Contacts of the helix formed by residues 606 - 620 (chain B) in PDB entry 4RG7
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 TYR 606 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573B PRO* 4.3 15.7 - - + -
574B GLU* 5.7 2.7 - - - +
599B ALA 4.9 0.7 - - - +
600B ILE* 5.6 0.2 - - - -
603B ASP* 3.0 31.6 + - + +
604B PRO 3.3 2.4 + - - -
605B ASN* 1.3 75.8 - - - +
607B ALA* 1.3 66.6 + - - +
608B TYR* 3.2 4.2 + - + +
609B ALA* 3.3 19.0 + - + +
610B TYR* 4.0 8.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 607 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605B ASN 3.8 3.4 + - - -
606B TYR* 1.3 73.3 - - - +
608B TYR* 1.3 57.6 + - - +
610B TYR* 2.9 37.3 + - - +
611B THR* 3.3 10.9 + - + +
633B ALA* 4.0 10.8 - - + +
636B VAL* 4.2 7.4 - - + +
637B ASN* 3.5 32.8 - - + -
640B HIS* 5.3 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 608 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543B GLU* 3.8 38.1 - - + +
544B ILE* 4.5 10.6 - - + +
547B THR* 2.6 40.1 + - - +
577B CYS* 5.0 2.7 - - + -
606B TYR 3.2 2.3 + - - -
607B ALA* 1.3 78.6 - - - +
609B ALA* 1.3 59.1 + - - +
611B THR* 2.8 26.6 + - - -
612B LEU* 3.2 42.3 + - + +
642B ASN* 5.4 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 609 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573B PRO* 5.5 1.1 - - + -
577B CYS* 5.4 5.1 - - + +
596B PHE* 4.0 14.9 - - - +
599B ALA* 3.7 31.9 - - + -
600B ILE* 4.1 10.1 - - + +
606B TYR* 3.3 14.6 + - + +
607B ALA 3.1 0.6 - - - -
608B TYR* 1.3 76.3 - - - +
610B TYR* 1.3 65.5 + - - +
612B LEU* 3.5 7.5 + - - +
613B LEU* 3.1 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 610 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600B ILE* 3.7 27.2 - - + +
604B PRO* 2.8 44.8 + - - +
606B TYR 4.2 5.2 - - - -
607B ALA* 2.9 22.8 + - - +
609B ALA* 1.3 78.0 - - - +
611B THR* 1.3 57.6 + - - +
613B LEU* 3.5 4.9 + - + +
614B GLY 3.0 21.0 + - - -
629B CYS* 3.2 36.2 - - + +
632B ASN* 4.3 19.7 - - + -
633B ALA* 3.8 19.1 - - + -
636B VAL* 4.2 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 611 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607B ALA* 3.3 3.8 + - + +
608B TYR* 2.8 37.7 + - - -
610B TYR* 1.3 74.1 - - - +
612B LEU* 1.3 59.2 + - - +
614B GLY 3.3 0.3 + - - -
615B HIS* 3.0 26.0 + - - +
630B PHE* 3.4 16.4 - - + -
633B ALA* 3.7 23.1 - - + -
640B HIS* 6.1 2.5 - - + -
642B ASN* 3.9 15.3 - - + +
643B ALA* 3.7 28.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 612 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543B GLU 5.6 0.2 - - - +
546B SER* 5.7 0.9 - - - +
547B THR* 4.5 12.1 - - + +
577B CYS* 4.1 26.9 - - + +
581B ASN* 5.8 8.3 - - + +
596B PHE* 5.0 6.7 - - + -
608B TYR* 3.2 59.0 + - + +
609B ALA* 4.0 5.2 - - - +
611B THR* 1.3 75.0 - - - +
613B LEU* 1.3 64.5 + - - +
615B HIS* 3.6 8.6 + - + +
616B GLU* 3.1 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 613 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593B ILE* 5.2 7.9 - - + +
