Contacts of the helix formed by residues 617 - 629 (chain C) in PDB entry 6NYY
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 617 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641B ARG* 4.5 25.1 - - + +
642B ILE 3.3 11.2 - - - -
643B THR* 3.8 22.4 - - + +
587C HIS* 5.6 0.7 - - - -
615C LEU* 4.5 4.0 - - + +
616C TYR* 1.3 76.8 - - - +
618C LYS* 1.3 65.8 + - - +
619C GLU* 3.7 10.9 + - - +
620C GLN* 3.2 39.4 + - - +
621C LEU* 3.4 23.2 + - - +
666C MET* 4.5 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 618 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641B ARG* 6.0 0.2 - - - -
642B ILE* 3.0 24.4 + - + +
617C THR* 1.3 77.0 - - - +
619C GLU* 1.3 75.7 + - + +
621C LEU* 3.5 5.9 + - - +
622C LEU* 3.2 20.8 + - - +
660C GLN* 5.3 8.6 + - - +
666C MET* 3.2 49.3 + - + +
667C ASN* 5.4 0.2 - - - +
668C GLU 5.8 0.8 - - - +
704C LEU* 5.8 7.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 619 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640B GLY 5.0 4.2 - - - +
641B ARG* 3.4 38.1 - - - +
587C HIS* 4.6 14.1 - - + +
617C THR* 3.7 2.5 + - - +
618C LYS* 1.3 88.9 + - + +
620C GLN* 1.3 64.4 + - - +
622C LEU* 3.5 11.4 + - + +
623C ASP* 3.3 30.2 + - - +
711C ARG* 5.2 2.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 620 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587C HIS* 3.4 50.6 + - + +
613C GLN* 2.9 35.8 + - - +
615C LEU 3.6 3.2 + - - +
616C TYR* 3.5 12.1 - - + -
617C THR* 3.2 40.7 + - - +
618C LYS 3.3 0.4 - - - -
619C GLU* 1.3 78.0 - - - +
621C LEU* 1.3 62.1 + - - +
623C ASP* 3.6 3.6 + - - +
624C ARG* 3.5 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 621 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644B THR* 4.0 22.2 - - + -
616C TYR* 3.9 29.6 - - + -
617C THR 3.4 20.3 + - - +
618C LYS* 3.5 5.1 + - - +
619C GLU 3.3 0.2 - - - -
620C GLN* 1.3 76.3 - - - +
622C LEU* 1.3 62.4 + - - +
624C ARG* 3.6 17.8 + - - +
625C MET* 3.4 24.1 + - - +
656C SER* 5.6 6.5 - - - -
660C GLN* 3.3 36.0 + - + +
664C PHE* 4.3 8.1 - - + -
666C MET* 4.4 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 622 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618C LYS 3.2 16.6 + - - +
619C GLU* 3.8 12.6 - - + +
620C GLN 3.3 0.6 - - - -
621C LEU* 1.3 78.8 - - - +
623C ASP* 1.3 51.1 + - - +
624C ARG 3.2 0.4 - - - -
625C MET* 3.0 13.8 + - - +
626C CYS* 2.7 40.7 + - - -
660C GLN* 4.7 1.3 - - - +
704C LEU* 4.8 13.0 - - + -
707C ASP* 5.1 3.8 - - + +
708C ALA* 3.8 31.0 - - + +
711C ARG* 3.4 28.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 623 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585C LEU* 3.7 22.2 - - + +
586C GLU* 2.8 30.0 + - - +
587C HIS* 4.0 7.5 - - + -
588C ALA* 4.2 13.1 - - - +
619C GLU* 3.3 19.0 + - - +
620C GLN 3.6 4.5 + - - +
621C LEU 3.4 0.4 - - - -
622C LEU* 1.3 74.3 - - - +
624C ARG* 1.3 61.5 + - - +
626C CYS* 3.9 5.8 - - - +
627C MET* 3.3 21.5 + - - +
