Contacts of the helix formed by residues 413 - 425 (chain B) in PDB entry 2AXT
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 ASP 413 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B PHE* 3.5 2.8 - - + -
412B THR* 1.3 78.9 + - - +
414B PRO* 1.3 72.5 - - - +
415B PRO* 3.1 21.5 - - - +
416B THR* 2.9 39.8 + - - +
417B VAL* 3.1 10.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 414 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B PHE* 5.5 3.8 - - + -
393B GLU* 3.5 44.9 - - + +
397B VAL 5.9 0.7 - - - +
412B THR 3.4 10.2 - - - +
413B ASP* 1.3 86.1 - - - +
415B PRO* 1.3 73.7 - - + +
417B VAL* 3.1 8.4 + - + +
418B LYS* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 415 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B ASP* 3.1 23.3 - - - +
414B PRO* 1.3 89.2 - - + +
416B THR* 1.3 58.8 + - - +
418B LYS* 3.1 19.7 + - + +
419B SER* 2.8 30.0 + - - -
422B ARG* 5.0 0.9 + - - -
38U GLU* 5.9 2.7 - - - +
40U VAL* 6.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 416 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B PHE* 3.6 27.5 - - + -
413B ASP* 2.9 28.7 + - - +
415B PRO* 1.3 71.8 - - - +
417B VAL* 1.3 67.2 + - - +
419B SER* 3.6 7.0 - - - -
420B TYR* 3.0 56.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 417 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B PHE* 3.9 6.7 - - + -
392B PHE* 3.8 23.3 - - + -
397B VAL* 4.1 8.3 - - + +
398B THR* 4.0 19.5 - - - +
399B VAL* 3.9 21.1 - - + -
411B PHE 3.6 22.9 - - - +
412B THR 3.9 5.6 - - - -
413B ASP 3.1 24.4 + - - +
414B PRO* 3.4 7.2 - - + +
416B THR* 1.3 77.1 - - - +
418B LYS* 1.3 57.8 + - - +
420B TYR* 3.2 3.6 + - - +
421B ALA* 2.9 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 418 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B ILE* 3.7 32.9 - - + +
382B PRO* 6.4 0.2 - - + -
392B PHE* 3.6 28.0 - - + +
393B GLU* 2.7 28.7 + - - +
414B PRO* 2.9 27.1 + - - +
415B PRO* 3.4 16.2 - - - +
417B VAL* 1.3 73.9 - - - +
419B SER* 1.3 68.1 + - - +
421B ALA* 2.7 13.5 + - - +
422B ARG* 2.9 23.0 + - - +
195O ASP* 4.6 10.2 + - - +
44U ASP* 4.0 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 419 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B PRO 2.8 19.7 + - - -
416B THR* 3.6 9.6 - - - -
418B LYS* 1.3 74.0 - - - +
420B TYR* 1.3 65.8 + - - +
422B ARG* 3.1 34.6 + - - +
423B LYS* 3.2 19.7 + - - +
205O GLU* 3.4 21.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 420 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B LYS* 3.2 32.1 + - - -
346B PHE* 3.7 12.3 - - + -
399B VAL* 4.7 4.9 - - + -
401B PHE* 3.3 36.3 - + + -
406B LEU* 3.1 25.8 - - + +
411B PHE* 4.3 13.7 - + - -
416B THR* 3.0 45.2 + - + +
417B VAL* 3.5 5.2 - - - +
419B SER* 1.3 83.0 + - - +
421B ALA* 1.3 61.1 + - - +
423B LYS* 3.6 4.8 + - + +
424B ALA* 3.2 17.8 + - - +
429B ILE* 3.3 23.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 421 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B PHE* 3.6 20.6 - - + -
356B VAL* 3.9 12.0 - - + +
368B VAL* 4.0 14.9 - - + +
370B LEU* 5.1 0.4 - - + -
381B ILE* 5.1 0.4 - - + -
392B PHE* 3.9 23.1 - - + -
417B VAL 2.9 12.7 + - - +
418B LYS* 2.7 15.2 + - - +
420B TYR* 1.3 70.9 - - - +
422B ARG* 1.3 63.6 + - - +
423B LYS 3.2 0.2 - - - -
424B ALA* 3.1 17.1 + - - +
425B ILE* 3.4 5.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 422 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B VAL* 4.4 12.1 - - + -
381B ILE* 4.1 20.3 - - + +
415B PRO 5.0 0.6 + - - -
418B LYS* 2.9 12.3 + - - +
419B SER* 3.1 29.8 + - - +
421B ALA* 1.3 76.3 - - - +
423B LYS* 1.3 72.0 + - - +
425B ILE* 3.6 22.6 - - + +
426B PHE* 4.0 12.5 - - - -
195O ASP* 3.4 30.1 + - - +
196O SER* 4.3 22.9 + - - -
205O GLU* 2.8 31.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 423 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B SER* 3.2 17.3 + - - +
420B TYR* 4.0 8.1 - - + +
421B ALA 3.2 0.6 - - - -
422B ARG* 1.3 87.0 + - - +
424B ALA* 1.3 62.5 + - - +
425B ILE 3.3 1.1 - - - -
426B PHE* 3.5 25.2 + - + +
427B GLY 3.9 2.3 - - - +
428B GLU 5.0 0.5 - - - +
429B ILE* 3.7 28.1 - - + +
201O PRO 3.6 13.4 + - - -
202O GLN* 3.0 36.1 - - - +
203O ALA 4.8 8.2 + - - -
205O GLU* 3.4 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 424 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B ALA* 5.8 0.4 - - + -
346B PHE* 4.0 9.0 - - + -
356B VAL* 3.7 25.6 - - + +
358B ARG* 4.8 3.8 - - - +
420B TYR 3.2 14.1 + - - +
421B ALA* 3.1 13.9 + - - +
423B LYS* 1.3 74.2 - - - +
425B ILE* 1.3 55.8 + - - +
426B PHE 2.9 2.9 - - - -
427B GLY* 2.5 38.4 + - - +
429B ILE* 4.0 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 425 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B TRP* 4.2 1.4 - - - -
356B VAL* 4.0 16.0 - - + +
357B ARG 3.7 16.4 - - - +
358B ARG* 3.5 8.9 - - - +
359B MET* 3.1 44.8 + - + +
366B PHE* 3.6 22.2 - - + +
367B PRO 3.3 28.3 - - - +
368B VAL* 4.0 8.7 - - + -
421B ALA 3.4 4.3 + - - +
422B ARG* 3.6 17.0 - - + +
424B ALA* 1.3 79.2 - - - +
426B PHE* 1.3 70.5 + - + +
427B GLY 3.2 3.8 + - - -
----------------------------------------------------------
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