Contacts of the helix formed by residues 443 - 448 (chain C) in PDB entry 2JJD
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 MET 443 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438C ILE* 4.6 11.4 - - - -
439C MET 3.5 15.7 - - - +
440C LYS* 3.3 18.5 + - - +
441C GLU 3.3 0.6 - - - -
442C ASN* 1.3 74.3 - - - +
444C ARG* 1.3 67.1 + - - +
445C THR* 3.3 2.8 + - - -
446C GLY* 3.4 9.2 + - - -
447C ASN* 3.1 26.8 + - - +
458C ILE 5.0 3.1 - - - +
459C GLN 4.3 11.4 - - - +
461C ILE* 3.0 57.4 - - + +
462C PRO 3.9 9.9 - - - +
463C TYR* 3.6 24.0 - - + -
464C ASP 4.5 2.5 - - - +
670C PRO* 4.7 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 444 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440C LYS 4.9 0.2 + - - -
441C GLU 4.6 6.0 + - - +
442C ASN 3.8 1.4 - - - -
443C MET* 1.3 76.9 - - - +
445C THR* 1.3 68.0 + - - +
447C ASN* 2.9 18.8 + - - +
448C LEU* 3.3 10.4 + - - +
464C ASP* 4.8 3.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 445 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443C MET 3.3 1.2 + - - -
444C ARG* 1.3 77.6 - - - +
446C GLY* 1.3 59.8 + - - +
447C ASN 3.5 0.2 + - - -
448C LEU* 3.8 10.0 + - - +
451C ASN* 2.8 24.1 + - - -
462C PRO* 5.9 1.6 - - - -
464C ASP* 4.6 17.1 - - - +
467C ARG* 3.7 41.3 - - - -
481C TYR* 4.3 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 446 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443C MET 3.4 4.4 + - - -
444C ARG 2.9 2.0 + - - -
445C THR* 1.3 76.7 - - - +
447C ASN* 1.3 59.1 + - - +
448C LEU 3.6 0.4 - - - -
451C ASN* 3.9 16.9 - - - +
452C MET* 4.3 2.3 + - - -
461C ILE* 2.9 32.0 - - - +
462C PRO 5.3 1.8 + - - -
481C TYR* 3.4 31.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 447 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440C LYS 5.1 2.0 + - - -
443C MET* 3.1 45.0 + - - +
444C ARG* 2.9 9.7 + - - +
446C GLY* 1.3 75.6 - - - +
448C LEU* 1.3 68.8 + - - +
449C PRO* 3.4 4.7 - - - +
452C MET* 4.8 6.4 - - - +
458C ILE* 4.7 10.3 - - - +
461C ILE* 4.8 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 448 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444C ARG 3.3 8.1 + - - +
445C THR* 3.8 13.5 - - - +
446C GLY 3.6 0.4 - - - -
447C ASN* 1.3 79.1 - - - +
449C PRO* 1.3 78.4 - - + +
450C ALA 3.3 2.7 - - - +
451C ASN* 3.0 19.9 + - - +
452C MET 3.2 6.9 + - - -
478C TYR* 4.9 16.6 - - + -
----------------------------------------------------------
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