Contacts of the helix formed by residues 359 - 367 (chain I) in PDB entry 4K4I
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 SER 359 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337I LEU* 4.2 6.5 - - - -
338I PHE* 3.9 6.2 - - - -
357I PHE 3.8 0.4 - - - -
358I ARG* 1.3 82.2 - - - +
360I LEU* 1.3 63.3 + - - +
361I GLU* 3.3 11.0 + - - +
362I ASP* 3.1 29.3 + - - +
363I ILE* 3.1 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 360 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337I LEU* 4.1 30.3 - - + +
338I PHE* 4.5 6.3 - - + -
341I ILE* 4.0 26.9 - - + -
359I SER* 1.3 69.7 - - - +
361I GLU* 1.3 60.5 + - - +
363I ILE* 3.0 6.0 + - + +
364I ARG* 2.8 49.3 + - - +
377I LEU* 4.0 10.1 - - + +
380I TYR* 3.8 45.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 361 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359I SER* 3.2 9.7 + - - +
360I LEU* 1.3 78.9 - - - +
362I ASP* 1.3 60.5 + - - +
364I ARG* 3.3 28.2 + - - +
365I SER* 2.7 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 362 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356I GLY 4.5 1.9 - - - +
357I PHE* 3.8 24.8 - - + -
358I ARG* 2.9 27.0 + - - +
359I SER* 3.1 26.9 + - - +
361I GLU* 1.3 78.1 - - - +
363I ILE* 1.3 63.2 + - - +
365I SER* 3.4 6.0 + - - -
366I GLN* 3.0 41.0 + - - +
367I ALA 3.6 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 363 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338I PHE* 3.6 27.4 - - + -
341I ILE* 4.5 4.7 - - + -
352I TRP* 3.5 45.1 - - + -
357I PHE* 3.7 15.9 - - + -
359I SER 3.4 12.3 - - - +
360I LEU* 3.0 13.3 + - + +
362I ASP* 1.3 78.6 - - - +
364I ARG* 1.3 62.3 + - - +
367I ALA* 2.9 40.4 + - + +
369I LEU* 4.0 14.6 - - + +
377I LEU* 3.9 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 364 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360I LEU* 2.8 40.8 + - - +
361I GLU* 3.5 25.4 + - - +
363I ILE* 1.3 78.5 - - - +
365I SER* 1.3 59.0 + - - +
367I ALA 4.9 1.7 + - - +
369I LEU* 4.8 6.7 - - - +
377I LEU* 3.6 48.2 + - + +
378I LYS* 4.7 5.3 - - - +
380I TYR* 6.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 365 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361I GLU* 2.7 31.0 + - - +
362I ASP* 3.4 4.0 + - - -
364I ARG* 1.3 76.2 - - - +
366I GLN* 1.3 80.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 366 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357I PHE* 3.7 30.1 - - + -
362I ASP* 3.0 31.9 + - - +
365I SER* 1.3 100.0 + - - +
367I ALA* 1.3 65.2 + - - +
368I SER 3.8 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 367 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352I TRP* 3.7 20.4 - - + +
357I PHE* 3.9 16.1 - - + -
362I ASP 3.6 1.0 + - - -
363I ILE* 2.9 43.8 + - + +
364I ARG 5.2 1.4 - - - +
366I GLN* 1.3 80.8 - - - +
368I SER* 1.3 62.2 + - - +
369I LEU* 3.5 11.0 + - + +
----------------------------------------------------------
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