Contacts of the helix formed by residues 668 - 685 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666A PRO* 3.7 0.9 - - - +
667A HIS* 1.3 82.5 - - - +
669A PHE* 1.3 63.9 + - - +
670A GLU* 3.1 24.1 + - - +
671A ASP* 3.0 44.3 + - - +
672A CYS* 3.5 9.9 + - - -
744A ILE* 3.8 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 669 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668A ASN* 1.3 75.9 - - - +
670A GLU* 1.3 64.3 + - - +
672A CYS* 2.9 15.3 + - + +
673A ILE* 3.0 30.7 + - + +
735A ALA* 3.5 35.2 - - + -
736A SER* 3.9 5.4 - - - -
739A ALA* 4.0 12.1 - - + -
744A ILE* 3.7 6.7 - - - +
745A LYS 3.9 14.5 + - - +
746A SER* 3.5 29.4 - - - -
747A ASP* 3.7 33.7 - - + +
748A ASP* 3.3 20.6 - - - -
757A GLU* 4.4 0.4 - - - -
758A TYR* 3.3 22.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 670 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668A ASN* 3.1 18.3 - - - +
669A PHE* 1.3 77.0 - - - +
671A ASP* 1.3 58.7 + - - +
673A ILE* 3.0 28.3 + - - +
674A LYS* 3.0 45.8 + - - +
747A ASP* 5.2 2.2 + - - -
761A VAL* 3.8 26.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 671 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665A LYS 4.7 0.3 - - - +
666A PRO* 3.7 19.0 - - + +
667A HIS* 2.8 34.7 + - - +
668A ASN* 3.0 26.9 + - - +
670A GLU* 1.3 77.6 - - - +
672A CYS* 1.3 58.8 + - - +
674A LYS* 3.6 21.1 + - - +
675A TRP* 3.0 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 672 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666A PRO* 3.7 28.7 - - - -
668A ASN 3.7 8.7 - - - -
669A PHE* 2.9 13.1 + - + +
671A ASP* 1.3 78.7 - - - +
673A ILE* 1.3 62.5 + - - +
675A TRP* 3.4 8.3 + - - +
676A ALA* 3.1 24.3 + - - +
735A ALA* 3.6 26.3 - - + +
738A ARG* 4.0 7.4 - - + -
739A ALA* 3.8 30.7 - - - -
744A ILE* 4.4 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 673 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669A PHE* 3.0 40.5 + - + +
670A GLU* 3.0 10.5 + - - +
672A CYS* 1.3 77.0 - - - +
674A LYS* 1.3 63.4 + - - +
676A ALA* 3.2 4.5 + - - +
677A ARG* 2.9 22.4 + - - +
731A VAL* 4.0 7.7 - - + +
735A ALA* 4.0 5.6 - - + -
757A GLU* 4.3 13.9 - - + +
758A TYR* 3.7 42.4 - - + +
761A VAL* 3.9 34.3 - - + -
762A ILE* 4.1 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 674 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670A GLU* 3.0 41.5 + - - +
671A ASP* 3.7 19.5 + - - +
673A ILE* 1.3 75.4 - - - +
675A TRP* 1.3 62.7 + - - +
677A ARG 3.3 0.7 + - - -
678A LEU* 2.8 34.0 + - + +
761A VAL* 4.1 11.2 - - + -
765A MET* 3.7 39.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 675 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623A TYR* 3.9 40.4 - + + -
624A PHE* 4.0 21.3 - + - -
664A SER* 4.4 11.5 + - - -
671A ASP 3.0 17.9 + - - +
672A CYS 3.6 5.4 - - - +
674A LYS* 1.3 77.4 - - - +
676A ALA* 1.3 85.2 + - + +
678A LEU* 3.2 8.6 + - - +
679A GLU* 2.8 59.7 + - + +
730A PHE* 6.2 1.1 - + - -
734A GLY* 4.1 9.4 - - - -
738A ARG* 3.1 60.4 - - + +
833A PHE* 6.0 0.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 676 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672A CYS 3.1 14.0 + - - +
673A ILE 3.7 3.4 - - - +
675A TRP* 1.3 93.5 - - + +
677A ARG* 1.3 52.7 + - - +
679A GLU* 3.2 3.1 + - - +
680A PHE* 2.8 30.7 + - - +
730A PHE* 3.3 12.7 - - + +
731A VAL* 3.7 32.8 - - - +
734A GLY* 4.1 5.2 - - - -
735A ALA 3.8 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 677 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673A ILE 2.9 17.2 + - - +
