Contacts of the helix formed by residues 779 - 793 (chain C) in PDB entry 3T6A
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 LYS 779 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520C PHE* 4.1 17.3 - - + -
559C MET* 2.9 26.7 - - + -
562C ARG* 5.1 4.3 - - - +
775C ASN* 3.9 18.8 - - - +
776C GLU* 2.9 47.9 + - - +
778C CYS* 1.3 78.6 - - - +
780C THR* 1.3 65.2 + - - +
781C GLU* 4.2 8.3 - - + +
782C PHE* 3.0 14.2 + - + +
783C GLN* 2.9 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 780 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515C PHE* 3.7 41.4 - - + -
559C MET* 4.2 2.4 - - - +
563C VAL* 5.4 0.2 - - - +
600C GLU* 4.6 0.7 - - + -
601C ARG* 2.9 54.0 + - - +
604C THR* 4.5 8.1 - - - +
778C CYS 3.5 3.0 + - - -
779C LYS* 1.3 72.4 - - - +
781C GLU* 1.3 56.6 + - - +
783C GLN* 3.2 10.2 + - - +
784C MET* 2.8 50.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 781 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514C SER 4.7 0.7 - - - +
515C PHE* 3.0 37.2 - - + +
516C ARG* 2.8 34.0 + - - -
517C PRO* 3.4 5.8 - - + +
520C PHE* 3.5 38.1 - - + +
779C LYS* 3.1 8.9 - - + -
780C THR* 1.3 77.4 - - - +
782C PHE* 1.3 62.7 + - - +
784C MET* 3.5 6.6 + - - +
785C ARG* 3.2 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 782 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520C PHE* 3.9 23.2 - + + -
522C SER* 4.5 3.1 - - - -
524C PHE* 3.9 28.7 - - + -
525C LEU* 3.7 30.5 - - + +
536C LEU* 5.2 3.8 - - + -
540C ALA* 5.9 1.8 - - + -
773C GLU* 6.5 0.2 - - + -
776C GLU* 3.2 35.7 - - + +
777C ILE* 3.7 30.1 - - + -
779C LYS* 3.0 6.3 + - + +
781C GLU* 1.3 80.7 - - - +
783C GLN* 1.3 64.2 + - - +
785C ARG* 3.2 5.5 + - - +
786C LEU* 3.0 43.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 783 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601C ARG* 4.3 5.2 - - - +
604C THR* 3.6 17.0 - - + +
605C MET* 3.7 39.6 + - - +
608C GLY* 6.0 2.1 - - - -
777C ILE* 3.1 23.7 + - + +
778C CYS* 3.1 29.1 + - - +
779C LYS 2.9 8.8 + - - +
780C THR* 3.6 9.8 + - - +
782C PHE* 1.3 78.8 - - + +
784C MET* 1.3 62.1 + - - +
786C LEU* 3.4 9.0 + - + +
787C LEU* 3.0 32.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 784 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513C SER* 5.6 1.8 - - - +
515C PHE* 4.2 14.6 - - + -
517C PRO* 3.7 25.4 - - + -
600C GLU* 4.0 11.7 - - + +
604C THR* 3.9 16.8 - - + +
780C THR* 2.8 39.1 + - + +
781C GLU* 3.9 4.0 - - - +
782C PHE 3.3 0.2 - - - -
783C GLN* 1.3 73.4 - - - +
785C ARG* 1.3 58.1 + - - +
788C TRP* 2.9 46.0 + - + +
793C ALA* 3.7 26.6 - - + +
800C ARG* 3.7 28.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 785 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517C PRO* 2.8 46.9 + - + +
518C ASN 3.8 8.0 + - - -
520C PHE* 2.8 26.4 + - + +
525C LEU* 3.5 30.2 + - + +
526C PRO 3.4 10.1 + - - -
527C PRO* 3.3 24.9 + - - +
529C ASN* 2.6 43.5 + - - +
781C GLU 3.2 14.1 + - - +
782C PHE 3.2 4.8 + - - +
784C MET* 1.3 77.5 - - - +
786C LEU* 1.3 60.7 + - - +
789C GLY* 2.9 26.4 + - - +
790C SER* 3.5 27.2 - - - +
