Contacts of the helix formed by residues 376 - 389 (chain A) in PDB entry 2A72
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 GLU 376 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A ARG* 3.1 35.6 + - + -
373A PRO* 3.0 31.4 + - + +
375A LYS* 1.3 78.1 - - - +
377A VAL* 1.3 58.6 + - - +
378A PRO* 3.5 0.7 - - - -
379A SER* 3.1 14.1 + - - +
380A ARG* 2.9 48.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 377 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A LEU* 4.2 11.2 - - + +
372A ARG* 4.4 2.0 - - + +
373A PRO 3.3 14.3 + - - +
374A ILE* 2.9 26.6 + - + +
376A GLU* 1.3 77.6 - - - +
378A PRO* 1.3 59.6 - - + +
380A ARG* 4.4 5.4 - - - -
381A VAL* 2.7 42.2 + - + +
414B PRO 3.8 7.9 - - - +
415B GLY* 3.5 33.2 - - - -
416B ARG* 3.7 30.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 378 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A ILE 3.4 11.0 - - - +
375A LYS* 3.5 14.6 - - - +
376A GLU 3.6 0.7 - - - -
377A VAL* 1.3 94.3 - - + +
379A SER* 1.3 61.4 + - - +
381A VAL* 3.4 6.7 + - + +
382A GLN* 3.1 30.0 + - + +
414A PRO* 6.5 1.6 - - + -
414B PRO 5.8 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A LYS 5.0 1.6 + - - -
376A GLU* 3.1 22.7 + - - +
378A PRO* 1.3 79.2 - - - +
380A ARG* 1.3 59.2 + - - +
382A GLN* 3.2 8.7 + - - +
383A GLU* 2.9 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 380 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A ASP* 5.7 1.1 - - - +
369A LEU* 3.7 19.3 - - + -
372A ARG* 4.2 12.6 - - + +
376A GLU* 2.9 56.4 + - + +
377A VAL 3.8 0.2 - - - +
379A SER* 1.3 75.0 + - - +
381A VAL* 1.3 66.4 + - - +
383A GLU* 3.1 17.7 + - - +
384A ILE* 2.9 32.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 381 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A LEU* 4.1 11.6 - - + +
377A VAL* 2.7 37.7 + - + +
378A PRO* 3.5 6.7 - - + +
380A ARG* 1.3 71.5 - - - +
382A GLN* 1.3 69.0 + - - +
384A ILE* 3.3 1.4 + - - -
385A TRP* 3.0 25.1 + - - +
410A ASN 5.3 1.3 - - - +
411A VAL* 4.1 14.8 - - + -
414A PRO* 6.3 1.8 - - + -
415B GLY* 3.5 26.0 - - - +
418B THR* 3.9 26.2 - - + +
419B PHE* 3.5 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 382 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A PRO 3.1 18.5 + - - +
379A SER* 3.5 10.3 - - - +
380A ARG 3.2 0.4 - - - -
381A VAL* 1.3 82.8 - - - +
383A GLU* 1.3 58.5 + - + +
385A TRP* 3.4 10.1 + - - +
386A GLN* 3.0 39.9 + - + +
411A VAL* 3.1 42.4 + - - +
412A LYS* 5.4 2.9 - - - -
414A PRO* 5.1 5.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 383 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A SER* 2.9 26.0 + - - +
380A ARG* 3.1 22.0 + - - +
382A GLN* 1.3 76.7 - - + +
384A ILE* 1.3 61.8 + - + +
386A GLN* 3.5 7.1 + - - +
387A GLU* 3.1 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 384 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A PHE* 4.0 23.6 - - + -
365A ALA* 3.8 34.3 - - + +
366A VAL* 4.6 3.8 - - + +
369A LEU* 3.9 22.4 - - + -
380A ARG* 2.9 23.7 + - + +
381A VAL 3.8 3.8 - - - +
383A GLU* 1.3 73.7 - - + +
385A TRP* 1.3 65.5 + - - +
387A GLU* 3.4 1.5 + - - +
388A PHE* 3.1 37.2 + - + +
389A LEU* 4.9 0.5 - - - +
419B PHE* 3.7 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 385 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A VAL 3.0 14.7 + - - +
382A GLN* 3.6 12.8 - - - +
383A GLU 3.3 0.2 - - - -
384A ILE* 1.3 74.8 - - - +
386A GLN* 1.3 70.8 + - - +
389A LEU* 2.9 51.2 + - + -
390A ALA* 2.6 56.8 + - + +
391A PRO* 4.7 6.9 - - + +
404A TYR* 3.9 16.2 - + - -
407A THR* 4.4 2.5 - - + -
408A THR* 3.3 42.0 - - + -
411A VAL* 3.6 36.3 - - + -
412A LYS* 3.5 32.9 - - - +
419B PHE* 4.2 3.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 386 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A GLN* 3.0 26.9 + - + +
383A GLU* 3.7 7.9 - - - +
385A TRP* 1.3 97.5 - - - +
387A GLU* 1.3 59.6 + - - +
390A ALA* 3.6 16.8 - - - +
391A PRO 5.3 0.9 - - - +
393A ALA* 3.3 19.8 - - - +
394A PRO* 3.7 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 387 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A ARG* 4.5 3.0 + - - +
383A GLU 3.1 17.7 + - - +
384A ILE* 4.7 0.9 - - - -
385A TRP 3.4 0.2 - - - -
386A GLN* 1.3 76.1 - - - +
388A PHE* 1.3 84.0 + - + +
393A ALA* 3.4 2.8 - - - +
394A PRO* 3.4 24.5 - - - +
395A SER* 2.7 57.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A GLU 3.6 5.8 - - - -
361A ARG* 3.6 24.9 - - + -
362A PHE* 3.5 55.0 - + + -
365A ALA* 4.0 15.5 - - + -
384A ILE* 3.1 23.3 + - + +
387A GLU* 1.3 93.5 - - + +
389A LEU* 1.3 67.4 + - + +
393A ALA* 3.7 6.5 - - - -
395A SER* 3.0 37.0 - - - +
396A ALA* 3.4 3.3 - - - +
397A ILE* 3.1 37.1 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
362A PHE* 4.0 17.3 - - + -
385A TRP* 2.9 35.7 + - + +
388A PHE* 1.3 92.6 - - + +
390A ALA* 1.3 67.7 + - - +
391A PRO* 4.6 0.2 - - - +
393A ALA* 3.6 1.0 - - - +
397A ILE* 3.7 22.2 - - + +
399A LEU* 3.8 21.8 - - + +
404A TYR* 4.4 21.7 + - + -
407A THR* 3.8 29.2 - - + -
419B PHE* 3.9 17.0 - - + -
----------------------------------------------------------
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