Contacts of the helix formed by residues 429 - 433 (chain C) in PDB entry 4K9N
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 GLY 429 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LEU 5.0 0.3 - - - +
428C ASP* 1.3 78.9 - - - +
430C SER* 1.3 63.9 + - - +
431C ALA 3.2 0.9 + - - -
432C ASN* 3.3 20.0 + - - +
433C TYR* 3.5 16.8 - - - -
458C TYR* 3.5 29.2 + - - -
478C VAL* 4.4 6.7 - - - +
602C TZD 3.1 13.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 430 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375C GLU* 3.2 42.7 + - - +
377C THR* 5.0 0.5 - - - +
403C LEU* 3.4 23.0 - - - +
404C GLY* 4.4 1.4 + - - -
407C LEU* 6.1 0.5 - - - +
426C ILE* 3.9 4.9 - - - +
427C GLY 3.3 2.9 + - - -
429C GLY* 1.3 73.0 - - - +
431C ALA* 1.3 63.6 + - - +
432C ASN 3.0 1.2 + - - -
433C TYR* 3.2 28.1 + - - +
434C SER 4.6 1.2 + - - -
602C TZD 2.6 30.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 431 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407C LEU* 3.8 12.7 - - + +
426C ILE* 3.6 15.2 - - + +
427C GLY 2.9 17.0 + - - +
428C ASP 3.9 1.6 - - - +
429C GLY 3.2 1.2 - - - -
430C SER* 1.3 76.6 - - - +
432C ASN* 1.3 61.8 + - - +
433C TYR 3.5 0.3 + - - -
434C SER 4.0 0.9 + - - -
435C ILE* 3.5 26.0 + - + +
452C ILE* 4.1 15.9 - - + -
483C PHE* 3.6 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 432 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LEU* 3.7 37.2 - - + +
46A GLN* 4.8 0.3 - - - +
436A SER* 4.1 10.9 + - - -
490A TYR* 2.9 33.5 + - - +
428C ASP 2.9 27.2 + - - -
429C GLY* 3.3 13.4 + - - +
430C SER 3.0 1.2 + - - -
431C ALA* 1.3 75.0 - - - +
433C TYR* 1.3 67.1 + - - +
434C SER 3.2 3.8 + - - -
435C ILE* 3.5 16.3 + - - +
478C VAL* 5.5 0.2 - - - +
481C ILE* 3.5 18.5 - - - +
483C PHE* 3.9 11.0 - - - -
486C LEU* 4.3 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 433 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ASN* 2.7 26.6 + - - -
45A LEU 3.7 15.7 - - - -
46A GLN* 3.4 45.6 + - + +
47A GLU* 3.5 15.7 - - - -
77A ASN* 4.0 2.5 - - - +
46C GLN* 5.4 2.8 - - - +
48C ALA* 5.5 0.2 - - - +
403C LEU* 3.7 22.7 - - + +
404C GLY* 3.6 19.5 - - - -
429C GLY 3.5 17.9 - - - -
430C SER* 3.2 17.9 + - - +
432C ASN* 1.3 79.0 - - - +
434C SER* 1.3 61.6 + - - +
435C ILE 3.7 0.4 + - - -
458C TYR* 4.1 4.0 + + - -
602C TZD 3.2 50.8 - + + +
----------------------------------------------------------
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