Contacts of the helix formed by residues 378 - 386 (chain B) in PDB entry 3H8E
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 THR 378 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B ARG* 4.0 8.3 - - - +
376B THR 3.8 1.0 - - - -
377B LEU* 1.3 83.6 - - + +
379B GLY* 1.3 64.7 + - - +
380B ALA* 3.7 10.5 - - - -
381B CYS* 3.1 6.9 + - - +
382B ILE 3.9 0.7 + - - -
443B GLY 3.7 20.9 - - - +
444B THR* 2.9 22.5 + - - -
447B ALA* 3.8 19.7 - - + -
464B ASP* 2.6 24.8 + - - +
466B ALA* 3.1 20.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 379 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B THR* 1.3 72.7 - - - +
380B ALA* 1.4 61.2 + - - +
382B ILE* 3.0 28.4 + - - +
383B VAL* 3.2 15.1 + - - +
466B ALA* 5.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 380 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A VAL* 4.0 21.3 - - + +
378B THR* 3.0 3.8 - - - +
379B GLY* 1.4 76.9 - - - +
381B CYS* 1.3 56.1 + - - +
382B ILE 3.2 0.2 - - - -
383B VAL* 3.3 11.4 + - - +
384B ALA* 3.0 26.2 + - - +
443B GLY* 3.9 12.6 - - - +
444B THR* 3.1 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 381 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B THR* 3.1 23.2 + - - +
380B ALA* 1.3 76.3 - - - +
382B ILE* 1.3 54.7 + - + +
384B ALA* 4.3 3.8 - - - +
385B LEU* 2.7 40.6 + - - +
386B GLY 3.4 3.4 + - - +
389B THR 5.0 1.8 - - - -
391B GLY* 3.8 23.8 - - - -
417B LEU* 5.2 0.4 - - - -
444B THR* 2.8 17.4 + - - +
464B ASP* 3.5 34.5 - - - +
466B ALA* 4.7 3.8 - - + -
467B GLY* 5.4 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 382 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A LYS* 3.5 42.3 - - + +
442A ALA 3.3 5.7 + - - -
378B THR 4.1 4.3 - - - +
379B GLY* 3.0 18.8 + - - +
381B CYS* 1.3 75.3 - - - +
383B VAL* 1.3 63.3 + - + +
386B GLY* 2.8 37.1 + - - +
466B ALA* 3.7 22.9 - - + +
467B GLY* 3.9 20.0 - - - +
470B TRP* 6.0 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 383 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A ALA* 4.2 23.4 - - + +
383A VAL* 4.1 23.1 - - + -
440A PRO* 3.9 19.3 - - + +
442A ALA* 2.6 30.0 + - - +
443A GLY 3.4 3.9 + - - +
379B GLY 3.2 12.4 + - - +
380B ALA* 3.3 13.7 + - - +
382B ILE* 1.3 78.9 - - + +
384B ALA* 1.3 55.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 384 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A ALA 6.0 0.2 - - - -
383A VAL* 6.1 0.4 - - + -
384A ALA* 4.3 27.1 - - + -
417A LEU* 5.4 5.1 - - + +
442A ALA* 3.9 5.0 - - - -
444A THR* 6.1 0.5 - - - -
445A ILE* 3.4 22.7 - - - +
380B ALA 3.0 16.7 + - - +
381B CYS* 3.8 6.1 - - - +
382B ILE 3.3 0.2 - - - -
383B VAL* 1.3 80.8 - - - +
385B LEU* 1.3 68.1 - - + +
386B GLY 3.7 0.2 - - - -
417B LEU* 4.8 15.9 - - + -
444B THR* 5.0 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 385 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A LEU* 5.3 4.3 - - + -
418A PRO* 4.2 4.3 - - + -
423A TYR* 2.8 40.9 + - - +
442A ALA* 4.2 1.1 - - - -
445A ILE* 4.1 10.5 - - + -
381B CYS* 2.7 17.9 + - - +
384B ALA* 1.3 82.9 - - + +
386B GLY* 1.3 67.6 + - - +
387B SER 3.7 0.5 + - - -
388B HIS 3.9 0.2 + - - -
389B THR* 3.5 22.6 + - + +
390B THR 4.1 3.6 - - - +
391B GLY* 3.6 33.2 - - - +
415B TRP* 4.0 35.2 - - + +
417B LEU* 4.4 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 386 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A TYR* 4.8 1.8 - - - -
426A GLN* 5.5 1.3 - - - -
441A LYS* 4.0 16.4 - - - -
442A ALA* 4.2 5.3 - - - +
381B CYS 3.4 2.5 + - - +
382B ILE* 2.8 30.0 + - - -
384B ALA 3.7 0.2 - - - -
385B LEU* 1.3 83.2 - - - +
387B SER* 1.3 61.1 + - - -
388B HIS 3.7 0.3 + - - -
389B THR 4.4 5.5 - - - +
467B GLY* 3.5 18.7 - - - -
----------------------------------------------------------
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