596B PHE* 4.0 20.7 - - + +
597B GLN* 6.0 4.9 - - + -
609B ALA 3.1 17.5 + - - +
610B TYR* 3.6 7.4 - - + +
612B LEU* 1.3 76.4 - - - +
614B GLY* 1.3 52.5 + - - +
616B GLU* 3.1 8.0 + - - +
617B PHE* 2.8 35.3 + - - +
629B CYS* 4.0 16.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 614 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610B TYR 3.0 12.9 + - - -
611B THR 3.3 4.2 + - - -
612B LEU 3.2 0.4 - - - -
613B LEU* 1.3 76.4 - - - +
615B HIS* 1.3 61.1 + - - +
617B PHE* 2.9 8.6 + - - +
618B VAL* 2.9 24.9 + - - +
626B ALA* 3.8 3.9 - - - +
629B CYS* 4.0 11.8 - - - +
630B PHE* 3.6 24.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 615 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611B THR 3.0 15.5 + - - +
612B LEU* 4.0 11.0 - - + +
613B LEU 3.4 0.2 - - - -
614B GLY* 1.3 74.6 - - - +
616B GLU* 1.3 62.3 + - - +
618B VAL* 3.0 30.5 - - + +
619B LEU* 3.1 8.8 + - - +
630B PHE* 3.6 6.0 - - + -
681B ILE* 5.9 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 616 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584B SER* 5.5 6.7 - - - +
589B HIS* 5.1 4.6 - - + +
592B ALA* 5.0 13.7 - - + -
593B ILE* 4.2 22.6 - - + +
596B PHE* 6.3 0.4 - - + -
612B LEU 3.1 18.0 + - - +
613B LEU* 3.1 7.9 + - - +
615B HIS* 1.3 76.7 - - - +
617B PHE* 1.3 58.4 + - - +
619B LEU* 3.7 8.4 - - - +
620B THR* 3.3 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 617 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593B ILE* 5.3 3.3 - - + +
613B LEU 2.8 12.8 + - - +
614B GLY* 2.9 8.7 + - - +
616B GLU* 1.3 76.7 - - - +
618B VAL* 1.3 62.3 + - - +
619B LEU 3.2 0.2 - - - -
620B THR* 2.9 15.6 + - - +
621B GLU 3.1 0.5 + - - -
622B GLU* 2.9 35.2 + - + +
625B LYS* 4.7 5.6 - - + -
626B ALA* 3.7 24.7 - - + +
629B CYS* 5.5 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 618 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614B GLY 2.9 15.9 + - - +
615B HIS* 3.0 24.2 - - + +
617B PHE* 1.3 72.6 - - - +
619B LEU* 1.3 61.2 + - + +
621B GLU* 2.8 26.1 + - - +
622B GLU 4.7 0.9 - - - +
623B LEU* 5.7 3.1 - - + +
626B ALA* 3.7 16.4 - - + -
630B PHE* 4.2 13.2 - - + -
646B GLY 5.7 1.1 - - - +
650B ILE* 5.8 6.7 - - + -
685B GLN* 6.4 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 619 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589B HIS* 6.3 0.9 - - + -
615B HIS 3.1 8.4 + - - +
616B GLU* 3.7 13.0 - - - +
618B VAL* 1.3 85.0 - - + +
620B THR* 1.3 59.4 - - + +
621B GLU* 3.3 4.2 + - - +
685B GLN* 5.1 16.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 620 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589B HIS* 3.6 31.4 - - + -
590B ASP* 5.6 2.0 - - - +
593B ILE* 6.0 1.7 - - + +
616B GLU 3.3 11.6 + - - +
617B PHE* 2.9 17.5 + - - -
619B LEU* 1.3 76.7 - - + +
621B GLU* 1.3 69.3 + - - +
622B GLU* 3.1 11.2 + - - +
----------------------------------------------------------
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