Contacts of the strand formed by residues 819 - 831 (chain C) in PDB entry 4OIR
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 VAL 819 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711C GLU* 4.1 14.4 - - + +
712C ALA 4.0 2.9 - - - +
713C ARG* 4.0 13.0 - - + -
808C ARG* 4.0 17.1 - - - +
815C LEU* 4.1 14.7 - - + +
816C LYS* 3.1 46.5 + - + +
817C PRO 4.6 2.0 - - - +
818C GLY* 1.3 77.6 - - - +
820C ARG* 1.3 64.3 + - - +
821C GLU 3.7 22.4 - - - +
822C VAL* 3.9 18.6 - - + -
532D GLY 5.5 5.2 - - - +
305F GLU* 4.3 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 820 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712C ALA 2.9 13.4 + - - +
713C ARG 3.6 10.3 - - - -
714C ASP* 3.3 29.7 + - - +
719C PRO* 4.0 16.4 - - - +
720C GLU 3.4 25.7 + - - -
721C ARG* 5.2 5.8 - - - +
807C ARG* 4.5 0.2 - - - +
808C ARG* 2.7 65.6 + - - +
815C LEU* 4.0 1.4 - - - +
818C GLY 3.6 0.2 + - - -
819C VAL* 1.3 72.7 - - - +
821C GLU* 1.3 68.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 821 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710C ILE 4.1 0.3 - - - +
711C GLU* 3.4 3.5 - - - -
712C ALA* 2.9 44.0 + - + +
720C GLU 4.7 0.9 - - - +
721C ARG* 4.0 6.1 - - - +
722C ILE* 3.3 33.4 + - + +
805C ARG* 2.4 38.8 + - - +
806C LEU 3.3 13.2 - - - +
807C ARG* 3.4 13.8 - - + +
815C LEU* 4.8 1.3 - - - -
819C VAL* 3.6 3.0 - - - +
820C ARG* 1.3 91.0 + - + +
822C VAL* 1.3 66.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 822 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709C GLU* 3.8 28.9 - - + +
710C ILE 3.6 8.3 - - - +
711C GLU* 4.1 14.8 - - + +
804C VAL 3.8 0.9 - - - +
805C ARG* 3.6 2.3 - - - -
806C LEU* 2.8 47.3 + - + +
815C LEU* 4.0 19.7 - - + -
819C VAL* 3.9 16.8 - - + -
821C GLU* 1.3 77.7 - - - +
823C VAL* 1.3 68.8 + - - +
824C ARG* 4.5 10.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 823 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708C TYR 4.0 0.5 - - - +
709C GLU* 3.5 2.3 - - - +
710C ILE* 2.9 49.0 + - + +
722C ILE* 3.7 31.9 - - + -
742C VAL* 4.1 17.9 - - + -
756C VAL* 3.6 26.4 - - + +
790C LEU* 5.4 0.3 - - - +
803C THR* 5.7 0.2 - - - -
804C VAL 3.4 9.4 - - - +
805C ARG* 4.0 23.3 - - + +
821C GLU* 5.1 0.7 - - - +
822C VAL* 1.3 79.7 - - - +
824C ARG* 1.3 68.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 824 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C GLU 3.7 20.8 + - - -
86C LYS 5.2 1.6 - - - -
87C ASP* 3.8 17.0 + - - +
707C ARG* 3.5 43.8 - - + +
708C TYR 3.3 6.5 - - - +
709C GLU* 2.4 50.3 + - + -
803C THR* 3.3 4.9 - - - -
804C VAL* 2.7 59.4 + - + +
806C LEU* 4.1 22.0 - - - +
822C VAL* 4.3 8.5 - - + +
823C VAL* 1.3 74.9 - - - +
825C VAL* 1.3 64.9 + - - +
826C TYR* 4.2 14.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 825 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708C TYR* 2.9 41.7 + - + +
742C VAL* 4.6 2.2 - - + -
743C VAL* 4.2 14.1 - - + -
755C LEU* 4.4 16.6 - - + +
756C VAL* 3.7 28.9 - - + -
