Contacts of the helix formed by residues 383 - 395 (chain A) in PDB entry 2X1L
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 383 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A GLU* 4.4 7.4 - - - +
382A PHE* 1.3 74.1 - - - +
384A ASP* 1.3 61.1 + - - +
385A GLU* 3.6 14.4 + - - +
386A ASP* 2.9 16.4 + - - -
387A THR* 2.9 31.4 + - - -
446A ARG* 3.0 41.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 384 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A THR* 1.3 75.4 - - - +
385A GLU* 1.3 67.4 + - - +
387A THR* 4.1 6.6 + - - -
388A ALA* 3.2 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 385 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A THR* 3.1 18.2 + - - +
384A ASP* 1.3 86.1 + - - +
386A ASP* 1.3 63.9 + - - +
388A ALA* 3.6 4.9 + - - +
389A LEU* 3.3 22.5 + - - +
426A TYR* 4.1 12.3 - - + -
430A GLN* 4.3 20.6 + - - +
446A ARG* 5.4 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 386 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A PHE* 3.5 22.6 - - + -
383A THR* 2.9 33.3 + - - +
385A GLU* 1.3 77.8 - - - +
387A THR* 1.3 55.8 + - - +
389A LEU* 3.5 2.9 + - - +
390A LEU* 3.1 34.7 + - - +
426A TYR* 2.6 33.7 + - - -
446A ARG* 2.8 31.5 + - - -
449A THR* 3.5 4.0 - - - +
453A THR* 3.9 11.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 387 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A PHE* 4.1 13.7 + - - +
383A THR 2.9 16.9 + - - -
384A ASP* 4.1 8.0 + - - -
386A ASP* 1.3 75.4 - - - +
388A ALA* 1.3 60.5 + - - +
390A LEU* 3.8 8.7 - - + +
391A ALA* 2.9 33.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A ASP 3.2 20.7 + - - +
385A GLU* 4.0 6.1 - - - +
386A ASP 3.4 0.2 - - - -
387A THR* 1.3 76.1 - - - +
389A LEU* 1.3 61.0 + - - +
391A ALA* 3.8 6.1 + - - +
392A ALA* 3.4 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A GLU 3.3 15.1 + - - +
386A ASP 3.8 3.1 - - - +
387A THR 3.2 0.4 - - - -
388A ALA* 1.3 77.6 - - - +
390A LEU* 1.3 64.9 + - - +
392A ALA* 3.3 7.1 + - + +
393A ALA* 3.1 21.3 + - - +
419A VAL* 4.2 6.0 - - + +
422A ALA* 3.7 19.1 - - + +
423A ALA* 3.6 34.1 - - + +
426A TYR* 3.6 36.8 - - + -
453A THR* 3.9 18.4 - - + +
454A THR* 5.3 0.9 - - - +
457A VAL* 3.8 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A PHE* 4.1 33.0 - - + -
386A ASP 3.1 23.4 + - - +
387A THR* 3.9 6.5 - - - +
389A LEU* 1.3 73.2 - - - +
391A ALA* 1.3 56.0 + - - +
393A ALA* 3.3 6.9 + - + +
394A ASP* 2.8 41.2 + - - +
452A TYR* 5.9 1.3 - - + -
453A THR* 3.8 22.0 - - + +
456A GLU* 3.7 33.9 - - + -
457A VAL* 4.5 5.6 - - + -
460A ILE* 5.6 0.2 - - + -
495A ARG* 3.8 27.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A THR* 2.9 22.4 + - + +
388A ALA* 4.0 6.7 - - - +
390A LEU* 1.3 76.0 - - - +
392A ALA* 1.3 57.5 + - - +
394A ASP* 3.4 8.2 + - - +
395A ALA* 3.1 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A ALA 3.4 12.5 + - - +
389A LEU* 3.3 11.9 + - + +
390A LEU 3.3 0.6 - - - -
391A ALA* 1.3 79.3 - - - +
393A ALA* 1.3 61.0 + - - +
395A ALA* 3.7 11.0 + - - +
396A LEU* 3.6 9.9 + - - +
399A ARG* 5.2 2.9 + - - -
419A VAL* 3.5 27.4 - - + +
422A ALA* 5.9 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 393 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A LEU 3.1 13.2 + - - +
390A LEU* 3.6 8.1 - - - +
392A ALA* 1.3 76.8 - - - +
394A ASP* 1.3 64.3 + - - +
396A LEU* 3.4 27.2 + - + +
397A LEU 4.8 0.5 + - - -
419A VAL* 4.0 13.9 - - + +
457A VAL* 4.0 18.6 - - + -
460A ILE* 3.5 34.9 - - + +
492A ILE* 5.5 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 394 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A LEU 2.8 28.5 + - - +
391A ALA* 3.8 8.7 + - - +
393A ALA* 1.3 72.9 - - - +
395A ALA* 1.3 59.0 + - - +
396A LEU 3.2 2.2 + - - -
397A LEU* 4.3 8.8 + - - +
398A GLU* 5.3 1.9 + - - +
460A ILE* 3.7 11.1 - - - +
492A ILE* 5.0 10.1 - - - +
495A ARG* 3.0 40.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A ALA 3.1 17.0 + - - +
392A ALA* 4.0 8.7 - - - +
393A ALA 3.3 0.6 - - - -
394A ASP* 1.3 76.6 - - - +
396A LEU* 1.3 62.4 + - - +
397A LEU 3.6 0.7 - - - -
398A GLU* 3.8 8.1 + - - +
399A ARG* 3.4 33.4 + - + +
----------------------------------------------------------
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