Contacts of the helix formed by residues 829 - 846 (chain C) in PDB entry 3CMM
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 HIS 829 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732C VAL* 4.8 4.5 - - + +
733C ALA* 3.8 11.9 - - + +
736C SER* 3.8 35.6 + - - -
737C LEU* 3.9 11.9 - - + +
748C ASP* 4.4 10.5 + - - +
751C SER* 4.7 19.3 - - - -
826C ASP 4.6 3.8 + - - -
827C THR 3.4 15.0 + - - -
828C ASN* 1.3 89.3 - - - +
830C HIS* 1.3 58.5 + - - +
831C ILE 3.6 1.3 - - - -
832C GLU* 2.5 41.2 + - - +
833C PHE* 2.8 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 830 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620C PHE* 3.8 14.5 - + + -
737C LEU* 3.8 11.5 - - + +
819C VAL* 3.4 22.9 - - + +
820C ASP 3.5 16.6 + - - -
821C PHE* 3.9 21.1 - - + -
822C GLU* 3.0 33.1 - - - +
828C ASN* 3.0 46.0 + - + +
829C HIS* 1.3 75.0 - - - +
831C ILE* 1.3 58.3 + - + +
833C PHE* 3.1 5.0 + - - +
834C ILE* 2.9 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 831 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821C PHE* 4.1 26.9 - - + -
822C GLU 5.2 0.4 - - - +
823C LYS* 3.7 28.0 - - + +
825C ASP 5.7 3.1 - - - +
826C ASP* 5.7 4.9 - - - +
828C ASN* 4.5 1.4 - - - +
830C HIS* 1.3 76.2 - - + +
832C GLU* 1.3 68.6 + - - +
834C ILE* 3.0 8.6 + - + +
835C THR* 2.7 43.5 + - - +
852C ARG* 3.7 31.0 - - + +
853C GLN* 5.6 0.4 - - - +
855C THR* 4.8 1.3 - - + -
856C LYS* 4.0 29.6 - - + +
859C ALA* 5.2 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 832 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729C HIS* 2.9 33.2 + - + +
732C VAL* 3.9 11.3 - - - +
733C ALA* 3.6 15.8 - - + +
753C PRO* 5.9 0.3 - - - +
826C ASP 6.0 1.6 - - - +
829C HIS* 2.5 48.6 + - - +
831C ILE* 1.3 76.4 - - - +
833C PHE* 1.3 61.1 + - - +
835C THR* 4.0 1.5 - - - -
836C ALA* 3.0 26.0 + - - +
852C ARG* 3.7 38.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 833 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616C ALA 4.4 1.1 - - - -
619C LEU 4.8 0.4 - - - -
620C PHE* 3.8 39.0 - + + -
623C TYR* 3.8 22.9 - + - -
624C PHE* 3.9 16.6 - + - -
675C TRP* 5.9 0.9 - + - -
730C PHE* 3.7 40.2 - + - -
733C ALA* 3.6 10.3 - - + +
734C GLY* 3.9 26.2 - - - -
737C LEU* 3.8 11.7 - - + -
829C HIS 2.8 21.4 + - - +
830C HIS 3.1 4.2 + - - +
832C GLU* 1.3 73.4 - - - +
834C ILE* 1.3 62.6 + - - +
836C ALA* 3.2 2.2 + - - +
837C CYS* 2.8 49.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 834 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613C ILE* 4.4 4.7 - - + +
616C ALA* 3.6 15.8 - - + +
617C LYS* 4.4 14.6 - - + +
620C PHE* 4.0 31.9 - - + -
821C PHE* 3.4 36.8 - - + -
830C HIS 2.9 19.0 + - - +
831C ILE* 3.9 5.8 - - + +
833C PHE* 1.3 75.9 - - - +
835C THR* 1.3 58.2 + - - +
838C SER* 2.9 34.1 + - - -
855C THR* 3.6 21.3 - - + -
859C ALA* 4.1 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 835 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726C ASP* 5.3 0.7 - - - +
831C ILE* 2.7 39.5 + - - +
832C GLU* 4.0 4.0 - - - -
834C ILE* 1.3 72.6 - - - +
836C ALA* 1.3 57.9 + - - +
838C SER* 3.7 1.3 - - - -
839C ASN* 2.9 52.5 + - - +
850C ALA 3.7 7.9 - - - +
851C ASP* 4.0 10.5 - - - -
852C ARG* 3.5 14.7 - - + +
855C THR* 3.4 28.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 836 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726C ASP* 3.6 18.7 - - - +
729C HIS* 3.8 12.1 - - + -
730C PHE* 3.4 32.8 - - - +
832C GLU 3.0 19.1 + - - +
833C PHE 3.9 1.8 - - - +
835C THR* 1.3 76.0 - - - +
837C CYS* 1.3 58.0 + - - +
839C ASN* 3.3 2.3 + - - +
840C CYS* 2.9 35.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 837 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615C TRP* 3.5 24.5 - - - -
616C ALA* 3.6 16.2 - - + -
619C LEU* 3.7 19.7 - - - -
684C PHE* 3.7 8.2 - - - -
730C PHE* 3.7 28.9 - - + -
833C PHE* 2.8 26.6 + - + +
836C ALA* 1.3 75.4 - - - +
838C SER* 1.3 65.5 + - - +
840C CYS 3.3 0.7 + - - -
