Contacts of the helix formed by residues 609 - 621 (chain A) in PDB entry 1W6J
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 CYS 609 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568A ARG* 5.6 0.4 - - - +
596A PHE* 4.1 11.7 - - - -
601A GLN* 4.0 24.8 + - - +
602A THR 4.9 1.2 + - - -
608A ALA* 1.3 80.6 - - - +
610A ALA* 1.3 67.8 + - - +
611A GLU* 3.3 20.1 + - - +
612A VAL* 3.4 30.6 + - - -
613A SER* 3.0 18.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 610 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608A ALA 3.8 0.6 + - - -
609A CYS* 1.3 72.6 - - - +
611A GLU* 1.3 64.0 + - - +
613A SER* 3.7 5.9 - - - -
614A ARG* 2.9 52.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 611 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568A ARG* 3.0 43.0 + - + +
571A GLN* 2.9 45.4 + - - +
577A TRP* 5.4 1.1 - - - -
596A PHE* 3.7 27.4 - - + -
609A CYS* 3.3 21.5 - - - +
610A ALA* 1.3 84.1 + - - +
612A VAL* 1.3 62.2 + - - +
614A ARG* 4.3 11.2 + - - +
615A ALA* 3.1 12.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 612 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577A TRP* 6.2 0.4 - - - -
593A LEU* 4.3 9.9 - - + -
596A PHE* 3.9 20.9 - - + -
601A GLN* 3.8 20.9 - - + +
602A THR 5.1 0.4 - - - -
603A TYR* 3.7 24.0 - - + -
608A ALA* 3.7 9.6 - - + -
609A CYS* 3.4 25.3 + - - +
611A GLU* 1.3 76.0 - - - +
613A SER* 1.3 63.0 + - - +
615A ALA* 3.4 1.4 + - - +
616A CYS* 3.1 24.4 + - - -
662A VAL* 3.8 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 613 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A TYR* 3.5 20.8 + - - -
607A THR* 5.3 0.7 + - - -
608A ALA* 3.3 18.2 + - - +
609A CYS 3.0 18.4 + - - -
610A ALA* 3.7 7.6 - - - -
612A VAL* 1.3 77.1 - - - +
614A ARG* 1.3 63.5 + - - +
616A CYS* 3.3 3.5 + - - +
617A ASP* 3.1 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 614 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571A GLN* 3.9 15.4 + - - +
572A ARG 3.5 16.2 + - - -
573A ALA* 3.4 31.8 + - - +
574A ASP 3.6 6.1 - - - +
575A GLY* 3.8 14.3 - - - +
610A ALA* 2.9 39.9 + - + +
611A GLU* 4.0 13.4 + - - +
613A SER* 1.3 76.0 - - - +
615A ALA* 1.3 58.9 + - - +
617A ASP* 3.3 9.2 + - - +
618A PHE* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 615 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571A GLN* 3.7 2.7 - - - +
575A GLY* 3.3 26.2 - - - +
577A TRP* 4.0 8.1 - - + -
589A THR* 4.2 8.1 - - + +
593A LEU* 3.8 20.0 - - + -
611A GLU 3.1 18.4 + - - +
612A VAL 3.7 4.9 - - - +
614A ARG* 1.3 78.0 - - - +
616A CYS* 1.3 61.2 + - - +
618A PHE* 3.4 5.5 + - - +
619A LEU* 3.2 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 616 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593A LEU* 4.3 9.4 - - - -
603A TYR* 4.0 5.6 - - - +
612A VAL* 3.1 23.7 + - - +
613A SER 3.8 3.4 - - - +
614A ARG 3.3 0.2 - - - -
615A ALA* 1.3 73.1 - - - +
617A ASP* 1.3 60.3 + - - +
619A LEU* 3.3 3.9 + - - +
620A LEU* 2.8 37.3 + - - +
659A LEU* 3.9 19.5 - - + -
662A VAL* 3.6 30.3 - - - -
664A HIS* 3.5 28.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 617 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613A SER 3.1 14.1 + - - +
614A ARG* 3.5 12.8 - - - +
616A CYS* 1.3 73.0 - - - +
618A PHE* 1.3 64.6 + - - +
620A LEU* 4.5 4.8 - - - +
621A SER* 2.8 43.4 + - - -
664A HIS* 5.7 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 618 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574A ASP* 3.5 45.7 + - + +
575A GLY 4.5 0.2 - - - -
576A SER* 3.6 32.3 - - - +
585A PHE* 4.1 12.6 - + + -
589A THR* 4.8 2.9 - - - -
614A ARG 2.9 14.1 + - - +
615A ALA 3.4 10.1 - - - +
617A ASP* 1.3 77.7 - - - +
619A LEU* 1.3 77.0 + - + +
621A SER* 4.8 0.2 - - - -
622A ARG* 2.9 67.8 + - - +
641A TYR* 3.8 32.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 619 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A THR* 4.3 19.5 - - + +
589A THR* 4.1 21.3 - - + -
590A TRP 5.7 0.7 - - - +
593A LEU* 3.8 29.4 - - + -
615A ALA 3.2 12.3 + - - +
616A CYS* 3.7 5.8 - - - +
617A ASP 3.2 0.2 - - - -
618A PHE* 1.3 88.9 - - + +
620A LEU* 1.3 58.1 + - - +
622A ARG* 2.9 17.0 + - - +
629A TRP* 2.8 29.4 + - + +
641A TYR* 6.0 0.4 - - + -
654A TRP 5.4 0.2 - - - +
655A ALA* 4.0 40.4 - - + +
658A GLY* 5.1 0.9 - - - -
659A LEU* 4.3 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 620 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A CYS 2.8 24.3 + - - +
617A ASP* 4.3 4.9 - - - +
619A LEU* 1.3 73.8 - - - +
621A SER* 1.3 61.6 + - - +
622A ARG 3.2 0.7 + - - -
623A GLN* 3.3 24.5 + - - +
629A TRP* 4.5 4.0 - - + -
659A LEU* 4.0 26.5 - - + -
664A HIS* 3.3 38.8 - - + +
666A ASP* 4.6 6.3 - - + +
669A ALA* 3.6 31.9 - - + -
672A ARG* 5.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 621 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A ASP* 2.8 35.1 + - - -
618A PHE* 3.9 5.6 - - - -
620A LEU* 1.3 77.6 - - - +
622A ARG* 1.3 69.3 + - - +
623A GLN 3.5 3.2 - - - +
----------------------------------------------------------
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