Contacts of the strand formed by residues 4050 - 4057 (chain F) in PDB entry 1Y1S
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 PHE4050 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1069A ILE* 4.0 20.4 - - + -
4008F HIS* 4.0 15.9 - - + -
4009F LEU* 3.5 38.6 - - + +
4045F ALA 4.1 0.9 - - - +
4046F SER* 3.7 2.4 + - - -
4047F HIS* 2.9 39.4 + - - +
4048F ARG* 3.0 8.2 - - + -
4049F GLU* 1.3 81.1 - - + +
4051F THR* 1.3 61.8 + - - +
4052F SER* 3.9 1.7 + - - -
4065F CYS* 4.5 2.2 - - - -
4066F SER 3.4 19.1 - - - +
4067F THR 3.5 12.3 - - - -
4073F SER* 3.1 40.8 - - - -
4076F ILE* 3.7 23.6 - - + -
4077F ALA* 3.8 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR4051 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4028F PRO* 3.3 32.8 + - - +
4031F VAL* 3.3 7.9 - - + +
4032F GLU 5.8 0.2 - - - +
4043F LYS* 5.5 4.3 - - - -
4045F ALA 3.6 9.6 - - - +
4046F SER* 3.7 19.0 + - - +
4048F ARG 4.9 2.9 + - - -
4050F PHE* 1.3 74.1 - - - +
4052F SER* 1.3 62.6 + - - +
4053F TRP* 4.1 21.8 - - + +
4065F CYS* 3.3 2.1 - - - -
4066F SER* 2.8 39.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER4052 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4009F LEU* 4.6 1.6 + - - -
4011F LEU* 3.5 40.6 - - - +
4043F LYS* 4.4 0.5 - - - +
4044F LEU* 3.2 19.3 + - - +
4045F ALA* 2.9 21.9 + - - +
4050F PHE 3.9 2.2 + - - -
4051F THR* 1.3 75.2 - - - +
4053F TRP* 1.3 74.1 + - - +
4063F ILE* 4.9 3.1 - - - -
4064F VAL 3.2 7.2 - - - -
4065F CYS* 4.0 15.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP4053 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4031F VAL* 3.5 24.9 - - + -
4032F GLU* 3.5 42.6 + - + +
4035F ALA* 3.9 27.4 - - + -
4041F PRO* 3.8 21.5 - - + -
4042F VAL 3.4 24.5 - - - -
4043F LYS* 3.6 43.6 - - + +
4044F LEU* 4.1 5.6 - - - +
4051F THR* 4.1 12.3 - - + +
4052F SER* 1.3 90.9 - - - +
4054F ARG* 1.3 60.8 + - - +
4063F ILE* 3.4 11.6 - - - +
4064F VAL* 2.8 28.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG4054 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4015F ASP* 3.1 26.3 + - - +
4016F LEU 4.2 5.8 - - - +
4017F GLN* 3.6 33.3 - - - +
4040F LYS* 3.7 4.0 + - - +
4041F PRO* 3.2 3.5 - - - +
4042F VAL* 2.8 63.0 + - + +
4044F LEU* 3.9 24.5 - - + +
4053F TRP* 1.3 78.2 - - - +
4055F ALA* 1.3 72.9 + - - +
4061F ALA* 4.7 3.1 - - - -
4062F VAL 3.5 13.0 - - - +
4063F ILE* 3.9 10.5 - - + -
4064F VAL* 5.9 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA4055 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4035F ALA* 4.4 5.8 - - + +
4038F MET* 3.5 42.8 - - + -
4039F ASP 3.3 7.2 - - - +
4040F LYS* 4.0 6.1 - - - -
4041F PRO* 4.2 7.6 - - + -
4054F ARG* 1.3 84.2 - - - +
4056F GLU* 1.3 64.6 + - - +
4061F ALA* 3.6 5.7 - - - -
4062F VAL* 2.9 27.2 + - + +
4064F VAL* 5.4 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU4056 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4038F MET* 3.5 4.5 - - - +
4039F ASP* 2.6 52.7 + - + +
4040F LYS* 3.0 41.6 + - + +
4055F ALA* 1.3 77.8 - - - +
4057F LEU* 1.3 63.3 + - - +
4058F ASP 4.2 0.2 - - - -
4059F GLY* 4.0 18.6 + - - +
4060F LYS 3.0 22.7 - - - +
4061F ALA* 4.9 0.7 - - - +
4062F VAL* 4.4 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU4057 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4037F LEU 5.6 1.1 - - - +
4038F MET* 3.9 37.0 - - + -
4039F ASP* 4.8 2.7 - - - +
4056F GLU* 1.3 71.7 - - - +
4058F ASP* 1.3 74.8 + - - +
4059F GLY 3.1 0.7 - - - -
4060F LYS* 2.7 32.5 + - - +
4062F VAL* 4.5 7.2 - - + +
4246F VAL* 3.7 17.9 - - + +
4249F ALA* 4.0 11.9 - - + -
4250F ARG* 3.5 52.3 - - + +
4253F LEU* 3.5 16.2 - - + +
----------------------------------------------------------
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