Contacts of the strand formed by residues 922 - 930 (chain A) in PDB entry 1JV2
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 SER 922 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778A HIS* 3.1 33.1 - - - -
780A TYR* 2.5 29.7 + - - -
797A LEU* 3.4 10.0 - - - +
798A GLN 3.8 5.6 + - - -
799A TRP* 3.7 11.9 - - - -
800A PRO* 4.5 2.0 - - - -
921A LYS* 1.3 74.6 - - - +
923A SER* 1.3 59.9 + - - +
946A LEU* 2.9 7.3 - - - +
947A VAL 2.5 34.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 923 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780A TYR* 3.7 1.1 - - - -
796A HIS 4.0 0.2 - - - +
797A LEU* 3.3 4.5 - - - +
798A GLN* 2.7 52.2 + - - +
874A CYS* 6.4 1.3 - - - -
921A LYS* 4.8 11.9 - - - -
922A SER* 1.3 78.4 + - - +
924A ALA* 1.3 65.4 + - - +
925A SER* 5.0 0.5 + - - -
944A SER* 5.0 6.1 + - - -
945A THR 3.4 11.1 + - - -
946A LEU* 4.4 7.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 924 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744A ILE* 3.2 17.9 - - + +
780A TYR* 3.6 29.4 + - + -
795A LEU* 4.9 6.1 - - + -
796A HIS 3.0 12.1 - - - +
797A LEU* 4.0 14.4 - - + -
923A SER* 1.3 76.7 + - - +
925A SER* 1.3 60.9 + - - +
944A SER* 4.2 2.5 - - - -
945A THR 2.9 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 925 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744A ILE* 4.4 1.3 - - - -
795A LEU* 3.6 4.2 - - - +
796A HIS* 2.7 49.5 + - - +
798A GLN* 5.6 1.8 + - - -
923A SER* 5.0 0.4 + - - -
924A ALA* 1.3 74.4 - - - +
926A PHE* 1.3 66.6 + - - +
943A ASN 3.3 13.5 - - - -
944A SER* 3.7 12.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 926 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742A VAL* 3.5 46.7 - - + -
744A ILE* 4.1 16.8 - - + -
782A LEU* 3.3 33.7 - - + -
793A ALA* 5.1 1.3 - - + -
794A MET 2.9 14.1 - - - +
795A LEU* 4.1 7.9 - - + -
796A HIS* 5.5 1.6 - - - -
925A SER* 1.3 79.3 - - - +
927A ASN* 1.3 65.4 + - - +
928A VAL* 3.8 19.3 - - + -
941A ILE* 4.0 8.3 - - + -
942A THR* 3.4 32.2 - - - +
943A ASN* 3.0 48.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 927 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793A ALA* 3.1 3.7 - - - -
794A MET* 2.8 40.9 + - + +
796A HIS* 5.9 2.7 - - + -
926A PHE* 1.3 75.9 - - - +
928A VAL* 1.3 97.3 + - - +
929A ILE* 3.3 15.8 + - + +
940A ASP* 3.8 19.8 - - - +
941A ILE 3.4 5.3 + - - -
942A THR* 3.4 20.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 928 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742A VAL* 4.2 9.0 - - + -
790A PHE* 3.7 34.8 - - + -
792A LYS 3.8 6.7 - - - +
793A ALA* 3.7 5.6 - - + -
926A PHE* 3.8 18.2 - - + -
927A ASN* 1.3 79.7 + - - +
929A ILE* 1.3 59.8 + - - +
930A GLU 4.3 1.3 - - - +
931A PHE* 3.7 23.0 - - + -
940A ASP* 2.9 24.1 - - - +
941A ILE* 2.7 43.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 929 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792A LYS* 2.9 30.7 + - + +
793A ALA* 3.9 7.0 - - - +
794A MET* 3.5 32.8 - - + -
927A ASN* 3.3 23.3 + - - +
928A VAL* 1.3 75.9 - - - +
930A GLU* 1.3 63.9 + - + +
931A PHE* 5.0 2.5 - - - -
938A ILE* 4.8 9.2 - - - +
940A ASP* 4.1 12.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 930 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790A PHE* 3.7 2.1 - - - +
791A SER* 2.6 25.6 + - - +
792A LYS* 2.6 70.8 + - + +
928A VAL* 3.7 2.0 - - - +
929A ILE* 1.3 82.4 - - + +
931A PHE* 1.3 69.9 + - - +
938A ILE* 5.7 1.6 - - - -
----------------------------------------------------------
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