Contacts of the helix formed by residues 393 - 404 (chain A) in PDB entry 2AAT
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 393 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ASP 3.8 11.7 + - - +
51A GLU* 3.8 11.4 - - - +
52A THR* 5.8 1.6 - - - -
329A ARG* 3.4 10.0 + - - -
333A MET* 4.1 8.1 - - - -
390A ALA 5.2 0.9 + - - -
391A GLY 4.3 3.4 + - - -
392A MET* 1.3 77.3 + - - +
394A PRO* 1.3 87.9 - - + +
395A ASP* 3.1 11.2 - - + +
396A ASN* 3.0 32.4 - - - +
397A MET* 2.4 40.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 394 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A GLU* 3.9 26.5 - - + +
329A ARG* 4.6 4.5 - - - +
332A ARG* 5.5 10.8 - - - +
333A MET* 4.5 6.4 - - - -
336A LEU* 6.1 3.4 - - + -
393A THR* 1.3 101.1 - - + +
395A ASP* 1.3 78.3 - - + +
397A MET* 3.7 13.2 - - + +
398A ALA* 4.5 5.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A GLU 4.7 6.4 - - - +
393A THR* 3.9 9.0 - - + -
394A PRO* 1.3 91.8 - - - +
396A ASN* 1.3 65.5 + - - +
398A ALA* 4.2 3.5 - - - +
399A PRO* 3.5 16.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 396 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LYS* 2.3 47.3 + - - +
41A ILE* 4.9 0.2 - - - +
391A GLY 2.8 22.5 - - - +
392A MET* 4.0 0.2 - - - -
393A THR* 3.0 31.9 + - - +
395A ASP* 1.3 73.7 - - - +
397A MET* 1.3 74.5 - - - +
398A ALA 2.7 4.8 + - - -
399A PRO* 3.0 18.9 - - + +
400A LEU* 3.3 9.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 397 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A MET* 4.5 12.6 - - - -
336A LEU* 4.2 19.5 - - + -
337A PHE* 3.6 52.3 - - + +
340A THR* 4.0 20.0 - - + -
392A MET* 4.6 6.5 - - - +
393A THR 2.4 33.5 + - - +
394A PRO* 3.7 11.2 - - + +
395A ASP 3.4 0.6 - - - -
396A ASN* 1.3 71.9 - - - +
398A ALA* 1.3 52.5 + - + +
400A LEU* 3.4 6.4 + - + -
401A CYS* 2.6 51.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A THR* 4.8 7.9 - - + -
394A PRO 4.8 4.0 - - - +
395A ASP 4.2 5.6 - - - +
396A ASN 2.7 2.4 + - - -
397A MET* 1.3 74.9 - - + +
399A PRO* 1.3 64.1 - - + +
401A CYS* 2.7 33.3 + - - +
402A GLU* 3.0 7.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LYS* 6.0 3.8 - - + -
395A ASP 3.5 12.6 - - - +
396A ASN* 3.0 18.2 - - + +
398A ALA* 1.3 92.3 - - + +
400A LEU* 1.3 47.3 + - - +
402A GLU* 2.8 25.4 + - - +
403A ALA* 2.4 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LYS* 3.2 51.0 - - + +
43A LEU* 4.3 8.3 - - + -
337A PHE* 4.7 13.6 - - + -
379A VAL* 4.4 12.6 - - + -
387A VAL* 6.1 0.4 - - + -
392A MET* 3.3 34.5 - - + -
396A ASN* 3.3 17.6 + - + +
397A MET* 4.0 12.6 - - + +
399A PRO* 1.3 74.2 - - - +
401A CYS* 1.3 63.7 + - - +
403A ALA* 3.3 17.7 + - - +
404A ILE* 3.9 15.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A PHE* 4.5 2.2 - - - -
340A THR* 3.2 44.6 - - + -
341A LEU* 3.1 39.8 - - - +
344A LYS* 4.8 10.5 - - + +
345A GLY 5.2 0.2 + - - -
397A MET* 2.6 28.8 + - + +
398A ALA 2.7 12.5 + - - +
400A LEU* 1.3 75.9 - - - +
402A GLU* 1.3 51.6 + - - +
404A ILE* 2.8 28.1 - - - +
405A VAL* 3.6 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A LYS* 5.1 17.8 - - + +
377A PHE* 4.3 9.9 - - + -
398A ALA 3.0 7.6 + - - +
399A PRO* 2.8 23.9 + - - +
401A CYS* 1.3 77.1 - - - +
403A ALA* 1.3 64.5 + - - +
404A ILE 3.4 1.1 - - - -
405A VAL* 3.3 24.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 403 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LYS* 6.0 0.2 - - + -
373A LEU* 4.0 6.1 - - + -
377A PHE* 2.7 45.8 - - + -
379A VAL* 3.4 35.4 - - + -
399A PRO 2.4 20.2 + - - +
400A LEU* 3.3 15.1 + - - +
402A GLU* 1.3 75.2 - - - +
404A ILE* 1.3 58.7 + - + +
405A VAL 3.5 0.7 + - - -
406A ALA 4.2 1.0 + - - -
407A VAL* 3.3 3.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A PHE* 4.5 24.0 - - + -
341A LEU* 3.9 13.5 - - + -
345A GLY* 5.6 0.7 - - - -
350A PHE* 4.9 13.9 - - + -
363A SER* 6.4 0.7 - - - -
365A LEU* 4.5 18.2 - - + -
373A LEU* 4.9 5.4 - - + -
400A LEU* 3.9 12.6 - - + +
401A CYS 2.8 30.5 - - - +
403A ALA* 1.3 70.5 - - + +
405A VAL* 1.3 74.2 + - + +
406A ALA 3.4 1.8 - - - -
407A VAL* 2.7 39.5 - - + +
408A LEU* 2.8 18.9 + - - +
----------------------------------------------------------
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