Contacts of the helix formed by residues 499 - 509 (chain q) in PDB entry 6FF7
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 ASP 499 (chain q).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452q THR* 4.2 18.2 - - - -
453q GLN 2.9 16.0 + - - +
454q PRO* 4.8 6.5 - - + +
497q MET 3.8 0.4 + - - -
498q THR* 1.3 72.5 - - - +
500q GLY* 1.3 62.8 + - - +
502q LEU* 3.2 5.8 + - - +
503q LEU* 3.0 22.3 + - - +
527q THR* 6.1 1.3 - - - -
529q HIS* 3.7 22.4 - - + +
530q THR* 4.1 18.4 - - - +
533q LEU* 5.6 5.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 500 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498q THR* 3.1 5.7 - - - -
499q ASP* 1.3 77.7 - - - +
501q MET* 1.3 55.3 + - - +
503q LEU* 3.2 6.8 + - - +
504q ARG* 3.0 25.3 + - - +
529q HIS* 3.7 14.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 501 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481q SER* 4.0 29.2 - - - +
482q ILE* 5.1 6.5 - - - +
483q ARG* 5.4 2.7 - - - +
497q MET* 4.3 6.5 - - + -
498q THR* 3.1 16.6 + - - +
500q GLY* 1.3 74.7 - - - +
502q LEU* 1.3 60.4 + - - +
504q ARG* 2.9 10.4 + - - +
505q GLU* 2.9 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 502 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450q ALA* 5.7 9.4 - - + -
452q THR* 5.2 9.2 - - - -
497q MET* 5.1 5.3 - - + +
498q THR 3.3 8.3 + - - +
499q ASP* 3.2 10.6 + - - +
501q MET* 1.3 76.9 - - - +
503q LEU* 1.3 58.3 + - - +
505q GLU* 2.9 11.3 + - - +
506q PHE* 2.8 26.6 + - - +
533q LEU* 6.3 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 503 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499q ASP 3.0 13.5 + - - +
500q GLY* 3.4 12.3 - - - +
502q LEU* 1.3 77.1 - - - +
504q ARG* 1.3 63.2 + - - +
506q PHE* 3.0 12.1 + - - +
507q LEU* 3.0 19.4 + - - +
529q HIS* 5.1 13.0 - - + +
532q ILE* 5.9 4.7 - - + -
533q LEU* 6.0 4.9 - - + +
767q LEU* 6.3 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 504 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500q GLY 3.0 11.6 + - - +
501q MET* 2.9 12.8 + - - +
503q LEU* 1.3 77.4 - - - +
505q GLU* 1.3 60.7 + - - +
507q LEU* 3.1 22.5 + - - +
508q SER* 3.4 6.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 505 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501q MET 2.9 11.5 + - - +
502q LEU* 2.9 12.3 + - - +
504q ARG* 1.3 75.6 - - - +
506q PHE* 1.3 58.0 + - - +
508q SER* 3.1 9.2 + - - +
509q GLU* 2.9 29.4 + - - +
512q LEU* 6.1 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 506 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502q LEU 2.8 11.1 + - - +
503q LEU* 3.0 15.9 + - - +
505q GLU* 1.3 76.5 - - - +
507q LEU* 1.3 64.3 - - - +
509q GLU 2.9 28.6 - - - +
510q PRO* 3.1 13.5 - - + +
512q LEU* 5.6 5.6 - - + +
536q LEU* 5.9 7.4 - - + -
771q LEU* 5.6 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 507 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503q LEU 3.0 7.9 + - - +
504q ARG* 3.1 15.6 + - - +
506q PHE* 1.3 82.2 - - - +
508q SER* 1.3 60.3 + - - +
510q PRO 5.0 0.7 - - - -
767q LEU* 5.5 2.2 - - - +
770q SER* 4.0 37.9 - - - +
771q LEU* 5.1 4.4 - - - +
817q ALA* 5.6 7.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 508 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504q ARG 3.4 4.8 + - - -
505q GLU* 3.1 10.8 + - - -
507q LEU* 1.3 83.0 - - - +
509q GLU* 1.3 60.6 + - - +
510q PRO 4.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 509 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505q GLU 2.9 9.7 + - - +
506q PHE* 2.9 17.3 - - - +
508q SER* 1.3 78.5 - - - +
510q PRO* 1.3 66.2 - - - +
511q ASP* 3.2 2.2 - - + +
512q LEU* 3.0 21.5 + - - +
513q ALA* 5.0 5.4 - - + +
----------------------------------------------------------
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