793C ALA* 4.5 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 786 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525C LEU* 4.9 3.7 - - + +
529C ASN* 4.6 2.0 - - - +
530C LYS 4.6 0.3 - - - +
532C LEU* 2.9 33.7 + - - +
533C GLU 5.3 1.6 - - - +
536C LEU* 3.5 44.9 - - + +
537C LEU* 4.2 23.0 - - + +
540C ALA* 4.3 20.9 - - + -
777C ILE* 5.2 4.3 - - + -
782C PHE* 3.0 35.4 + - + +
783C GLN* 3.6 12.3 - - + +
785C ARG* 1.3 77.3 - - - +
787C LEU* 1.3 63.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 787 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531C PRO* 3.8 12.1 - - - +
532C LEU* 3.8 10.2 - - + +
537C LEU* 5.9 2.0 - - + -
604C THR* 3.8 34.1 - - + +
607C ILE* 4.1 12.3 - - + -
608C GLY* 4.3 9.4 - - - +
611C VAL* 3.9 18.8 - - + -
783C GLN* 3.0 24.5 + - + +
786C LEU* 1.3 85.4 - - + +
788C TRP* 1.3 79.2 + - + +
804C PHE* 3.3 47.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 788 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531C PRO* 3.8 15.7 - - - +
604C THR* 3.8 20.0 - - + -
607C ILE* 3.9 22.9 - - + -
784C MET* 2.9 43.2 + - + +
787C LEU* 1.3 85.4 - - + +
789C GLY* 1.3 65.7 + - - +
792C GLY* 3.6 18.7 + - - -
793C ALA* 3.7 16.8 - - - +
800C ARG* 3.0 75.7 + - + -
801C TYR* 3.9 13.0 - + - -
803C LYS* 4.8 9.6 - - + -
804C PHE* 3.3 26.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 789 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529C ASN* 3.9 0.7 - - - -
530C LYS 3.5 3.8 - - - -
531C PRO* 3.5 25.5 - - - +
785C ARG* 2.9 23.1 + - - -
787C LEU 3.7 1.0 - - - -
788C TRP* 1.3 82.2 - - - +
790C SER* 1.3 60.0 + - - -
791C LYS 3.0 11.8 + - - -
792C GLY 4.2 0.2 - - - -
793C ALA* 3.2 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 790 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518C ASN* 3.0 26.7 + - - +
527C PRO 3.6 15.4 + - - -
528C GLU* 3.8 9.4 + - - -
529C ASN* 2.8 35.6 + - - -
530C LYS* 4.4 0.2 - - - +
785C ARG* 3.5 19.1 - - - +
789C GLY* 1.3 69.6 - - - -
791C LYS* 1.3 70.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 791 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518C ASN* 3.6 16.0 + - - +
789C GLY 3.0 0.6 + - - -
790C SER* 1.3 93.5 - - - +
792C GLY* 1.3 62.7 + - - +
793C ALA 3.2 2.8 + - - -
794C GLN* 3.7 4.7 + - - +
795C VAL* 4.7 2.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 792 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788C TRP* 3.6 20.7 + - - +
791C LYS* 1.3 75.7 - - - +
793C ALA* 1.3 60.0 + - - +
794C GLN 3.0 7.3 + - - -
795C VAL* 3.1 32.4 + - - +
800C ARG* 3.7 9.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 793 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517C PRO* 3.7 30.4 - - + +
518C ASN* 3.7 11.2 - - - +
784C MET* 3.7 33.7 - - + +
785C ARG* 4.5 2.7 - - - -
788C TRP* 3.6 10.3 + - - -
789C GLY 3.2 20.1 + - - +
791C LYS 3.2 0.8 - - - -
792C GLY* 1.3 76.9 - - - +
794C GLN* 1.3 57.9 + - - +
795C VAL 3.5 0.4 - - - -
800C ARG* 3.7 9.4 + - - +
----------------------------------------------------------
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