Contacts of the helix formed by residues 933 - 942 (chain C) in PDB entry 6CIM
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 THR 933 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726C ILE* 4.8 2.2 - - - -
799C GLY* 5.0 5.1 - - - -
932C ILE* 1.3 78.8 - - - +
934C ASN* 1.3 68.1 + - - +
935C TYR* 4.0 15.2 - - + +
936C PHE* 3.2 23.0 + - - +
937C HIS* 3.0 24.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 934 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709C GLU* 2.8 41.8 + - - +
721C SER* 5.0 10.0 + - - +
726C ILE* 3.7 32.0 - - - +
727C CYS* 5.6 0.2 - - - -
734C ARG* 5.8 1.4 + - - -
932C ILE 5.0 0.7 - - - +
933C THR* 1.3 74.3 - - - +
935C TYR* 1.3 74.0 + - + +
937C HIS* 3.7 6.7 - - - +
938C LYS* 2.9 41.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 935 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709C GLU* 5.2 10.2 - - + +
791C ILE* 3.9 17.9 - - + +
795C HIS* 3.1 69.6 + + + +
798C ILE* 5.6 6.5 - - + -
799C GLY* 4.7 7.9 - - - -
933C THR* 3.1 11.6 - - - +
934C ASN* 1.3 96.2 + - + +
936C PHE* 1.3 53.9 + - - +
938C LYS* 3.4 3.1 + - + +
939C THR* 2.7 37.7 + - - -
44G A 4.1 17.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 936 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741C LEU* 5.6 1.6 - - + -
799C GLY* 4.2 18.1 - - - +
800C ASN* 3.0 36.1 - - - -
803C GLU* 4.2 32.1 - - + -
804C PHE* 6.5 0.2 - + - -
916C PHE* 3.8 15.7 - + - -
920C LEU* 4.6 8.1 - - + -
932C ILE* 3.8 24.7 - - + -
933C THR* 3.2 21.2 + - - +
935C TYR* 1.3 76.3 - - - +
937C HIS* 1.3 67.5 + - - +
939C THR* 3.2 6.0 + - - -
940C LEU* 2.9 60.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 937 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726C ILE* 4.1 18.6 - - + -
727C CYS* 3.1 25.0 - - + +
730C CYS* 3.2 7.8 - - - -
732C THR* 3.5 10.7 - - + +
737C ALA* 3.7 17.2 + - + +
741C LEU 4.8 4.6 + - - -
744C HIS* 4.1 19.0 + + - -
932C ILE* 4.1 10.8 - - + +
933C THR 3.0 16.8 + - - +
934C ASN* 3.7 6.1 - - - +
936C PHE* 1.3 77.2 - - - +
938C LYS* 1.3 66.8 + - + +
940C LEU* 3.8 3.2 - - - +
941C ALA* 2.9 33.9 + - + +
942C HIS* 3.9 2.7 - - - -
1101C ZN 2.0 37.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 938 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709C GLU* 3.6 27.0 + - - +
727C CYS* 4.6 6.5 - - - +
728C THR* 3.8 30.0 + - - +
729C LEU* 4.9 11.8 - - + +
789C PRO* 5.2 1.4 - - - +
790C SER 3.8 19.1 + - - +
791C ILE* 3.9 32.7 - - + +
934C ASN* 2.9 25.6 + - - +
935C TYR* 3.9 5.0 - - + +
937C HIS* 1.3 80.7 - - + +
939C THR* 1.3 58.5 + - - +
942C HIS* 2.9 48.9 + - + +
943C VAL* 3.5 9.1 + - - +
946C ILE* 5.4 1.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 939 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791C ILE* 5.1 0.7 - - - +
796C CYS* 3.4 29.1 + - + +
800C ASN* 3.6 27.6 - - - +
893C TRP* 3.7 24.7 - - + -
909C TYR* 2.9 26.0 + - - +
935C TYR 2.7 23.4 + - - -
936C PHE* 3.2 9.5 + - - -
938C LYS* 1.3 78.4 - - - +
940C LEU* 1.3 67.3 + - + +
943C VAL* 3.5 13.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 940 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741C LEU* 3.9 37.5 - - + +
742C VAL* 3.9 16.1 - - + +
800C ASN* 4.8 2.7 - - - +
889C MET* 4.1 19.7 - - + -
909C TYR* 5.0 3.0 - - - -
913C SER* 3.0 24.6 + - - +
916C PHE* 3.9 31.4 - - + -
920C LEU* 4.9 0.2 - - + -
932C ILE* 5.3 0.9 - - + -
936C PHE* 2.9 58.9 + - + +
937C HIS* 4.1 0.9 - - - +
939C THR* 1.3 83.5 - - + +
941C ALA* 1.3 59.8 + - - +
943C VAL 5.3 0.2 - - - -
944C PRO* 5.5 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 941 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741C LEU 3.9 10.8 - - - +
742C VAL 3.7 17.9 - - - +
744C HIS* 3.6 26.7 - - + +
937C HIS* 2.9 22.1 + - + +
940C LEU* 1.3 79.5 - - - +
942C HIS* 1.3 69.6 + - + +
943C VAL 3.8 1.3 - - - -
944C PRO* 4.7 5.1 - - - +
945C GLU* 3.4 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 942 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727C CYS* 3.5 5.2 - - - -
729C LEU* 3.7 33.4 - - + +
730C CYS* 3.6 0.8 - - + -
744C HIS* 3.8 9.4 - - + -
745C SER 3.6 37.2 - - - -
746C ILE* 4.0 7.4 - - + +
937C HIS* 3.9 2.4 - - - -
938C LYS* 2.9 23.5 + - + +
941C ALA* 1.3 79.3 + - + +
943C VAL* 1.3 64.1 + - - +
944C PRO 3.5 1.8 - - - -
945C GLU* 3.4 17.4 + - - -
946C ILE* 2.9 31.5 + - + +
1101C ZN 2.0 37.4 - - - -
----------------------------------------------------------
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