711C ARG* 2.8 40.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 624 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587C HIS 5.1 8.6 + - - +
588C ALA* 5.7 2.9 - - - -
589C ASP* 2.8 41.1 + - - +
610C PRO* 5.0 4.2 - - - +
611C LYS* 4.5 11.1 + - - +
613C GLN* 5.5 0.4 + - - -
616C TYR* 3.7 39.1 + - - -
620C GLN* 3.5 16.8 + - - +
621C LEU* 3.9 19.3 - - + +
622C LEU 3.2 0.6 - - - -
623C ASP* 1.3 77.9 - - - +
625C MET* 1.3 57.8 + - + +
626C CYS 3.3 0.2 - - - -
627C MET* 3.3 15.3 + - + +
628C THR* 2.7 40.2 + - - +
1I ALA* 4.5 16.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 625 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621C LEU 3.4 10.7 + - - +
622C LEU* 3.0 14.2 + - - +
624C ARG* 1.3 79.2 - - + +
626C CYS* 1.3 59.2 + - - +
628C THR* 4.4 0.7 - - - +
629C LEU* 3.1 35.0 + - - +
653C VAL* 3.7 38.8 - - + +
656C SER* 3.4 36.1 - - - +
657C ALA* 4.0 7.4 - - + -
660C GLN* 3.7 14.8 - - - -
704C LEU* 4.2 10.5 - - + -
705C ILE* 3.9 18.8 - - + -
708C ALA* 4.0 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 626 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581C ALA* 3.9 6.8 - - - +
585C LEU* 3.7 22.0 - - + +
622C LEU* 2.7 30.2 + - - +
623C ASP* 4.2 2.7 - - - +
625C MET* 1.3 74.2 - - - +
627C MET* 1.3 57.6 + - - +
629C LEU 4.3 0.9 - - - -
630C GLY 4.0 0.2 + - - -
708C ALA* 3.3 30.7 - - - -
711C ARG* 3.6 31.0 - - + -
712C THR* 2.8 37.3 + - - +
715C LEU* 5.3 0.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 627 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577C GLY 4.6 0.2 - - - +
578C HIS* 3.6 19.1 + - - +
581C ALA* 4.2 5.6 - - - -
582C GLY* 3.7 23.8 - - - +
585C LEU* 4.6 3.6 - - + -
588C ALA* 5.0 2.7 - - + -
589C ASP* 5.2 15.3 - - - +
608C TYR* 3.2 52.0 - - + +
623C ASP 3.3 17.7 + - - +
624C ARG* 3.3 16.7 + - + +
625C MET 3.1 0.4 - - - -
626C CYS* 1.3 77.6 - - - +
628C THR* 1.3 72.0 + - - +
629C LEU 3.2 1.3 - - - -
630C GLY* 2.9 18.5 + - - -
4I ALA* 5.2 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 628 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578C HIS* 3.6 10.2 - - + -
624C ARG* 2.7 27.5 + - - +
625C MET* 4.6 0.2 - - - -
627C MET* 1.3 83.5 - - - +
629C LEU* 1.3 60.4 + - - +
630C GLY 3.2 0.6 + - - -
631C GLY 4.2 0.3 + - - -
632C ARG 5.3 0.5 + - - -
649C ASP* 3.4 60.3 - - + +
652C LYS* 4.1 21.0 - - + +
653C VAL* 3.9 11.7 - - + -
4I ALA* 5.3 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 629 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625C MET 3.1 21.7 + - - +
628C THR* 1.3 74.8 - - - +
630C GLY* 1.3 61.8 - - - +
631C GLY 3.3 2.9 + - - -
632C ARG* 3.5 9.7 + - + +
633C VAL* 3.3 23.1 + - + +
649C ASP* 5.1 2.0 - - + +
650C LEU* 3.8 27.1 - - + -
653C VAL* 3.8 25.1 - - + -
705C ILE* 4.0 17.7 - - + +
708C ALA* 4.1 5.2 - - + -
709C TYR* 3.8 42.6 - - + +
712C THR* 4.4 8.3 - - - +
672D GLN* 4.0 10.5 - - - +
----------------------------------------------------------
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