Contacts of the helix formed by residues 383 - 395 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381C GLU* 4.4 7.0 - - + +
382C PHE* 1.3 73.1 - - - +
384C ASP* 1.3 57.5 + - - +
385C GLU* 3.6 14.8 + - - +
386C ASP* 2.8 31.7 + - - -
387C THR* 2.7 35.4 + - - -
430C GLN* 5.1 0.2 + - - -
446C ARG* 3.5 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 384 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383C THR* 1.3 74.6 - - - +
385C GLU* 1.3 68.6 + - - +
387C THR* 3.8 6.9 + - - -
388C ALA* 3.0 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 385 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383C THR* 3.2 15.5 + - - +
384C ASP* 1.3 85.0 + - - +
386C ASP* 1.3 64.8 + - - +
388C ALA* 3.5 5.4 + - - +
389C LEU* 3.3 22.5 + - - +
426C TYR* 4.0 11.1 - - + -
430C GLN* 3.8 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 386 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382C PHE* 3.5 19.9 - - + -
383C THR* 2.8 23.9 + - - +
385C GLU* 1.3 75.0 - - - +
387C THR* 1.3 57.4 + - - +
389C LEU* 3.4 3.5 + - - +
390C LEU* 3.0 35.1 + - - +
426C TYR* 2.6 34.9 + - - -
446C ARG* 2.7 37.8 + - - -
449C THR* 3.4 12.3 - - - +
453C THR* 4.0 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 387 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382C PHE* 4.1 13.3 + - - +
383C THR 2.7 23.5 + - - -
384C ASP* 3.8 8.8 + - - -
386C ASP* 1.3 77.3 - - - +
388C ALA* 1.3 56.2 + - - +
390C LEU* 3.4 7.8 + - - +
391C ALA* 2.9 32.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 388 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384C ASP 3.0 18.5 + - - +
385C GLU* 4.0 5.6 - - - +
386C ASP 3.4 0.2 - - - -
387C THR* 1.3 76.3 - - - +
389C LEU* 1.3 60.7 + - - +
391C ALA* 3.8 6.6 + - - +
392C ALA* 3.4 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 389 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385C GLU 3.3 14.4 + - - +
386C ASP 3.8 4.3 - - - +
387C THR 3.3 0.4 - - - -
388C ALA* 1.3 76.8 - - - +
390C LEU* 1.3 63.4 + - - +
392C ALA* 3.2 8.6 + - + +
393C ALA* 3.1 20.5 + - - +
419C VAL* 4.1 9.1 - - + +
422C ALA* 3.8 17.9 - - + +
423C ALA* 3.6 31.6 - - + +
426C TYR* 3.6 39.0 - - + -
453C THR* 4.0 11.4 - - + +
454C THR* 5.4 0.9 - - - +
457C VAL* 3.8 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 390 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382C PHE* 3.9 34.8 - - + -
386C ASP 3.0 21.9 + - - +
387C THR* 3.9 6.1 - - - +
389C LEU* 1.3 75.4 - - - +
391C ALA* 1.3 57.1 + - - +
393C ALA* 3.3 5.9 + - + +
394C ASP* 2.8 37.5 + - - +
452C TYR* 5.8 0.9 - - + -
453C THR* 3.8 22.7 - - + +
456C GLU* 3.8 32.8 - - + -
457C VAL* 4.7 5.2 - - + -
495C ARG* 4.0 28.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 391 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387C THR* 2.9 21.3 + - + +
388C ALA* 3.9 8.1 - - - +
389C LEU 3.3 0.2 - - - -
390C LEU* 1.3 77.2 - - - +
392C ALA* 1.3 55.6 + - - +
394C ASP* 4.0 6.9 - - - +
395C ALA* 3.1 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 392 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388C ALA 3.4 11.6 + - - +
389C LEU* 3.2 13.6 + - + +
391C ALA* 1.3 78.7 - - - +
393C ALA* 1.3 60.3 + - - +
395C ALA* 3.7 10.8 + - - +
396C LEU* 3.6 9.7 + - - +
399C ARG* 5.2 3.3 + - - -
419C VAL* 3.6 29.2 - - + +
422C ALA* 5.9 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 393 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389C LEU 3.1 12.4 + - - +
390C LEU* 3.3 9.8 + - + +
392C ALA* 1.3 76.1 - - - +
394C ASP* 1.3 63.6 + - - +
396C LEU* 3.3 27.9 + - + +
397C LEU 4.7 0.5 + - - -
419C VAL* 4.1 13.6 - - + +
457C VAL* 4.3 17.5 - - + +
460C ILE* 3.6 34.6 - - + +
492C ILE* 5.4 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 394 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390C LEU 2.8 22.7 + - - +
391C ALA* 3.6 7.2 + - - +
392C ALA 3.5 0.2 - - - -
393C ALA* 1.3 73.8 - - - +
395C ALA* 1.3 59.2 + - - +
396C LEU 3.2 1.4 + - - -
397C LEU* 4.3 9.8 + - - +
398C GLU* 5.3 1.4 + - - +
460C ILE* 3.6 11.6 - - - +
492C ILE* 5.2 9.0 - - - +
495C ARG* 2.7 44.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 395 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391C ALA 3.1 18.3 + - - +
392C ALA* 4.0 7.6 - - - +
393C ALA 3.2 0.4 - - - -
394C ASP* 1.3 75.7 - - - +
396C LEU* 1.3 62.3 + - - +
397C LEU 3.5 1.1 + - - -
398C GLU* 3.7 8.7 + - - +
399C 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