Contacts of the strand formed by residues 107 - 111 (chain H) in PDB entry 2OSL
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 TYR 107 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99H SER* 3.3 5.3 - - - -
100H THR* 3.0 40.6 + - + +
101H TYR* 4.7 9.2 - + + -
105H ASP 4.3 3.6 - - - +
106H TRP* 1.3 80.6 - - - +
108H PHE* 1.3 63.4 + - - +
109H ASN* 2.8 38.9 + - + +
33L HIS* 4.3 9.9 - - + -
35L PHE* 5.1 4.3 - + - -
45L PRO* 3.3 24.5 - - + +
46L TRP 5.5 0.2 - - - -
47L ILE 5.3 2.0 - - - -
48L TYR* 3.6 47.5 - + + -
54L ALA* 3.2 31.2 - - - +
55L SER 5.0 0.3 + - - -
90L TRP* 4.2 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 108 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H HIS* 3.4 41.1 - + + -
37H VAL* 4.9 5.2 - - + -
47H TRP* 4.2 13.0 - + - -
97H ALA* 3.9 16.2 - - + -
98H ARG 3.6 9.9 - - - +
99H SER* 4.4 2.0 - - - -
107H TYR* 1.3 74.0 - - - +
109H ASN* 1.3 59.0 + - - +
110H VAL 3.4 2.7 - - - -
111H TRP* 2.8 36.1 + + + +
33L HIS* 5.7 0.2 + - - -
35L PHE* 3.5 20.1 - + + -
45L PRO* 3.9 2.1 - - - +
88L GLN* 3.7 30.1 - - - -
90L TRP* 3.3 32.9 - + - +
95L PRO* 5.1 2.5 - - + -
97L PHE* 4.0 24.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 109 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98H ARG* 3.1 31.0 + - - +
100H THR* 3.4 18.4 - - - +
107H TYR* 2.8 43.5 + - + +
108H PHE* 1.3 71.5 - - - +
110H VAL* 1.3 64.7 + - - +
111H TRP* 4.6 0.7 - - - -
45L PRO* 4.0 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 110 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2H VAL* 3.9 39.0 - - + +
3H GLN* 4.7 0.2 - - - -
4H LEU* 3.4 26.8 - - + +
97H ALA* 3.3 4.5 - - - +
98H ARG* 2.9 50.0 + - + +
108H PHE 3.4 1.2 - - - -
109H ASN* 1.3 100.1 + - - +
111H TRP* 1.3 64.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 111 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H LEU* 4.0 13.0 + - - +
37H VAL* 4.2 18.6 - - + -
45H LEU* 4.7 2.0 - - + -
95H TYR* 3.9 33.0 - + + -
96H CYS 3.7 4.7 - - - -
97H ALA* 3.9 9.0 - - + -
108H PHE* 2.8 47.4 + + + +
110H VAL* 1.3 81.8 - - - +
112H GLY* 1.3 68.1 + - - +
35L PHE* 3.7 17.6 - + - -
42L SER* 4.2 8.0 + - - +
43L PRO* 3.3 53.5 + - + +
45L PRO* 4.3 7.6 - - + -
97L PHE* 3.9 29.6 - + - -
----------------------------------------------------------
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