Contacts of the strand formed by residues 916 - 925 (chain C) in PDB entry 4OQB
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 ILE 916 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675C MET* 3.7 41.5 - - + -
834C ILE* 3.6 31.9 - - + -
866C THR* 5.7 5.8 - - + +
910C THR* 3.1 13.6 - - - +
914C ASP* 3.3 26.2 - - - +
915C PRO* 1.3 86.9 - - + +
917C GLY* 1.3 59.3 + - - +
1004C LYS* 4.6 5.6 - - + -
1005C LEU 3.5 5.2 - - - +
1006C LYS* 4.9 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 917 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675C MET* 5.2 2.0 - - - -
866C THR* 5.6 6.1 - - - -
908C CYS* 4.5 9.2 - - - -
910C THR* 4.0 11.7 - - - -
915C PRO 3.8 0.2 + - - -
916C ILE* 1.3 76.3 - - - +
918C LEU* 1.3 64.9 + - - -
1004C LYS* 3.6 3.4 - - - +
1005C LEU* 2.8 39.5 + - - +
1007C PHE* 4.4 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 918 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672C LEU* 3.9 20.6 - - + -
675C MET* 4.5 11.0 - - - -
676C ILE* 3.6 30.7 - - + -
837C PHE* 6.1 0.2 - - + -
864C SER 3.6 9.6 + - - +
866C THR* 4.4 14.2 - - - +
869C PHE* 3.5 43.5 - - + -
908C CYS* 3.1 18.8 - - - +
917C GLY* 1.3 75.6 - - - +
919C ILE* 1.3 61.1 + - - +
1002C LEU* 3.9 6.5 - - + -
1003C LEU 3.3 15.7 - - - +
1004C LYS* 3.9 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 919 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
861C TRP* 3.6 28.9 - - + -
862C HIS 3.8 4.3 - - - +
863C GLY* 3.6 19.5 - - - +
869C PHE* 4.1 2.0 - - - -
901C VAL* 3.4 36.3 - - + +
904C SER* 3.6 8.5 - - - -
905C ALA* 3.4 22.0 - - + +
908C CYS* 4.3 4.0 - - - -
918C LEU* 1.3 74.3 - - - +
920C LEU* 1.3 64.6 + - - +
1002C LEU* 3.6 2.4 - - - +
1003C LEU* 2.9 32.5 + - + +
1005C LEU* 3.3 26.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 920 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839C ILE* 3.5 32.1 - - + -
861C TRP* 3.4 13.9 - - - -
862C HIS* 2.8 59.1 + - + +
869C PHE* 3.7 22.0 - - + -
872C ILE* 3.8 28.9 - - + -
873C LEU* 5.3 2.7 - - + -
877C LEU* 4.3 0.7 - - + -
897C PHE* 6.2 0.2 - - + -
919C ILE* 1.3 72.8 - - - +
921C LEU* 1.3 61.9 + - - +
999C LEU* 4.1 21.5 - - + -
1001C TYR 3.6 2.0 - - - +
1002C LEU* 3.7 19.7 - - + -
1003C LEU* 5.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 921 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
814C ILE* 4.2 15.3 - - + -
817C TYR* 3.6 12.1 - - + -
859C LEU* 3.5 32.8 - - + -
860C LEU 3.5 10.8 - - - +
861C TRP* 3.2 49.6 - - + -
920C LEU* 1.3 73.9 - - - +
922C GLY* 1.3 57.5 + - - +
999C LEU* 4.1 1.2 - - - -
1000C LYS* 2.8 23.7 + - - +
1001C TYR* 2.8 37.3 + - + +
1003C LEU* 3.7 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 922 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
858C ARG 3.4 0.2 - - - +
859C LEU* 3.8 4.2 - - - +
860C LEU 3.1 29.3 + - - +
897C PHE* 4.7 9.8 - - - -
920C LEU 4.2 0.6 - - - -
921C LEU* 1.3 75.6 - - - +
923C GLU* 1.3 61.4 + - - -
924C VAL* 3.0 14.3 + - - +
997C VAL* 4.9 1.3 - - - -
998C ASN 3.4 11.0 - - - -
999C LEU* 3.9 14.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 923 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
848C TYR* 3.2 34.1 + - - +
852C LYS* 3.6 15.3 + - - -
857C ARG* 3.2 30.4 + - + -
858C ARG 3.8 4.5 - - - -
859C LEU* 3.8 7.6 - - + +
922C GLY* 1.3 66.7 - - - -
924C VAL* 1.3 58.3 + - - +
925C ALA 3.7 0.2 + - - -
967C VAL* 3.4 33.6 - - + +
996C GLN 3.7 0.2 - - - +
998C ASN* 2.7 34.7 + - + +
1000C LYS* 2.9 38.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 924 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
848C TYR* 4.4 0.4 - - - -
857C ARG* 4.9 0.4 - - - -
858C ARG 3.1 22.9 + - - +
860C LEU* 3.5 34.8 - - + -
897C PHE* 3.8 32.8 - - + -
922C GLY 3.0 11.2 + - - +
923C GLU* 1.3 70.9 - - - +
925C ALA* 1.3 59.3 + - - +
926C LEU* 3.0 16.3 + - + +
991C VAL* 3.4 35.4 - - + -
996C GLN 3.6 7.6 - - - +
997C VAL* 4.4 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 925 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
848C TYR* 3.6 20.2 + - + +
851C PHE* 3.7 34.5 - - + +
854C LEU* 3.9 9.6 - - + +
857C ARG* 4.5 12.1 - - + -
923C GLU 3.7 1.8 + - - -
924C VAL* 1.3 67.4 - - - +
926C LEU* 1.3 64.5 + - - +
927C GLY 3.6 1.1 - - - -
991C VAL* 4.2 0.9 - - - +
996C GLN* 3.0 38.3 + - - +
----------------------------------------------------------
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