Contacts of the strand formed by residues 920 - 923 (chain A) in PDB entry 4YOC
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 ARG 920 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
917A LEU* 2.9 57.4 + - + +
918A ASP 3.7 0.6 - - - -
919A SER* 1.3 87.2 - - - +
921A VAL* 1.3 67.6 + - - +
922A LEU* 3.6 17.4 - - + +
998A GLU* 2.8 41.1 + - - -
1000A PHE* 4.0 36.5 - - + -
1001A CYS 3.6 11.4 - - - +
1002A PRO* 4.4 2.7 - - + -
1003A LYS* 4.3 2.8 - - - +
1017A ARG* 4.4 14.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 921 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
913A GLN* 3.0 28.9 - - - +
915A GLU 3.7 4.7 - - - +
916A ASP* 3.8 10.1 - - - +
920A ARG* 1.3 81.0 - - - +
922A LEU* 1.3 65.4 + - - +
923A TYR* 3.3 30.5 - - + +
1000A PHE* 3.1 4.3 - - - -
1001A CYS 2.9 34.4 + - - +
1003A LYS* 3.7 23.1 - - + -
1009A PRO* 3.7 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 922 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
913A GLN* 3.4 8.3 - - - +
914A LEU* 2.9 35.4 + - + -
915A GLU* 2.7 51.1 + - + +
917A LEU* 4.7 7.0 - - + -
920A ARG* 3.6 35.0 - - + +
921A VAL* 1.3 74.8 - - - +
923A TYR* 1.3 61.0 + - - +
998A GLU* 4.1 16.6 - - + +
999A ILE 3.4 5.2 - - - +
1000A PHE* 3.5 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 923 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
910A VAL* 3.4 38.4 - - + -
911A LEU 4.7 2.7 - - - -
912A GLU 3.7 7.9 - - - +
913A GLN* 3.3 35.9 - - + -
914A LEU* 3.6 12.0 - - - +
921A VAL* 3.3 39.4 - - + +
922A LEU* 1.3 71.6 - - - +
924A TYR* 1.3 61.5 + - - +
925A SER 4.4 6.5 - - - +
935A VAL* 3.7 7.8 - - - +
999A ILE* 2.9 37.8 + - + +
1000A PHE* 4.4 1.3 - - - -
1001A CYS* 3.6 20.9 - - + -
1009A PRO* 3.7 17.3 - - - +
1011A GLU* 3.6 16.3 + - - +
----------------------------------------------------------
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