Contacts of the helix formed by residues 664 - 683 (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 ASP 664 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660C ALA* 4.9 3.7 - - + +
661C ASP* 2.8 29.8 + - + +
662C GLU 3.3 0.2 - - - -
663C SER* 1.3 74.4 - - - +
665C HIS* 1.3 62.8 + - - +
667C THR* 2.6 34.8 + - - +
668C LEU* 2.9 21.9 + - - +
34D LYS* 3.0 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 665 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663C SER 3.2 6.3 + - - +
664C ASP* 1.3 74.0 + - - +
666C GLU* 1.3 71.4 + - - +
668C LEU* 4.3 5.8 - - + -
669C THR* 3.0 59.6 + - + +
714C GLU* 3.0 55.2 + - + +
781C ALA* 5.7 1.6 - - + -
782C LYS 5.1 2.4 + - - -
784C PHE* 4.4 7.7 - + - -
35D GLY* 4.7 12.8 - - - -
36D TRP* 3.4 23.5 + + - -
99D PRO 3.4 11.0 - - - +
100D ASN* 3.0 19.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 666 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548C TYR* 4.7 5.4 - - + -
664C ASP* 3.2 0.4 - - - +
665C HIS* 1.3 77.9 + - - +
667C THR* 1.3 57.6 + - - +
669C THR* 2.9 17.5 + - - -
670C ALA* 3.0 16.5 + - - +
16D GLN* 4.1 6.6 + - - +
33D GLN 4.6 0.3 - - - +
34D LYS* 2.7 44.5 + - - +
35D GLY* 2.7 33.3 + - - -
73D ARG* 3.6 39.9 + - - +
99D PRO* 3.6 27.4 - - + +
101D ASN* 3.6 4.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 667 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538C LEU* 5.8 0.2 - - + -
541C LEU* 6.2 3.1 - - + -
548C TYR* 5.5 5.0 - - - -
552C THR* 3.5 35.0 - - + -
660C ALA* 4.2 9.2 - - + -
664C ASP* 2.6 32.7 + - - +
666C GLU* 1.3 75.6 - - - +
668C LEU* 1.3 65.4 + - - +
670C ALA* 3.3 5.8 + - + +
671C ILE* 3.0 34.5 + - + +
34D LYS* 5.1 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 668 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599C CYS* 5.6 0.7 - - - -
620C VAL* 4.4 19.7 - - + -
658C MET* 4.4 16.6 - - - -
660C ALA* 6.3 0.2 - - + -
661C ASP 4.9 4.2 + - - +
662C GLU* 3.9 21.3 - - - +
664C ASP 2.9 19.2 + - - +
665C HIS* 3.8 5.6 - - - +
667C THR* 1.3 77.6 - - - +
669C THR* 1.3 64.0 + - + +
671C ILE* 3.3 2.7 + - - +
672C LEU* 2.9 59.5 + - + +
711C LEU* 4.5 16.4 - - + -
714C GLU* 5.0 8.3 - - + +
715C VAL* 4.7 5.8 - - + -
784C PHE* 4.4 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 669 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665C HIS* 3.0 41.9 + - + +
666C GLU 2.9 19.2 + - - -
668C LEU* 1.3 75.3 - - + +
670C ALA* 1.3 62.9 + - - +
673C SER* 2.9 31.2 + - - -
784C PHE* 3.7 31.4 - - + -
99D PRO 3.2 11.8 + - - +
100D ASN* 3.4 28.5 - - - +
101D ASN* 3.9 0.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 670 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541C LEU* 4.4 22.9 - - + -
666C GLU 3.0 13.9 + - - +
667C THR* 3.7 7.4 - - - +
669C THR* 1.3 81.4 + - - +
671C ILE* 1.3 61.9 + - + +
673C SER* 3.8 3.5 + - - -
674C PRO* 3.6 8.3 - - - +
101D ASN* 3.5 31.2 - - - +
173D ASN* 2.9 25.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 671 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537C GLY 3.6 22.5 - - - +
538C LEU* 3.9 22.0 - - + -
539C SER* 4.8 0.3 + - - -
541C LEU* 5.8 0.4 - - + -
552C THR* 3.9 19.3 - - + +
554C ALA* 4.1 9.4 - - + -
556C ARG* 5.1 2.8 - - - -
656C CYS* 4.0 14.4 - - - -
658C MET* 3.5 41.7 - - + -
667C THR* 3.0 37.2 + - + +
668C LEU 4.1 1.8 - - - +
670C ALA* 1.3 81.5 - - + +
672C LEU* 1.3 58.3 + - - +
674C PRO* 3.3 15.2 - - - +
675C LEU* 4.7 6.2 + - - +
173D ASN* 5.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 672 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599C CYS* 4.4 19.3 - - - -
622C PHE* 3.9 25.6 - - + -
656C CYS* 4.7 1.3 - - - -
658C MET* 4.0 17.3 - - + -
668C LEU* 2.9 47.1 + - + +
671C ILE* 1.3 76.1 - - - +
673C SER* 1.3 65.2 + - - +
674C PRO 3.3 1.3 - - - -
675C LEU* 3.3 30.5 + - + +
676C ILE* 3.2 28.1 + - + +
715C VAL* 6.0 0.4 - - + -
784C PHE* 4.4 10.3 - - + -
785C ILE* 4.5 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 673 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669C THR* 2.9 20.5 + - - +
670C ALA* 3.8 4.9 + - - -
672C LEU* 1.3 76.2 - - - +
674C PRO* 1.3 79.0 - - - +
676C ILE* 3.1 9.1 + - - +
677C ALA* 2.9 22.5 + - - +
