Contacts of the helix formed by residues 336 - 348 (chain H) in PDB entry 1D00
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 ALA 336 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334H ALA 2.2 30.8 + - - +
335H MET 1.3 69.2 - - - +
337H ASP* 1.3 65.2 + - + +
338H LEU 3.2 0.9 + - - +
339H GLU* 3.6 18.0 + - - +
340H GLN* 4.3 2.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 337 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334H ALA 3.3 4.2 + - - +
336H ALA* 1.3 77.9 - - + +
338H LEU* 1.3 64.5 + - - +
339H GLU 3.2 1.1 - - - -
340H GLN* 3.8 8.2 + - - +
341H LYS* 3.5 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 338 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335F MET 4.5 7.0 - - - +
338F LEU* 4.0 25.6 - - + +
339F GLU* 3.7 47.6 - - + +
342F VAL* 4.7 13.5 - - + -
343F LEU* 5.3 4.9 - - + -
338G LEU* 4.4 11.2 - - + -
334H ALA* 3.1 23.7 + - - +
335H MET* 5.4 1.8 - - - +
337H ASP* 1.3 77.4 - - - +
339H GLU* 1.3 69.2 + - - +
341H LYS* 3.2 10.4 + - + +
342H VAL* 3.2 21.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 339 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338G LEU* 4.0 24.6 - - + +
334H ALA 4.8 0.2 + - - -
335H MET 5.7 1.1 - - - -
336H ALA* 3.6 16.0 + - - +
338H LEU* 1.3 77.0 - - - +
340H GLN* 1.3 55.3 + - - +
342H VAL* 2.5 29.6 + - - +
343H LEU* 2.9 25.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 340 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336H ALA 4.3 1.3 + - - +
337H ASP* 3.8 13.2 + - - +
338H LEU 3.6 0.2 - - - -
339H GLU* 1.3 77.1 - - - +
341H LYS* 1.3 53.1 + - - +
343H LEU* 3.0 17.3 + - + +
344H GLU* 2.8 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 341 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342F VAL* 4.9 10.3 - - + -
346F GLU* 6.0 2.2 - - - +
337H ASP 3.5 10.2 + - - +
338H LEU* 3.2 16.6 + - + +
339H GLU 2.8 2.0 + - - -
340H GLN* 1.3 76.5 - - - +
342H VAL* 1.3 58.8 + - - +
344H GLU* 3.6 5.5 + - - +
345H MET* 2.9 37.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 342 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342F VAL* 3.9 30.1 - - + -
345F MET* 6.3 0.2 - - + -
338G LEU* 4.0 26.0 - - + -
341G LYS* 4.6 9.9 - - + -
342G VAL* 4.5 8.7 - - + -
345G MET* 3.3 29.0 - - + +
338H LEU* 3.5 14.1 - - + +
339H GLU 2.5 14.5 + - - +
341H LYS* 1.3 71.0 - - - +
343H LEU* 1.3 60.7 + - + +
345H MET* 3.5 6.5 + - - -
346H GLU* 2.8 29.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 343 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338G LEU* 5.5 2.5 - - + -
339H GLU* 2.9 38.1 - - + +
340H GLN* 3.0 17.4 + - + +
342H VAL* 1.3 81.8 - - + +
344H GLU* 1.3 68.8 + - - +
346H GLU* 3.2 20.0 + - - +
347H ALA* 3.0 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 344 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340H GLN 2.8 18.1 + - - +
341H LYS* 3.8 6.1 - - - +
343H LEU* 1.3 69.9 - - - +
345H MET* 1.3 59.2 + - + +
347H ALA* 2.4 31.5 + - - +
348H SER* 3.0 13.6 + - - -
379H PRO* 5.2 8.0 - - + +
380H ALA* 5.4 4.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 345 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342F VAL* 3.2 38.4 - - + +
345F MET* 3.8 23.8 - - + -
346F GLU* 3.5 52.9 - - + +
345G MET* 3.9 9.3 - - + +
385G ARG* 4.5 0.5 + - - -
341H LYS* 2.9 25.0 + - + +
342H VAL* 3.6 6.7 - - - +
344H GLU* 1.3 79.0 - - + +
346H GLU* 1.3 61.8 + - - +
347H ALA 3.3 0.3 + - - -
348H SER* 3.4 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 346 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341G LYS* 6.1 1.0 - - - +
345G MET* 3.9 28.5 - - + +
350G TYR* 5.3 5.4 + - - +
385G ARG* 2.6 25.0 + - - -
342H VAL* 2.8 20.1 + - - +
343H LEU* 3.2 20.8 - - - +
344H GLU 2.7 0.6 + - - -
345H MET* 1.3 78.5 - - - +
347H ALA* 1.3 49.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 347 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385G ARG* 3.1 12.9 + - - +
386G TYR* 4.0 6.0 + - - -
343H LEU 3.0 9.5 + - - +
344H GLU 2.4 24.1 + - - +
346H GLU* 1.3 68.0 - - + +
348H SER* 1.3 59.7 + - - +
354H PHE* 3.5 20.9 - - + -
379H PRO* 3.6 31.6 - - + -
380H ALA 4.5 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 348 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385G ARG* 3.1 22.9 + - - +
344H GLU 3.0 8.8 + - - -
345H MET* 3.4 19.1 + - - +
347H ALA* 1.3 78.4 - - - +
349H THR* 1.3 60.3 + - - +
350H TYR* 3.5 23.6 + - - -
379H PRO* 5.4 0.2 - - - +
380H ALA* 3.2 23.1 + - - -
382H TYR* 4.1 18.4 - - - -
----------------------------------------------------------
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