Contacts of the helix formed by residues 862 - 876 (chain A) in PDB entry 5B16
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 MET 862 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576A ILE* 6.1 1.6 - - + -
578A VAL* 4.4 22.2 - - + -
620A VAL* 3.7 32.1 - - + -
622A ARG* 5.6 5.2 - - + -
627A TYR* 4.4 24.9 - - + -
629A ILE* 3.4 30.7 - - + +
858A GLN* 4.0 21.8 - - - +
859A HIS* 4.4 10.5 - - + +
860A ALA 3.2 0.8 - - - -
861A MET* 1.3 86.4 - - - +
863A LEU* 1.3 66.2 + - + +
864A PRO* 3.5 1.6 - - - -
865A VAL* 3.4 7.3 + - + +
866A LEU* 3.3 17.2 + - - +
906A PHE* 4.7 12.1 - - + -
917A LEU* 6.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 863 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576A ILE* 3.7 27.4 - - + -
604A PHE* 4.0 23.6 - - + -
653A PHE* 3.6 31.0 - - + -
662A TRP* 4.1 9.4 - - + -
681A PHE* 3.7 36.6 - - + -
859A HIS* 3.9 10.8 - - + +
860A ALA* 3.7 14.4 - - - +
862A MET* 1.3 77.6 - - + +
864A PRO* 1.4 72.0 - - + +
866A LEU* 3.2 5.4 + - + +
867A THR* 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 864 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659A LEU* 5.3 2.0 - - + -
662A TRP* 3.5 29.4 + - + +
860A ALA 3.4 15.7 - - - +
861A MET* 3.9 12.1 - - + +
862A MET 3.6 2.5 - - - -
863A LEU* 1.4 89.9 - - + +
865A VAL* 1.3 57.2 + - + +
867A THR* 2.7 21.7 + - - +
868A HIS* 2.9 19.2 + - - +
906A PHE* 5.8 1.6 - - + -
907A GLY* 3.9 4.0 - - - +
908A MET* 3.7 44.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 865 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618A CYS* 3.9 12.6 - - - -
619A LYS 5.4 0.7 - - - +
620A VAL* 3.8 30.7 - - + -
629A ILE* 4.1 2.7 - - + -
861A MET 4.4 3.1 - - - +
862A MET* 3.5 13.2 - - + +
863A LEU 3.2 0.4 - - - -
864A PRO* 1.3 76.9 - - - +
866A LEU* 1.3 57.6 + - - +
868A HIS* 3.6 3.9 - - + +
869A HIS* 2.9 28.2 + - + +
905A ASN 3.8 16.2 - - - +
906A PHE* 3.6 45.3 - - + -
907A GLY* 3.8 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 866 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576A ILE* 3.7 18.4 - - + -
606A MET* 3.5 30.7 - - - -
618A CYS* 3.8 15.9 - - + -
629A ILE* 3.7 32.1 - - + +
631A PHE* 4.0 34.5 - - + -
681A PHE* 4.9 1.6 - - + -
862A MET 3.3 9.0 + - - +
863A LEU* 3.2 10.2 + - + +
865A VAL* 1.3 78.9 - - - +
867A THR* 1.3 64.8 + - + +
869A HIS* 3.2 1.7 + - - +
870A ILE* 2.9 43.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 867 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662A TRP* 3.6 15.0 + - + -
664A LEU* 4.1 10.3 - - + +
679A PHE* 3.8 27.4 - - + -
681A PHE* 3.6 30.7 - - + -
863A LEU 2.9 18.5 + - - +
864A PRO* 2.7 26.9 + - - +
866A LEU* 1.3 81.2 - - + +
868A HIS* 1.3 59.2 + - - +
870A ILE* 3.8 2.2 - - - +
871A ARG* 2.9 38.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 868 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A ILE* 4.8 7.0 - - + -
548A ARG* 5.6 3.0 + - - -
552A TYR* 2.6 40.5 + + - +
864A PRO 2.9 18.9 + - - +
865A VAL* 3.6 4.5 - - + +
867A THR* 1.3 75.0 + - - +
869A HIS* 1.3 62.3 + - + +
871A ARG* 3.9 3.8 - - - +
872A TYR* 2.9 34.6 + - + +
902A HIS* 5.4 7.9 - + - -
905A ASN 5.3 4.0 - - - -
906A PHE 4.8 4.9 - - - -
907A GLY* 4.0 24.7 - - - -
1023A LEU* 4.1 27.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 869 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615A ILE* 3.9 8.7 - - + +
616A PRO* 3.3 28.6 - - - +
617A LEU 3.5 18.6 + - - -
618A CYS* 3.6 26.9 - - + +
619A LYS 5.4 1.1 - - - -
631A PHE* 5.3 1.4 - - - -
865A VAL 2.9 14.5 + - - +
