Contacts of the helix formed by residues 375 - 387 (chain B) in PDB entry 3LLM
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 ASP 375 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B GLN* 3.0 19.6 + - + +
372B LEU 3.4 13.8 - - - +
374B GLN* 1.3 74.3 - - - +
376B HIS* 1.3 62.1 + - - +
377B ASP* 3.1 26.0 + - - +
378B LEU* 3.7 31.7 + - + +
379B GLN* 4.2 3.6 + - - +
462B GLY* 4.6 16.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 376 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B LEU 5.3 0.4 - - - -
374B GLN 3.3 8.1 + - - +
375B ASP* 1.3 71.3 + - - +
377B ASP* 1.3 67.5 + - - +
378B LEU 3.2 1.1 + - - -
379B GLN* 3.5 19.4 + - - +
380B ALA* 4.2 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 377 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B ASP* 3.1 12.7 + - - +
376B HIS* 1.3 80.3 - - - +
378B LEU* 1.3 60.0 + - - +
380B ALA* 3.3 18.0 + - - +
381B ILE* 3.6 19.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 378 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B LEU* 6.1 4.7 - - + -
371B GLN* 4.1 28.9 - - + +
372B LEU* 4.3 20.2 - - + -
375B ASP* 3.5 26.0 + - + +
376B HIS 3.2 0.6 - - - -
377B ASP* 1.3 76.4 - - - +
379B GLN* 1.3 64.8 + - - +
381B ILE* 3.2 15.9 + - + +
382B LEU* 3.1 31.3 + - + +
460B GLU 4.2 10.1 - - - +
461B ARG* 3.7 14.8 - - - +
462B GLY* 3.5 32.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 379 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B LEU* 4.3 30.3 - - + +
375B ASP 4.3 2.5 - - - +
376B HIS* 3.5 12.7 + - - +
377B ASP 3.4 0.8 - - - -
378B LEU* 1.3 77.3 - - - +
380B ALA* 1.3 56.1 + - - +
382B LEU* 3.7 8.1 + - - +
383B GLN* 3.1 26.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
376B HIS 4.2 3.2 + - - +
377B ASP* 3.3 12.6 + - - +
378B LEU 3.2 0.8 - - - -
379B GLN* 1.3 75.8 - - - +
381B ILE* 1.3 60.5 - - + +
383B GLN* 3.2 8.9 + - - +
384B GLU* 2.9 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 381 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B ASP* 3.7 18.6 - - + +
378B LEU* 3.2 20.8 + - + +
380B ALA* 1.3 73.8 - - + +
382B LEU* 1.3 61.0 + - - +
383B GLN 3.1 1.1 - - - -
384B GLU* 3.1 9.6 + - + +
385B ARG* 2.8 31.0 + - + +
456B ARG* 5.5 3.4 - - - +
459B PHE* 3.8 46.7 - - + +
460B GLU* 3.9 33.9 - - + +
462B GLY* 5.5 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 382 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B LEU* 4.0 27.1 - - + -
378B LEU* 3.1 28.6 + - + +
379B GLN* 3.9 7.0 - - - +
381B ILE* 1.3 75.4 - - - +
383B GLN* 1.3 56.6 + - - +
385B ARG* 3.3 34.3 + - - +
386B GLU* 2.9 35.0 + - + +
460B GLU 3.9 17.5 - - - +
461B ARG* 5.7 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 383 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B GLN 3.1 14.8 + - - +
380B ALA* 3.2 13.5 - - - +
381B ILE 3.1 1.0 - - - -
382B LEU* 1.3 73.9 - - - +
384B GLU* 1.3 64.4 + - - +
386B GLU* 3.3 17.7 + - - +
387B LEU* 3.6 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 384 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B ALA 2.9 13.0 + - - +
381B ILE* 3.1 12.3 + - + +
383B GLN* 1.3 75.0 - - - +
385B ARG* 1.3 61.9 + - - +
387B LEU* 3.3 28.4 + - + +
388B LEU* 4.0 9.3 + - - +
456B ARG* 6.3 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 385 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B ILE* 2.8 19.2 + - + +
382B LEU* 3.3 38.8 - - - +
384B GLU* 1.3 68.3 - - + +
386B GLU* 1.3 62.7 + - + +
387B LEU 3.0 6.1 + - - -
388B LEU* 3.2 25.7 + - + +
391B LYS* 4.4 9.7 - - - +
420B GLN* 2.7 28.7 + - - +
423B GLN* 3.3 37.4 + - - +
424B PHE* 3.7 20.2 - - - -
427B ASP* 4.1 14.3 + - - -
460B GLU* 3.4 35.6 + - - +
461B ARG* 4.6 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 386 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B LEU* 2.9 26.4 + - + +
383B GLN* 3.3 11.4 + - - +
385B ARG* 1.3 73.1 - - + +
387B LEU* 1.3 65.3 + - + +
388B LEU 3.5 0.7 + - - +
391B LYS* 3.7 45.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 387 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B GLN 3.6 15.7 + - - +
384B GLU* 3.3 21.9 + - + +
385B ARG 3.0 1.4 - - - -
386B GLU* 1.3 84.4 - - + +
388B LEU* 1.3 63.9 + - - +
389B PRO* 3.7 4.5 - - - +
----------------------------------------------------------
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