Contacts of the helix formed by residues 668 - 685 (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 ASN 668 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667C HIS* 1.3 80.3 - - - +
669C PHE* 1.3 64.6 + - - +
670C GLU* 3.2 17.4 - - + +
671C ASP* 2.7 50.5 + - - +
672C CYS* 3.4 17.3 + - - -
744C ILE* 3.5 16.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 669 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668C ASN* 1.3 76.5 - - - +
670C GLU* 1.3 58.7 + - - +
672C CYS* 2.8 23.2 + - - +
673C ILE* 3.0 26.4 + - + -
735C ALA* 3.7 30.5 - - + -
736C SER* 3.7 11.7 - - - -
739C ALA* 3.6 15.5 - - + -
744C ILE* 3.5 6.9 - - - +
745C LYS 4.1 7.2 - - - +
746C SER* 3.5 29.4 - - - -
747C ASP* 3.4 35.1 + - + +
748C ASP* 4.1 4.9 - - - -
757C GLU* 3.7 17.0 - - - -
758C TYR* 3.2 29.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 670 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668C ASN* 3.2 14.8 - - + +
669C PHE* 1.3 77.4 - - - +
671C ASP* 1.3 51.2 + - - +
673C ILE* 2.9 11.3 + - - +
674C LYS* 2.8 42.5 + - + +
747C ASP* 4.3 6.6 - - - +
757C GLU* 3.8 28.9 - - - +
761C VAL* 3.4 26.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 671 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665C LYS 5.5 0.2 - - - -
666C PRO* 3.8 12.6 - - + +
667C HIS* 2.9 43.2 + - - +
668C ASN* 2.7 31.2 + - - +
670C GLU* 1.3 72.1 - - - +
672C CYS* 1.3 56.9 + - - +
674C LYS* 3.2 27.0 - - - +
675C TRP* 2.9 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 672 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666C PRO* 4.1 4.7 - - - -
668C ASN 3.4 16.6 - - - -
669C PHE* 2.8 12.4 + - + +
671C ASP* 1.3 72.3 - - - +
673C ILE* 1.3 65.3 + - - +
675C TRP* 3.3 8.4 + - - +
676C ALA* 3.0 24.6 + - - +
735C ALA* 3.5 26.6 - - + +
738C ARG* 3.9 13.7 - - + -
739C ALA* 3.6 34.8 - - + -
744C ILE* 4.0 10.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 673 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669C PHE* 3.0 39.3 + - + +
670C GLU* 2.9 14.6 + - - +
672C CYS* 1.3 72.6 - - - +
674C LYS* 1.3 64.8 + - - +
676C ALA* 3.1 3.6 + - - +
677C ARG* 3.0 23.1 + - - +
731C VAL* 4.0 9.5 - - + +
735C ALA* 3.9 6.1 - - + -
757C GLU* 4.0 22.2 - - + +
758C TYR* 3.6 42.2 - - + +
761C VAL* 3.7 22.7 - - + -
762C ILE* 4.0 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 674 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670C GLU* 2.8 25.8 + - + +
671C ASP* 3.2 29.8 - - - +
673C ILE* 1.3 72.7 - - - +
675C TRP* 1.3 64.3 + - - +
677C ARG* 3.2 2.8 + - - +
678C LEU* 3.1 30.2 + - + +
761C VAL* 4.4 11.9 + - + +
764C HIS 5.4 4.2 + - - -
765C MET* 4.1 34.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 675 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623C TYR* 3.6 47.6 - + + -
624C PHE* 3.8 26.0 - + - -
664C SER* 5.7 4.3 - - - -
666C PRO* 6.3 0.2 - - + -
671C ASP 2.9 17.4 + - - +
672C CYS* 3.4 7.9 - - - +
673C ILE 3.2 0.2 - - - -
674C LYS* 1.3 71.7 - - - +
676C ALA* 1.3 81.4 + - + +
678C LEU* 3.1 10.4 + - - +
679C GLU* 3.0 52.1 + - + +
730C PHE* 6.2 1.1 - + - -
734C GLY* 3.8 10.8 - - - -
738C ARG* 3.3 60.1 - - + +
833C PHE* 5.9 0.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 676 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672C CYS 3.0 15.9 + - - +
673C ILE 3.8 3.1 - - - +
675C TRP* 1.3 91.1 - - + +
677C ARG* 1.3 56.7 - - - +
679C GLU* 3.4 2.6 + - - -
680C PHE* 3.0 23.7 + - - +
730C PHE* 3.4 14.6 - - + +
731C VAL* 3.7 34.8 - - + +
734C GLY* 4.1 4.7 - - - -