866A LEU* 3.4 8.9 + - - +
868A HIS* 1.3 80.8 - - - +
870A ILE* 1.3 61.3 + - - +
872A TYR* 3.6 4.0 - + - +
873A HIS* 2.9 69.1 + + - -
894A GLN* 3.8 19.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 870 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606A MET* 3.8 23.6 - - + -
612A LEU* 3.8 9.0 - - + -
615A ILE* 3.6 17.2 - - + +
631A PHE* 4.0 23.6 - - + -
679A PHE* 3.6 17.5 - - + -
866A LEU* 2.9 43.1 + - + +
867A THR* 3.8 3.6 - - - +
869A HIS* 1.3 80.1 - - - +
871A ARG* 1.3 58.3 + - - +
873A HIS* 3.3 2.6 + - - +
874A GLN* 2.9 57.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 871 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550A SER* 4.1 10.3 + - - -
552A TYR* 3.4 33.7 + - + -
555A GLU* 2.4 48.4 + - - +
662A TRP* 5.9 0.4 - - - -
663A ASN 2.5 32.3 + - - -
664A LEU* 3.7 14.8 - - - +
665A LYS 4.9 8.9 + - - -
666A GLY* 5.5 1.0 - - - +
678A ARG* 4.0 17.6 - - + +
679A PHE* 3.6 24.7 - - + -
867A THR 2.9 25.3 + - - +
868A HIS* 3.9 3.4 - - - +
870A ILE* 1.3 76.4 - - - +
872A TYR* 1.3 58.0 + - - +
874A GLN* 3.2 12.0 + - - +
875A CYS* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 872 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A ILE* 3.6 25.4 - - + -
552A TYR* 4.2 5.1 - + + -
868A HIS* 2.9 28.4 + + + +
869A HIS* 3.6 5.4 - + - +
871A ARG* 1.3 77.2 - - - +
873A HIS* 1.3 62.4 + + - +
875A CYS* 3.0 20.7 + - - -
876A LEU* 2.9 58.4 + - + +
894A GLN* 4.2 29.6 - - + -
897A MET* 3.2 22.7 - - - +
1021A PHE* 2.4 35.3 + - - -
1023A LEU* 3.9 20.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 873 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614A ASN 5.1 5.0 - - - +
615A ILE* 4.1 17.6 - - + +
616A PRO* 3.4 21.6 - - + +
869A HIS* 2.9 57.1 + + - +
870A ILE 3.9 4.0 - - - +
872A TYR* 1.3 79.8 - + - +
874A GLN* 1.3 59.4 + - - +
875A CYS 3.4 0.2 - - - -
876A LEU* 3.8 24.9 + - + +
877A MET* 4.0 10.7 - - - +
890A ARG* 3.5 40.8 + - + +
894A GLN* 2.9 33.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 874 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A GLU* 5.1 5.1 - - + +
608A ALA* 5.8 0.4 - - - +
610A ALA* 4.8 12.2 + - - +
611A PRO 4.6 9.5 + - - -
612A LEU* 4.0 15.4 - - - +
615A ILE* 4.2 10.2 - - + +
678A ARG* 5.4 7.1 + - - -
679A PHE* 4.5 10.4 - - - -
870A ILE* 2.9 41.7 + - - +
871A ARG* 3.5 13.8 - - - +
872A TYR 3.1 0.2 - - - -
873A HIS* 1.3 78.9 - - - +
875A CYS* 1.3 59.5 + - - +
876A LEU 3.3 0.7 - - - -
877A MET* 3.7 25.7 + - - +
878A HIS* 4.0 9.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 875 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A ILE* 5.8 0.2 - - - -
552A TYR* 4.0 17.3 - - + -
553A PRO* 3.4 36.8 - - - +
554A GLY* 5.7 0.2 - - - -
555A GLU* 5.5 3.4 - - + -
871A ARG 2.9 11.0 + - - +
872A TYR* 3.0 39.9 + - - -
874A GLN* 1.3 73.5 - - - +
876A LEU* 1.3 67.5 + - - +
877A MET 3.1 2.9 - - - -
878A HIS* 3.2 14.2 + - - +
1020A ARG 5.7 0.7 - - - -
1021A PHE* 3.1 25.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 876 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872A TYR* 2.9 62.5 + - + +
873A HIS* 3.9 33.2 - - + +
874A GLN 3.3 0.6 - - - -
875A CYS* 1.3 77.1 - - - +
877A MET* 1.3 58.5 + - - +
878A HIS 3.1 2.7 - - - -
879A LEU* 2.8 28.3 + - + +
880A ASP* 3.0 18.4 + - - +
890A ARG* 4.1 12.1 - - - +
893A LEU* 3.7 34.0 - - + +
894A GLN 4.7 4.0 - - - +
897A MET* 5.8 0.4 - - + -
1021A PHE* 4.3 9.2 - - + -
----------------------------------------------------------
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