Contacts of the helix formed by residues 508 - 518 (chain F) in PDB entry 4CYM
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 508 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471F ALA 3.8 8.3 - - - -
472F VAL 3.5 6.5 + - - -
473F CYS 3.2 30.0 + - - -
474F GLY* 3.4 21.5 - - - -
503F ALA* 3.2 10.3 + - + +
506F LYS* 3.0 61.4 - - + -
507F GLY* 1.3 72.7 - - - +
509F GLN* 1.3 65.9 + - - +
510F SER* 3.1 4.5 + - - +
511F VAL* 3.1 16.1 + - + +
512F THR* 2.8 23.8 + - - +
544F CYS* 3.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 509 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C ILE 4.8 2.8 + - - -
59C GLY* 4.4 3.6 - - - -
60C VAL* 3.0 44.3 + - - +
62C PHE* 4.0 7.7 - - - -
95C TYR* 4.9 2.4 + - - -
507F GLY 3.3 6.1 + - - -
508F TYR* 1.3 71.9 - - - +
510F SER* 1.3 64.3 + - - +
512F THR* 3.3 9.2 + - - +
513F LEU* 2.9 47.4 + - + +
543F ASP* 3.0 58.5 + - - +
544F CYS* 3.5 3.0 - - - -
546F LYS* 5.4 0.4 - - - +
547F ALA* 4.1 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 510 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C MET* 3.3 38.7 - - - +
95C TYR* 5.5 4.0 - - - -
476F ALA* 4.8 10.2 - - - +
508F TYR* 3.1 1.9 + - - -
509F GLN* 1.3 79.6 + - - +
511F VAL* 1.3 60.8 + - - +
513F LEU* 3.5 2.8 + - - -
514F LEU* 3.0 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 511 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471F ALA* 4.3 9.0 - - + +
474F GLY* 4.0 35.0 - - - +
476F ALA* 4.8 7.0 - - + -
479F ILE* 3.6 29.6 - - + -
503F ALA* 3.5 19.7 - - + -
508F TYR* 3.1 17.1 + - + +
510F SER* 1.3 76.2 - - - +
512F THR* 1.3 68.0 + - - +
514F LEU* 2.9 8.7 + - - +
515F LEU* 2.8 31.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 512 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500F LEU* 3.8 12.8 - - - +
503F ALA* 4.1 11.9 - - + -
504F CYS* 3.8 24.7 - - - -
508F TYR 2.8 29.8 + - - +
509F GLN* 3.6 4.0 - - - -
511F VAL* 1.3 72.3 - - - +
513F LEU* 1.3 62.4 + - - +
515F LEU* 3.4 2.8 + - - +
516F LEU* 3.0 31.5 + - - +
544F CYS* 3.2 31.2 + - - -
547F ALA* 4.0 16.3 - - - +
548F LEU* 4.6 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 513 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C VAL* 4.8 3.1 - - + -
62C PHE* 4.8 10.8 - - + -
80C TRP* 4.9 7.0 - - + -
91C MET* 4.4 2.9 - - + -
94C VAL* 4.1 14.3 - - + +
95C TYR* 4.0 23.8 - - + -
509F GLN* 2.9 45.3 + - + +
510F SER* 3.8 5.4 - - - +
512F THR* 1.3 73.2 - - - +
514F LEU* 1.3 61.5 + - - +
516F LEU* 3.1 8.6 + - + +
517F HIS* 2.7 29.6 + - - +
547F ALA* 3.6 27.1 - - + +
551F TYR* 4.0 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 514 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C MET* 4.3 11.2 - - + +
93C ARG* 4.3 7.6 - - - +
94C VAL* 4.1 20.6 - - + -
476F ALA* 3.7 33.4 - - + +
479F ILE* 3.8 17.9 - - + -
480F ASP* 3.7 21.1 - - - +
510F SER 3.0 15.2 + - - +
511F VAL* 2.9 9.5 + - - +
513F LEU* 1.3 75.4 - - - +
515F LEU* 1.3 58.4 + - - +
517F HIS* 3.1 9.7 + - - +
518F TYR* 2.9 59.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 515 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467F LEU* 4.7 13.5 - - + -
471F ALA* 4.6 1.3 - - + -
479F ILE* 4.3 25.1 - - + -
489F VAL* 4.4 10.3 - - + +
499F PRO* 3.8 18.8 - - + +
500F LEU* 3.6 39.0 - - + +
503F ALA* 4.2 1.8 - - + -
511F VAL* 2.8 37.9 + - + +
512F THR 3.6 4.0 - - - +
514F LEU* 1.3 74.2 - - - +
516F LEU* 1.3 66.9 + - - +
518F TYR* 2.9 18.3 + - + +
519F LYS 3.1 0.5 + - - -
520F ALA* 3.1 28.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 516 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500F LEU* 4.0 21.3 - - + -
512F THR* 3.0 30.2 + - - +
513F LEU* 3.6 12.1 - - + +
515F LEU* 1.3 74.4 - - - +
517F HIS* 1.3 57.5 - - - +
519F LYS* 2.8 20.1 + - - +
520F ALA* 3.9 20.5 - - - +
522F ALA* 4.5 4.5 - - + -
547F ALA 4.2 9.4 - - - +
548F LEU* 4.2 15.0 - - + -
551F TYR* 3.6 47.1 + - + -
552F ASP* 4.0 16.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 517 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C ARG* 4.5 16.9 + - - +
94C VAL* 3.8 46.5 + - + +
97C LYS* 4.0 41.2 + - + +
513F LEU 2.7 13.8 + - - +
514F LEU* 3.1 15.0 - - - +
515F LEU 3.1 0.2 - - - -
516F LEU* 1.3 77.7 - - - +
518F TYR* 1.3 80.4 + + - +
519F LYS* 3.4 8.8 + - - +
551F TYR* 3.3 12.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 518 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C ARG* 3.6 9.1 + - - -
479F ILE* 4.2 6.5 - - + -
480F ASP* 2.5 33.6 + - - +
483F VAL* 3.6 38.4 - - + -
489F VAL* 3.6 27.6 - - + +
514F LEU* 2.9 49.6 + - + -
515F LEU* 2.9 14.1 + - + +
517F HIS* 1.3 90.2 - + - +
519F LYS* 1.3 71.7 + - - +
520F ALA 3.4 0.9 + - - -
----------------------------------------------------------
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