 28.3 - - + -
59A ILE 3.1 15.7 - - - +
60A GLY* 3.9 8.3 - - - +
61A LEU* 4.3 2.0 - - - -
6C LEU* 4.1 15.5 - - + -
7C LEU* 4.1 28.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 4.7 9.6 - - + -
19A VAL* 5.5 0.7 - - + -
21A VAL* 4.0 20.0 - - + -
33A LEU* 4.2 9.6 - - + -
35A ASP 3.6 8.3 - - - +
36A PHE* 3.7 14.6 - - + +
40A VAL* 1.3 80.6 - - - +
42A LEU* 1.3 59.2 + - - +
43A LEU* 3.5 24.9 - - + -
57A MSE 3.4 5.0 - - - +
58A LEU* 3.5 4.7 - - - -
59A ILE* 2.7 51.1 + - + +
61A LEU* 3.5 21.1 - - + -
64A ILE* 4.3 10.8 - - + -
67A ILE* 4.4 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 3.8 0.9 - - - +
34A GLU* 3.1 54.4 + - + +
35A ASP* 2.6 30.5 + - + +
36A PHE* 4.6 0.2 - - - +
41A ILE* 1.3 72.9 - - - +
43A LEU* 1.3 83.2 + - - +
56A GLN* 3.6 27.6 - - + +
57A MSE 3.4 9.9 - - - +
58A LEU* 4.7 7.9 - - + -
6C LEU* 4.9 6.5 - - + +
10C VAL* 3.8 26.5 - - + -
14C TRP* 4.1 8.3 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
19A VAL* 4.6 5.8 - - + +
21A VAL* 4.3 13.5 - - + -
29A PHE* 5.5 2.5 - - + +
30A THR* 4.6 4.5 - - - +
31A GLY* 4.1 27.1 - - - +
32A THR 3.4 10.1 - - - +
33A LEU* 4.3 9.4 - - + -
34A GLU* 4.5 0.4 - - - -
41A ILE* 3.5 32.1 + - + -
42A LEU* 1.3 84.7 - - - +
44A LYS* 1.3 60.0 + - - +
46A VAL* 3.9 19.7 - - + -
56A GLN* 3.2 6.2 - - - +
57A MSE 2.8 42.7 + - + +
59A ILE* 4.1 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLY* 3.8 1.2 - - - -
32A THR* 3.0 38.2 + - + +
34A GLU* 3.1 37.0 - - + +
43A LEU* 1.3 72.9 - - - +
45A ASP* 1.3 95.8 + - - +
46A VAL* 3.7 1.8 - - - -
55A LYS 3.7 8.3 - - - +
56A GLN* 4.6 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLY* 3.7 10.0 - - - -
32A THR* 4.2 8.2 + - - +
44A LYS* 1.3 96.6 - - - +
46A VAL* 1.3 60.1 + - - +
47A VAL* 3.9 2.8 + - - +
54A GLY 3.8 5.4 + - - -
55A LYS* 3.1 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A PHE* 4.2 19.5 - - + -
30A THR 3.5 11.2 - - - +
43A LEU* 3.9 33.7 - - + +
44A LYS 4.2 4.7 - - - +
45A ASP* 1.3 74.4 - - - +
47A VAL* 1.3 62.1 + - - +
52A ASN* 3.6 6.1 - - - +
53A ARG* 2.8 42.5 + - + -
54A GLY* 3.1 23.6 + - - +
56A GLN 4.4 1.8 - - - -
57A MSE 4.0 24.2 - - + -
68C MSE 5.4 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LYS* 6.0 2.2 - - - +
29A PHE* 3.7 7.4 - - - -
30A THR* 2.9 46.6 + - + +
31A GLY* 6.1 0.2 - - - -
45A ASP 3.9 2.0 + - - +
46A VAL* 1.3 76.7 - - - +
48A ASP* 1.3 66.0 + - - +
51A GLY 3.3 12.3 - - - +
52A ASN* 5.0 3.6 - - - +
53A ARG* 4.8 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A PHE* 4.2 20.0 - - + +
30A THR* 6.3 0.4 - - - -
47A VAL* 1.3 78.5 - - - +
49A VAL* 1.3 61.2 + - - +
50A ILE* 2.6 56.6 + - - +
51A GLY* 2.6 19.2 + - - +
53A ARG* 3.5 30.8 + - + -
----------------------------------------------------------
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