Contacts of the strand formed by residues 40 - 44 (chain C) in PDB entry 4Y1L
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 40 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C VAL* 6.0 1.2 - - - +
16C LEU* 4.3 25.3 - - + +
31C VAL* 3.8 19.1 - - + -
33C SER 3.3 11.7 - - - +
34C ARG* 4.1 17.5 + - - -
35C SER 5.1 0.5 + - - -
39C GLY* 1.3 74.0 - - - -
41C VAL* 1.3 69.7 + - - +
42C PHE* 4.2 9.5 + - + -
62C PHE 4.0 0.7 - - - +
63C HIS* 3.6 1.4 - - - -
64C LEU* 2.8 47.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 41 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C VAL* 3.5 2.1 - - - +
32C LEU* 2.6 52.7 + - + -
33C SER* 2.9 32.4 + - - +
39C GLY 5.3 1.3 - - - +
40C THR* 1.3 74.5 - - - +
42C PHE* 1.3 58.3 + - - +
61C VAL* 3.9 10.1 - - + -
62C PHE 3.4 11.7 - - - +
63C HIS* 3.4 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 42 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C LEU* 3.9 17.9 - - + -
19C LEU* 4.1 6.3 - - + -
29C TRP* 3.3 33.4 - + + -
30C GLU 3.0 18.2 - - - +
31C VAL* 4.0 8.5 - - + -
32C LEU* 3.8 6.1 - - - +
40C THR* 4.6 5.6 - - + -
41C VAL* 1.3 76.1 - - - +
43C ARG* 1.3 62.2 + - - +
44C ILE* 4.5 5.4 - - + -
61C VAL* 3.4 5.0 - - - +
62C PHE* 2.9 72.8 + + + +
64C LEU* 3.8 27.4 - - + -
107C VAL* 3.7 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 43 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C HIS* 3.4 27.9 + - - +
28C GLU 4.6 1.0 + - - +
29C TRP* 3.3 7.8 - - - -
30C GLU* 3.0 73.3 + - - +
32C LEU* 4.2 23.9 - - + +
42C PHE* 1.3 76.4 - - - +
44C ILE* 1.3 65.3 + - - +
45C HIS* 3.1 32.9 + - + +
59C GLU* 3.7 14.4 - - + +
60C LEU 3.5 6.3 - - - +
61C VAL* 4.5 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 44 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C PHE* 3.4 53.8 - - + -
28C GLU* 3.2 11.4 - - - +
29C TRP* 4.6 6.5 - - + -
42C PHE* 4.5 5.2 - - + -
43C ARG* 1.3 75.5 - - - +
45C HIS* 1.3 90.6 + - - +
46C THR* 3.9 9.0 + - + +
60C LEU* 2.9 53.9 + - + +
62C PHE* 4.2 16.6 - - + -
111C VAL* 4.6 8.3 - - + -
----------------------------------------------------------
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