790C LEU* 5.7 0.9 - - + -
800C VAL* 3.7 25.8 - - + -
802C ARG 3.6 2.2 - - - -
803C THR* 4.0 14.4 - - + -
823C VAL* 4.4 0.6 + - + -
824C ARG* 1.3 79.9 - - - +
826C TYR* 1.3 63.7 + - - +
827C VAL* 4.0 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 826 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630C ARG* 4.4 14.6 - - + -
705C ILE* 4.1 20.0 - - + -
706C GLU 3.7 1.8 - - - -
707C ARG* 3.3 45.9 + - + -
800C VAL* 3.6 4.2 - - - +
801C VAL* 2.9 33.5 + - + +
802C ARG* 2.9 46.3 + - + +
804C VAL* 4.1 23.8 - - + -
824C ARG* 4.2 17.3 + - + -
825C VAL* 1.3 76.8 - - - +
827C VAL* 1.3 61.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 827 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704C HIS 3.8 1.2 - - - +
705C ILE* 3.3 3.2 - - - -
706C GLU* 2.8 37.7 + - + +
708C TYR* 3.7 32.3 - - + +
749C VAL* 4.3 15.7 - - + -
755C LEU* 4.5 3.6 - - + -
792C VAL* 6.1 0.2 - - + -
797C GLY* 4.1 6.3 - - - +
798C GLY* 3.6 33.4 - - - +
799C ILE 3.4 11.0 - - - +
800C VAL* 4.3 6.1 - - + -
825C VAL* 4.0 13.7 - - + -
826C TYR* 1.3 76.5 - - - +
828C ALA* 1.3 64.5 + - - +
829C GLN* 4.2 2.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 828 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PHE* 3.7 23.4 - - + -
703C ILE* 4.5 4.5 - - + -
704C HIS 3.3 4.9 - - - +
705C ILE* 3.7 22.2 - - + -
799C ILE* 2.9 30.6 + - - +
801C VAL* 3.6 25.5 - - + +
826C TYR 4.1 1.2 + - - -
827C VAL* 1.3 75.3 - - - +
829C GLN* 1.3 60.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 829 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PHE* 4.2 4.7 - - - -
703C ILE* 3.4 2.6 - - - +
704C HIS* 2.8 47.3 + - + +
706C GLU* 6.1 2.3 - - - +
796C GLU* 5.0 7.2 + - - +
797C GLY 2.8 32.9 + - - +
798C GLY* 4.2 4.5 - - - -
799C ILE* 6.0 0.4 - - - -
827C VAL* 5.3 2.5 - - + +
828C ALA* 1.3 76.7 - - - +
830C LYS* 1.3 61.8 + - - +
831C ARG* 2.7 44.3 + - + +
1002C GLU* 3.1 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 830 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLU* 2.7 43.8 + - - +
65A PHE* 4.0 18.3 - - + -
76A VAL* 5.1 3.4 - - + -
79A ILE* 6.0 1.6 - - - +
154A GLU* 5.8 4.4 - - - +
166A PRO 5.6 2.4 + - - -
168A ASP* 4.8 8.5 + - - -
572C ILE* 4.8 9.0 - - + -
698C ASP* 5.3 3.4 + - - +
701C THR* 3.7 24.9 - - + -
702C SER 3.7 2.7 - - - +
703C ILE* 4.4 14.4 - - + +
829C GLN* 1.3 73.3 - - - +
831C ARG* 1.3 60.8 + - - +
832C LYS* 3.6 16.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 831 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701C THR* 3.3 4.4 - - - -
702C SER* 2.7 43.6 + - - +
704C HIS* 3.7 27.2 + - + +
796C GLU* 5.7 2.8 + - - -
829C GLN* 2.7 37.4 + - + +
830C LYS* 1.3 71.7 - - - +
832C LYS* 1.3 67.9 + - - +
834C GLN* 6.0 0.2 - - - +
996C LYS* 3.6 5.5 + - - +
1000C MET* 3.3 30.4 - - - +
1002C GLU* 3.5 35.7 + - - +
1003C ASP* 2.8 44.0 + - - -
----------------------------------------------------------
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