735C ALA 3.8 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 677 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673C ILE 3.0 15.4 + - - +
674C LYS 3.7 3.6 - - - +
676C ALA* 1.3 76.4 - - - +
678C LEU* 1.3 61.0 + - - +
680C PHE* 3.4 5.8 - - - +
681C GLU* 2.7 56.6 + - - +
720C PHE* 3.5 44.6 - - - +
731C VAL* 4.1 8.0 - - + +
762C ILE* 3.8 38.5 - - + +
765C MET* 3.5 31.6 - - + -
767C ILE* 3.6 25.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 678 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674C LYS* 3.1 20.8 + - + +
675C TRP* 3.6 10.5 - - + +
677C ARG* 1.3 75.9 - - - +
679C GLU* 1.3 65.2 + - - +
681C GLU* 3.2 9.2 + - + +
682C LYS* 3.0 35.4 + - - +
765C MET* 3.7 23.1 - - + -
766C ILE 4.6 2.9 - - - +
767C ILE* 4.7 6.1 - - + -
768C PRO* 3.9 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 679 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623C TYR* 2.6 42.1 + - + +
675C TRP* 3.0 50.1 + - + +
676C ALA* 3.7 9.0 - - - +
678C LEU* 1.3 72.8 - - - +
680C PHE* 1.3 67.6 + - - +
682C LYS* 2.9 40.3 + - - +
683C LYS* 3.0 38.8 + - - +
730C PHE* 4.4 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 680 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676C ALA 3.0 15.0 + - - +
677C ARG* 3.4 21.1 - - - +
679C GLU* 1.3 74.8 - - - +
681C GLU* 1.3 67.1 + - - +
684C PHE* 3.0 52.7 + + + +
718C LEU* 4.0 28.0 - - + -
720C PHE* 3.6 53.6 - + + -
727C HIS* 3.8 31.4 - + + -
730C PHE* 3.7 17.6 - + + -
731C VAL* 5.0 0.2 - - + -
840C CYS* 4.0 12.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 681 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677C ARG* 2.7 39.2 + - - +
678C LEU* 3.2 14.1 + - + +
680C PHE* 1.3 85.4 - - - +
682C LYS* 1.3 57.0 + - - +
685C ASN* 3.1 38.3 + - - +
686C HIS* 2.8 47.8 + - + +
718C LEU 4.5 2.8 - - - +
720C PHE 5.1 1.6 + - - -
767C ILE* 3.4 27.5 - - + +
768C PRO* 4.7 2.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 682 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660C ASP* 5.7 4.0 + - - -
678C LEU* 3.0 23.2 + - - +
679C GLU* 2.9 39.4 + - - +
681C GLU* 1.3 77.3 - - + +
683C LYS* 1.3 70.4 + - - +
686C HIS* 3.9 16.8 - - + -
687C ASP* 2.8 39.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 683 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615C TRP* 4.0 26.8 - - + -
619C LEU* 4.1 31.0 - - + +
623C TYR* 3.6 20.5 + - - +
679C GLU* 3.0 26.0 + - - +
682C LYS* 1.3 88.8 - - - +
684C PHE* 1.3 76.5 + - + +
685C ASN 3.6 0.2 - - - -
687C ASP* 3.6 31.3 + - - +
688C ILE* 3.9 14.7 - - - +
730C PHE* 5.2 1.3 - - + -
841C ARG* 5.6 2.3 + - - -
844C ASN* 4.3 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 684 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615C TRP* 3.8 18.8 - + - -
680C PHE* 3.0 42.9 + + + +
683C LYS* 1.3 88.2 - - + +
685C ASN* 1.3 60.4 + - - +
688C ILE* 3.9 3.7 - - - +
717C PRO* 3.7 1.6 - - - +
718C LEU* 3.0 40.9 + - + -
730C PHE* 3.6 38.6 - + - -
837C CYS* 3.7 16.4 - - - -
840C CYS* 3.4 31.6 - - + -
841C ARG* 3.6 10.8 - - + -
844C ASN* 3.0 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 685 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680C PHE* 3.9 1.1 + - + -
681C GLU* 3.1 39.7 + - - +
684C PHE* 1.3 79.8 - - - +
686C HIS* 1.3 88.1 + - - +
687C ASP 3.5 1.1 - - - -
688C ILE* 3.4 4.8 + - - +
689C LYS* 3.0 63.0 + - - +
717C PRO* 3.8 9.6 - - - +
718C LEU 3.3 18.2 - - - +
719C GLU* 5.2 2.8 - - - +
----------------------------------------------------------
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