Contacts of the helix formed by residues 606 - 618 (chain C) in PDB entry 2XER
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 606 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606B THR* 3.1 26.0 + - - +
646B HIS* 5.0 2.0 - - - +
605C SER* 1.3 74.6 - - - +
607C GLU* 1.3 59.4 + - + +
609C ALA* 3.9 1.1 - - - +
610C ALA* 2.9 31.4 + - + +
643C LEU* 4.0 13.3 - - + +
646C HIS* 4.8 7.4 - - + +
647C LEU* 3.9 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 607 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566C TYR* 5.4 0.2 - - - -
605C SER* 3.9 6.7 + - - +
606C THR* 1.3 76.5 - - + +
608C GLN* 1.3 67.6 + - + +
610C ALA* 3.1 6.9 + - - +
611C ASP* 2.9 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 608 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646B HIS* 4.2 6.3 - - - -
562C ILE* 4.3 4.4 - - - +
563C CYS* 4.9 16.0 - - - +
566C TYR* 3.5 57.0 - - + +
604C LEU* 3.7 17.0 - - + +
605C SER* 3.0 37.5 + - - +
607C GLU* 1.3 80.2 - - + +
609C ALA* 1.3 63.0 + - - +
611C ASP* 3.5 0.5 + - - +
612C ILE* 3.0 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 609 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601C LEU* 4.3 24.9 - - + +
604C LEU* 4.0 11.8 - - + +
605C SER 2.8 21.5 + - - +
608C GLN* 1.3 69.9 - - - +
610C ALA* 1.3 67.4 + - - +
612C ILE* 3.1 6.9 + - - +
613C LEU 2.9 18.0 + - - -
640C PHE* 4.3 1.2 - - - -
643C LEU* 3.5 30.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 610 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606C THR 2.9 20.6 + - - +
607C GLU* 3.5 6.5 - - - +
609C ALA* 1.3 76.9 - - - +
611C ASP* 1.3 52.7 + - - +
613C LEU* 3.1 5.7 + - - +
614C MET* 2.7 39.8 + - + +
643C LEU* 3.6 13.4 - - + +
647C LEU* 4.7 19.5 - - + -
651C SER* 6.0 2.0 - - - +
655C LEU* 5.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 611 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566C TYR* 2.6 29.1 + - - +
570C ARG* 3.3 32.2 + - - +
607C GLU 2.9 14.9 + - - +
608C GLN 3.6 2.7 - - - +
610C ALA* 1.3 77.1 - - - +
612C ILE* 1.3 57.1 + - - +
614C MET* 3.2 6.4 + - - +
615C THR* 2.9 35.9 + - - -
618C ARG* 4.6 5.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 612 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566C TYR* 3.5 27.4 - - + -
569C LEU* 4.9 9.9 - - + -
570C ARG* 4.2 10.3 - - + -
584C PHE* 3.9 32.6 - - + -
597C VAL* 4.2 7.2 - - + -
601C LEU* 3.6 24.7 - - + -
604C LEU* 3.9 12.1 - - + -
608C GLN 3.0 23.2 + - - +
609C ALA 3.1 7.2 + - - +
611C ASP* 1.3 76.7 - - - +
613C LEU* 1.3 59.5 + - - +
615C THR* 3.3 3.9 + - - +
616C THR* 2.8 34.9 + - - +
640C PHE* 3.6 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 613 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609C ALA 2.9 10.4 + - - +
610C ALA 3.4 8.5 - - - +
612C ILE* 1.3 76.6 - - - +
614C MET* 1.3 57.3 + - - +
616C THR* 3.4 1.9 + - - -
617C ALA* 2.9 32.3 + - + +
640C PHE* 3.5 46.7 - - + -
643C LEU* 3.8 19.1 - - + -
644C LEU* 3.6 22.0 - - + -
647C LEU* 4.9 2.2 - - + -
655C LEU* 3.5 32.1 - - + -
688C LEU* 4.2 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 614 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610C ALA* 2.7 20.6 + - + +
611C ASP* 3.4 13.0 - - - +
613C LEU* 1.3 74.0 - - - +
615C THR* 1.3 57.7 + - - +
617C ALA* 3.2 3.8 + - - +
618C ARG* 3.0 64.4 + - - +
654C SER* 4.5 9.6 - - - -
655C LEU* 3.8 28.3 - - + -
658C GLN* 3.4 40.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 615 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570C ARG* 3.3 32.4 + - - +
581C ASP* 3.6 29.4 - - + +
584C PHE* 3.5 27.5 - - + -
585C VAL* 4.7 1.1 - - + +
611C ASP* 2.9 20.1 + - - -
612C ILE 3.9 3.4 - - - -
614C MET* 1.3 72.4 - - - +
616C THR* 1.3 64.8 + - - +
618C ARG* 3.2 14.7 + - - +
619C ASN* 3.1 32.0 + - - +
623C LEU* 5.3 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 616 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584C PHE* 3.6 17.8 - - - -
588C MET* 4.6 11.0 - - + +
612C ILE* 2.8 27.9 + - - +
613C LEU* 3.6 8.7 - - + -
615C THR* 1.3 75.3 - - - +
617C ALA* 1.3 67.3 + - - +
619C ASN 3.3 3.1 - - - +
620C LEU* 3.0 40.0 + - + -
623C LEU* 4.1 21.2 - - + +
633C LEU* 5.7 1.1 - - + -
636C LEU* 5.2 1.3 - - + -
640C PHE* 4.1 17.1 - - + -
684C PHE* 5.0 7.6 - - + -
688C LEU* 5.8 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 617 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613C LEU* 2.9 20.2 + - + +
614C MET 3.4 5.4 - - - +
616C THR* 1.3 76.7 - - - +
618C ARG* 1.3 66.0 + - - +
620C LEU* 3.1 23.7 + - - +
621C PRO* 4.3 1.9 - - - +
655C LEU* 4.4 15.3 - - + +
658C GLN* 4.6 9.5 - - + +
659C LEU* 4.1 32.5 - - + +
688C LEU* 5.7 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 618 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570C ARG* 4.6 3.8 - - - +
581C ASP* 2.7 48.0 + - - +
611C ASP* 4.6 4.9 + - - -
614C MET* 3.0 51.2 + - - +
615C THR* 3.2 32.4 + - - +
616C THR 3.4 0.2 - - - -
617C ALA* 1.3 79.0 - - - +
619C ASN* 1.3 66.1 + - - +
620C LEU 3.4 1.9 + - - -
621C PRO* 4.3 6.1 - - - +
658C GLN* 3.0 34.0 + - - +
659C LEU 5.7 0.3 - - - +
661C ASN* 5.9 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