841C ARG* 3.2 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 838 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609C ILE* 4.1 1.6 - - - +
612C THR* 2.8 40.3 + - - +
613C ILE* 3.2 21.2 - - - +
616C ALA* 3.5 15.7 - - - +
834C ILE 2.9 19.4 + - - -
835C THR* 3.7 3.8 + - - -
837C CYS* 1.3 77.3 - - - +
839C ASN* 1.3 63.3 + - - +
841C ARG* 3.2 3.5 + - - +
842C ALA 2.9 22.7 + - - -
855C THR* 5.0 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 839 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609C ILE* 4.0 3.3 - - - +
726C ASP* 3.3 35.1 + - - +
835C THR* 2.9 29.8 + - - +
836C ALA 3.8 0.4 - - - +
838C SER* 1.3 81.9 + - - +
840C CYS* 1.3 58.9 + - - +
842C ALA* 3.5 5.5 - - - +
843C GLN* 2.8 34.2 + - - +
849C THR* 3.4 16.0 - - + +
850C ALA* 2.7 43.6 + - - +
855C THR* 5.2 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 840 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680C PHE* 4.0 19.1 - - - -
684C PHE* 3.4 35.0 - - + -
718C LEU* 3.3 17.3 - - + +
726C ASP* 3.3 30.5 - - - -
727C HIS* 4.1 4.5 - - - -
730C PHE* 4.3 3.8 - - - -
836C ALA 2.9 25.1 + - - +
838C SER 3.2 0.4 - - - -
839C ASN* 1.3 77.1 - - - +
841C ARG* 1.3 62.5 + - - +
843C GLN* 3.4 4.9 + - - +
844C ASN* 3.1 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 841 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602C LEU 2.9 27.7 + - - -
603C ARG 3.2 19.2 + - - -
604C SER* 4.6 0.2 - - - +
606C PRO* 3.6 22.3 - - + +
612C THR* 3.2 20.2 - - - +
615C TRP* 3.3 58.7 - - + +
683C LYS 5.6 2.6 + - - -
684C PHE* 3.6 3.0 - - + -
688C ILE* 4.6 8.7 - - - +
691C LEU* 5.8 0.4 - - - +
837C CYS 3.2 11.9 + - - +
838C SER 3.6 3.8 - - - +
840C CYS* 1.3 75.8 - - - +
842C ALA* 1.3 64.4 + - - +
844C ASN* 3.1 27.9 + - - +
845C TYR* 3.2 38.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 842 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609C ILE* 3.9 23.6 - - + -
612C THR* 3.5 7.1 + - - +
838C SER 2.9 13.7 + - - +
839C ASN* 3.5 11.0 - - - +
841C ARG* 1.3 74.6 - - - +
843C GLN* 1.3 66.4 + - - +
845C TYR 3.1 1.9 + - - -
846C PHE 3.0 20.1 + - - -
847C ILE* 3.0 37.3 + - + +
849C THR* 4.2 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 843 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A SER* 5.1 1.4 - - - -
716C THR* 5.9 0.3 - - - -
718C LEU* 4.0 15.3 - - + +
724C ASN* 3.2 25.1 + - - +
726C ASP* 2.9 36.0 + - - +
727C HIS* 2.7 28.7 + - - -
839C ASN 2.8 17.7 + - - +
840C CYS* 3.5 10.5 - - - +
842C ALA* 1.3 73.5 - - - +
844C ASN* 1.3 61.7 + - - +
845C TYR 3.0 1.6 + - - -
846C PHE* 3.2 18.1 + - - +
847C ILE 4.5 2.2 + - - -
849C THR* 4.3 11.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 844 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683C LYS 4.3 0.3 - - - +
684C PHE* 3.0 43.9 + - - -
688C ILE* 3.5 18.4 - - + +
715C PRO* 2.9 7.0 - - + +
716C THR* 2.7 55.7 + - - -
718C LEU* 3.5 8.9 - - - +
840C CYS 3.1 19.3 + - - +
841C ARG* 3.1 14.8 + - - +
843C GLN* 1.3 74.3 - - - +
845C TYR* 1.3 70.6 + - + +
846C PHE* 4.0 4.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 845 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604C SER 2.6 31.4 + - - -
605C PHE* 4.6 1.6 - - - -
606C PRO* 3.6 35.4 - - + +
688C ILE* 3.8 20.6 - - + +
691C LEU* 3.2 18.0 - - + +
708C TRP* 4.8 1.3 - + - -
713C ARG* 3.0 56.5 + - + +
714C ALA 4.9 1.1 - - - -
715C PRO* 3.9 16.6 - - + -
841C ARG* 3.2 39.2 + - + +
842C ALA 3.1 2.6 + - - -
844C ASN* 1.3 81.0 - - + +
846C PHE* 1.3 69.3 + - - +
847C ILE* 3.3 21.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 846 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C GLU* 4.6 1.4 - - - +
697C LYS* 6.2 0.4 - - - -
713C ARG* 2.8 29.9 + - - +
714C ALA 4.0 16.2 - - - -
716C THR* 3.3 35.2 - - + -
842C ALA 3.0 5.2 + - - -
843C GLN* 3.2 10.5 + - - +
844C ASN 4.1 4.3 - - - -
845C TYR* 1.3 82.7 - - - +
847C ILE* 1.3 60.3 + - - +
848C GLU* 4.2 0.9 + - - +
----------------------------------------------------------
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