Contacts of the strand formed by residues 128 - 132 (chain D) in PDB entry 1Y8R
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 ALA 128 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D ARG 3.6 2.0 + - - -
39D VAL* 3.7 15.9 - - + -
40D LEU 3.1 22.3 + - - -
126D PHE* 3.8 3.6 - - - +
127D ASP* 1.3 78.3 - - - +
129D VAL* 1.3 68.4 + - - +
151D ILE* 4.3 0.2 - - - -
152D LYS* 3.5 16.8 - - + +
154D PHE* 4.6 6.5 - - + -
314D ILE* 4.4 12.8 - - + -
318D LEU* 3.7 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 129 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D LEU* 3.3 34.3 - - + -
123D PHE* 4.3 14.4 - - + -
126D PHE* 4.4 8.1 - - + -
128D ALA* 1.3 81.8 - - - +
130D CYS* 1.3 64.1 + - - +
131D LEU* 3.6 20.9 - - + -
142D VAL* 4.3 9.9 - - + -
146D CYS* 3.9 25.4 - - - -
151D ILE* 4.0 9.9 - - + -
152D LYS 3.0 6.2 + - - +
153D PHE* 3.7 2.0 - - + -
154D PHE* 2.9 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 130 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D VAL* 5.2 4.0 - - + -
40D LEU 2.8 11.9 + - - +
41D LEU* 3.6 15.4 - - + +
42D VAL 3.0 26.5 + - - -
51D ILE* 4.1 11.9 - - + -
129D VAL* 1.3 75.8 - - - +
131D LEU* 1.3 69.8 + - - +
132D THR* 5.0 0.7 - - - -
154D PHE* 3.5 22.2 - - + -
155D THR 4.5 0.4 - - - -
310D LEU* 3.9 21.5 - - - -
314D ILE* 3.8 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 131 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D VAL* 4.1 15.9 - - + -
115D ILE* 5.2 2.9 - - + -
129D VAL* 3.6 26.7 - - + -
130D CYS* 1.3 74.5 - - - +
132D THR* 1.3 64.8 + - - +
134D CYS* 3.7 24.9 - - + -
138D VAL* 4.0 4.9 - - + +
139D ILE* 3.9 24.5 - - + -
142D VAL* 3.9 34.5 - - + -
153D PHE* 4.0 9.0 - - + -
154D PHE 3.0 13.0 + - - +
155D THR* 3.1 13.0 + - - +
156D GLY 3.0 26.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 132 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D LEU* 4.2 11.1 - - - +
42D VAL* 3.1 22.7 + - - +
43D GLY* 3.6 17.9 + - - +
45D LYS* 5.7 0.7 - - + +
47D LEU* 4.2 26.5 - - + +
48D GLY* 4.5 4.0 - - - +
51D ILE* 4.7 5.2 - - - +
130D CYS* 4.9 1.2 - - - -
131D LEU* 1.3 79.1 + - - +
133D CYS* 1.3 90.9 + - - +
134D CYS* 3.3 9.2 + - - -
156D GLY 3.5 12.6 + - - +
157D ASP* 3.5 8.5 - - - +
298D GLU* 6.0 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