Contacts of the helix formed by residues 373 - 382 (chain B) in PDB entry 2A1A
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 373 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B LYS 3.8 1.8 + - - +
372B GLY* 1.3 76.6 - - - -
374B LEU* 1.3 59.5 + - - +
375B GLU* 3.6 9.7 + - - +
376B GLN* 2.6 43.8 + - - +
377B TRP* 2.9 24.9 + - - +
417B PRO 4.0 7.4 - - - -
418B SER* 3.9 9.9 - - - +
420B ILE 3.4 7.2 - - - -
421B PHE* 3.5 31.0 - - + -
422B LEU* 3.9 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 374 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B THR* 1.3 68.2 - - - +
375B GLU* 1.3 60.5 + - - +
377B TRP* 3.0 18.4 + - + +
378B ILE* 2.8 38.0 + - + +
394B LEU* 3.9 28.5 - - + -
398B ILE* 3.8 27.8 - - + -
417B PRO* 3.3 22.4 - - + +
420B ILE* 2.9 33.9 + - + +
422B LEU* 3.7 13.9 - - + +
428B VAL* 4.9 3.8 - - + -
477B ILE* 4.5 10.5 - - + -
481B LEU* 4.2 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 375 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B THR* 3.2 8.5 + - - +
374B LEU* 1.3 75.2 - - - +
376B GLN* 1.3 65.4 + - + +
378B ILE* 3.4 5.4 + - - +
379B GLU* 3.0 33.8 + - - +
417B PRO* 2.9 24.1 + - + +
418B SER* 3.3 29.4 - - - +
453B ARG* 5.4 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 376 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B LYS 5.6 1.6 - - - +
372B GLY* 3.3 11.2 - - - -
373B THR* 2.6 48.5 + - - +
375B GLU* 1.3 81.3 - - + +
377B TRP* 1.3 55.3 + - - +
379B GLU* 3.1 9.4 - - + +
380B LYS* 2.9 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 377 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B THR 2.9 12.5 + - - +
374B LEU* 3.0 25.7 + - + +
376B GLN* 1.3 72.5 - - - +
378B ILE* 1.3 74.2 + - + +
380B LYS* 3.4 9.2 + - + +
381B ARG* 3.0 63.8 + - + +
387B ASP* 5.4 3.8 - - + -
390B LEU* 3.6 37.3 - - + +
391B ALA* 4.8 10.3 - - + -
394B LEU* 4.1 16.3 - - + +
422B LEU* 3.7 29.2 - - + +
425B THR* 6.4 0.4 - - - +
426B LYS 5.9 1.8 - - - +
481B LEU* 4.0 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 378 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B LEU* 2.8 29.7 + - + +
375B GLU* 3.7 4.9 - - - +
377B TRP* 1.3 84.3 - - + +
379B GLU* 1.3 65.0 + - - +
381B ARG* 3.0 42.8 + - - +
382B ARG* 3.3 22.7 + - + +
417B PRO* 3.9 20.9 - - + -
477B ILE* 6.5 0.2 - - + -
480B GLU* 3.7 42.0 - - + +
481B LEU* 4.6 10.1 - - + -
485B CYS* 5.9 2.0 - - + +
491B THR* 6.4 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 379 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 5.9 2.4 - - - +
74A ARG* 3.0 21.1 + - - +
375B GLU* 3.0 23.2 + - - +
376B GLN* 3.1 16.4 - - + +
378B ILE* 1.3 74.6 - - - +
380B LYS* 1.3 63.8 + - - +
381B ARG 3.1 1.2 + - - -
382B ARG* 2.8 62.0 + - - +
488B ALA* 5.7 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 380 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B GLN 2.9 12.9 + - - +
377B TRP* 3.5 10.5 - - + +
379B GLU* 1.3 80.9 - - - +
381B ARG* 1.3 60.8 + - - +
382B ARG 3.5 0.5 + - - -
383B GLY 4.6 2.4 + - - -
384B GLU* 3.4 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 381 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B TRP* 3.0 49.8 + - + +
378B ILE* 3.0 36.2 + - - +
380B LYS* 1.3 76.9 - - - +
382B ARG* 1.3 64.9 + - - +
383B GLY 3.3 1.8 - - - -
384B GLU* 2.8 39.0 + - - +
385B LYS 4.5 10.1 - - - -
386B LEU* 5.1 4.7 - - - +
387B ASP* 5.4 3.7 + - - +
391B ALA* 5.9 0.4 - - - +
480B GLU 3.6 15.0 + - - -
481B LEU* 3.3 30.9 + - - +
483B HIS 4.7 1.2 + - - -
484B VAL* 3.7 42.7 - - - +
485B CYS 4.9 1.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 382 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ARG* 3.5 25.6 - - - +
378B ILE* 3.3 19.0 + - + +
379B GLU* 2.8 50.3 + - - +
380B LYS 3.4 0.4 - - - -
381B ARG* 1.3 75.8 - - - +
383B GLY* 1.3 59.4 + - - +
384B GLU 3.3 0.3 + - - -
484B VAL* 3.6 8.1 - - - +
485B CYS* 2.7 40.9 + - - +
486B ASP* 2.4 53.7 - - - +
487B THR* 3.3 8.4 + - - +
488B ALA* 3.9 17.1 - - - +
491B THR* 3.0 28.3 + - - +
----------------------------------------------------------
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