674A LYS 3.8 2.7 - - - +
676A ALA* 1.3 76.0 - - - +
678A LEU* 1.3 60.7 + - - +
680A PHE* 3.3 5.7 - - - +
681A GLU* 2.6 51.8 + - - +
720A PHE* 3.3 51.0 - - - +
731A VAL* 3.9 9.1 - - + +
762A ILE* 3.6 37.4 - - + +
765A MET* 3.7 25.8 - - + -
767A ILE* 3.8 28.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 678 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674A LYS* 2.8 26.2 + - + +
675A TRP* 3.6 7.0 - - + +
677A ARG* 1.3 74.8 - - - +
679A GLU* 1.3 66.3 + - - +
681A GLU* 3.1 10.6 + - + +
682A LYS* 3.0 29.1 + - - +
765A MET* 3.7 20.0 - - + -
766A ILE 4.4 4.0 - - - +
767A ILE* 4.8 7.0 - - + -
768A PRO* 3.8 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 679 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623A TYR* 2.4 41.0 + - + +
675A TRP* 2.8 51.6 + - + +
676A ALA* 3.4 9.6 - - - +
678A LEU* 1.3 73.8 - - - +
680A PHE* 1.3 66.3 + - - +
682A LYS* 3.1 31.5 + - - +
683A LYS* 3.0 39.5 + - - +
730A PHE* 4.2 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 680 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676A ALA 2.8 13.9 + - - +
677A ARG* 3.3 19.1 - - - +
678A LEU 3.2 0.2 - - - -
679A GLU* 1.3 76.7 - - - +
681A GLU* 1.3 67.4 + - - +
684A PHE* 3.2 51.6 + + + +
685A ASN* 5.8 0.7 - - + -
718A LEU* 3.8 31.2 - - + -
720A PHE* 3.7 43.1 - + + -
727A HIS* 3.8 28.5 - + - -
730A PHE* 3.5 21.7 - + + -
731A VAL* 4.7 0.9 - - + -
840A CYS* 3.7 19.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 681 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677A ARG* 2.6 39.4 + - - +
678A LEU* 3.1 15.7 + - + +
680A PHE* 1.3 79.3 - - - +
682A LYS* 1.3 61.0 + - - +
685A ASN* 3.2 38.3 + - - +
686A HIS* 2.8 49.1 + - + +
718A LEU 4.8 3.3 - - - +
719A GLU* 5.7 0.5 - - - +
720A PHE* 5.2 1.2 + - - +
767A ILE* 3.5 27.3 - - + +
768A PRO* 4.7 1.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 682 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678A LEU* 3.0 17.2 + - - +
679A GLU* 3.1 36.6 + - - +
681A GLU* 1.3 77.9 - - - +
683A LYS* 1.3 71.0 + - + +
686A HIS* 4.1 13.2 - - + -
687A ASP* 2.9 40.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 683 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615A TRP* 4.0 25.7 - - + -
619A LEU* 3.7 34.0 - - + +
623A TYR* 3.5 27.2 + - - +
679A GLU* 3.0 23.4 + - - +
682A LYS* 1.3 86.0 - - - +
684A PHE* 1.3 76.7 + - + +
687A ASP* 3.7 28.1 + - - +
688A ILE* 4.1 8.5 - - - +
730A PHE* 5.4 1.6 - - + -
841A ARG* 5.2 2.9 + - - -
844A ASN* 4.2 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 684 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615A TRP* 4.0 18.2 - + - -
680A PHE* 3.2 50.6 + + + +
683A LYS* 1.3 86.3 - - + +
685A ASN* 1.3 61.7 + - - +
688A ILE* 3.5 7.8 - - - +
717A PRO* 3.6 0.3 - - - +
718A LEU* 3.0 41.3 + - + -
730A PHE* 3.8 34.5 - + - -
837A CYS* 3.8 16.8 - - - -
840A CYS* 3.6 26.5 - - + -
841A ARG* 3.8 10.5 - - + -
844A ASN* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 685 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680A PHE* 4.1 1.5 + - + +
681A GLU* 3.2 36.8 + - - +
683A LYS 3.7 0.2 - - - -
684A PHE* 1.3 80.6 - - - +
686A HIS* 1.3 77.9 + - - +
687A ASP 3.5 1.1 - - - -
688A ILE* 3.4 3.0 + - - +
689A LYS* 3.0 67.8 + - - +
717A PRO* 3.7 9.3 - - - +
718A LEU* 2.9 24.8 - - + +
719A GLU* 4.2 7.6 - - - +
----------------------------------------------------------
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