784C PHE* 4.8 10.3 - - - -
100D ASN 5.5 4.5 - - - -
101D ASN* 5.7 2.4 - - - +
172D TRP* 3.4 22.1 + - - -
173D ASN* 4.2 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 674 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539C SER* 3.4 24.2 - - - +
556C ARG* 3.7 7.4 - - - +
670C ALA 3.6 9.2 - - - +
671C ILE 3.3 13.9 - - - +
673C SER* 1.3 98.0 - - - +
675C LEU* 1.3 59.2 + - - +
677C ALA* 3.4 5.9 + - + +
678C GLU* 3.1 30.1 + - - +
169D THR* 3.5 21.6 - - - +
172D TRP* 3.4 28.9 - - + -
173D ASN* 4.4 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 675 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556C ARG* 3.3 30.7 - - - +
557C PHE 3.5 14.8 - - - +
559C TYR* 3.6 17.4 - - + -
622C PHE* 3.4 36.3 - - + -
655C LEU* 4.0 15.9 - - + +
656C CYS* 3.6 26.0 - - + -
671C ILE 5.0 2.7 - - - +
672C LEU* 3.3 20.4 + - + +
674C PRO* 1.3 79.9 - - - +
676C ILE* 1.3 58.8 + - + +
678C GLU* 3.4 10.0 + - - +
679C ARG* 3.0 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 676 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559C TYR* 6.2 0.2 - - + -
597C GLU* 4.2 16.8 - - - +
622C PHE* 4.4 10.8 - - + -
672C LEU* 3.2 17.9 + - + +
673C SER* 3.1 10.6 + - - +
675C LEU* 1.3 75.2 - - + +
677C ALA* 1.3 59.4 + - - +
679C ARG* 3.3 27.3 + - - +
680C GLU* 2.8 34.4 + - + +
784C PHE* 4.0 17.0 - - + +
785C ILE* 3.7 35.9 - - + -
786C GLU 5.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 677 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524C LYS 5.1 2.2 - - - +
525C ASN* 6.1 0.4 - - + -
526C VAL* 5.3 0.2 - - - -
673C SER 2.9 12.9 + - - +
674C PRO* 3.5 9.0 - - + +
676C ILE* 1.3 76.2 - - - +
678C GLU* 1.3 63.3 + - - +
680C GLU* 3.2 8.8 + - - +
681C ALA* 2.9 22.4 + - - +
169D THR* 3.8 16.8 - - + -
172D TRP* 4.1 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 678 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523C LEU* 5.2 0.6 - - + +
526C VAL* 3.9 19.5 - - + +
556C ARG* 3.0 32.6 + - - -
558C ARG* 3.1 19.6 - - + +
559C TYR* 2.9 34.9 + - + +
560C ASP* 5.3 2.9 - - - +
674C PRO 3.1 10.4 + - - +
675C LEU* 3.7 7.2 - - - +
677C ALA* 1.3 75.3 - - - +
679C ARG* 1.3 62.4 + - - +
681C ALA* 3.1 4.0 + - - +
682C MET* 3.0 28.6 + - + +
169D THR* 2.7 31.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 679 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559C TYR* 3.7 15.5 - - + -
597C GLU* 2.7 33.1 + - - -
675C LEU 3.0 16.5 + - - +
676C ILE* 3.7 23.9 - - - +
678C GLU* 1.3 73.2 - - - +
680C GLU* 1.3 82.4 + - - +
682C MET* 3.2 15.1 + - + +
683C LYS* 3.1 43.7 + - - +
702C PHE* 3.8 37.5 + - + +
704C GLY 4.6 5.7 - - - +
785C ILE* 5.1 0.2 - - - +
786C GLU* 3.1 42.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 680 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676C ILE* 2.8 26.3 + - + +
677C ALA* 3.4 7.9 - - - +
679C ARG* 1.3 85.5 + - - +
681C ALA* 1.3 63.4 + - - +
683C LYS* 3.0 55.0 + - - +
684C SER* 4.2 4.7 + - - -
786C GLU* 4.8 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 681 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523C LEU* 3.3 21.8 - - + +
524C LYS* 3.8 39.6 + - + +
526C VAL* 4.2 4.3 - - + -
677C ALA 2.9 12.9 + - - +
678C GLU 3.1 10.3 + - - +
680C GLU* 1.3 76.7 - - - +
682C MET* 1.3 61.7 + - - +
683C LYS 3.2 0.9 + - - -
684C SER* 3.4 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 682 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519C TRP* 3.5 29.7 - - + -
523C LEU* 3.6 17.7 - - + -
559C TYR* 3.6 30.1 - - + -
560C ASP* 3.6 27.8 - - + -
563C LEU* 3.7 13.7 - - - -
678C GLU 3.0 12.4 + - - +
679C ARG* 3.2 28.7 + - - +
681C ALA* 1.3 72.6 - - - +
683C LYS* 1.3 61.2 + - - +
684C SER 3.0 7.6 + - - -
685C SER 3.7 14.3 + - - +
700C PHE* 5.0 8.5 + - + +
702C PHE* 3.6 24.5 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
679C ARG* 3.1 36.8 + - - +
680C GLU* 3.0 52.9 + - - +
682C MET* 1.3 77.1 - - - +
684C SER* 1.3 58.5 + - - +
685C SER 3.9 0.7 - - - -
700C PHE 5.2 7.4 - - - +
702C PHE* 4.2 23.6 - - + +
786C GLU* 2.7 29.9 + - - +
----------------------------------------------------------
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