Contacts of the helix formed by residues 438 - 447 (chain C) in PDB entry 3FAA
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 VAL 438 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C ARG* 2.9 38.8 - - - +
376C LYS* 5.0 12.6 - - + +
379C MET* 5.1 11.4 - - - -
384C LEU* 3.0 48.5 - - + +
436C PRO 3.6 2.2 + - - -
437C SER* 1.3 72.4 + - - +
439C GLU* 1.3 59.8 + - - +
441C MET* 4.1 1.6 - - - -
442C ARG* 2.7 42.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 439 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437C SER* 2.8 18.7 + - - +
438C VAL* 1.3 81.8 - - - +
440C GLU* 1.3 72.8 + - - +
441C MET 3.2 2.8 + - - -
442C ARG* 4.8 0.4 - - - +
443C LYS* 3.7 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 440 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431C LEU 4.0 0.9 - - - +
432C VAL* 3.4 35.9 - - + +
433C PRO* 4.0 10.4 - - - +
434C SER 4.6 3.3 - - - +
435C ASP 4.8 4.2 - - - +
437C SER* 3.0 28.9 + - - +
439C GLU* 1.3 84.4 - - + +
441C MET* 1.3 61.8 + - - +
443C LYS* 5.5 1.6 - - - -
444C VAL* 3.8 17.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 441 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376C LYS* 4.1 4.7 - - + +
377C ARG* 3.3 42.0 - - + +
384C LEU* 3.9 17.5 - - + -
428C TYR* 3.7 22.4 - - + -
432C VAL* 3.5 23.1 - - + -
436C PRO* 3.0 46.2 - - - +
437C SER 3.1 10.5 - - - +
438C VAL* 3.1 2.8 + - - +
439C GLU 3.1 0.8 + - - -
440C GLU* 1.3 79.0 - - - +
442C ARG* 1.3 64.6 + - - +
443C LYS 3.3 0.9 - - - -
444C VAL* 2.9 8.9 + - - +
445C VAL* 2.9 32.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 442 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C ARG* 5.1 4.0 - - - +
384C LEU* 3.1 48.9 + - + +
385C ASP* 3.0 37.4 + - - +
438C VAL* 2.7 24.5 + - + +
439C GLU* 4.8 0.4 - - - +
441C MET* 1.3 70.5 - - - +
443C LYS* 1.3 61.1 + - - +
445C VAL 2.9 0.7 + - - -
446C CYS* 2.7 40.6 + - + +
447C GLU* 4.7 12.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 443 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439C GLU 3.7 17.5 + - - +
440C GLU* 5.5 0.9 - - - -
441C MET 3.3 0.2 - - - -
442C ARG* 1.3 79.7 - - - +
444C VAL* 1.3 60.3 + - + +
447C GLU* 3.2 41.0 + - + +
448C GLN* 2.9 43.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 444 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428C TYR* 5.7 4.0 - - + -
431C LEU* 4.0 28.5 - - + +
440C GLU* 3.8 25.4 - - - +
441C MET* 2.9 10.5 + - - +
443C LYS* 1.3 81.7 - - + +
445C VAL* 1.3 59.8 + - + +
448C GLN* 3.5 22.6 - - - +
450C LEU* 3.1 53.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 445 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381C PRO* 3.8 21.7 - - + +
384C LEU* 3.4 27.4 - - + -
402C TYR* 4.4 5.8 - - - +
428C TYR* 3.7 38.1 - - + +
441C MET* 3.0 15.7 - - + +
442C ARG 2.9 1.6 + - - -
444C VAL* 1.3 82.8 - - + +
446C CYS* 1.3 61.4 + - - +
449C LYS* 4.0 6.6 - - - +
450C LEU 4.2 3.1 - - - +
451C ARG* 2.7 44.1 + - - +
477C ALA* 6.0 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 446 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381C PRO* 4.0 12.8 - - - -
384C LEU* 4.0 10.8 - - - -
385C ASP* 3.3 46.9 - - + +
442C ARG* 2.7 29.2 + - + +
445C VAL* 1.3 76.5 - - - +
447C GLU* 1.3 68.7 + - + +
449C LYS* 4.0 16.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 447 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442C ARG* 4.7 15.4 + - - +
443C LYS* 3.2 40.2 + - + +
446C CYS* 1.3 81.8 - - + +
448C GLN* 1.3 60.0 + - + +
449C LYS* 3.1 19.8 + - - +
----------------------------------------------------------
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