Contacts of the helix formed by residues 401 - 410 (chain B) in PDB entry 2XAF
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 401 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A ARG* 4.1 10.7 + - - -
398B TYR* 3.5 18.3 + - + +
399B GLY 3.9 0.4 - - - -
400B ARG* 1.3 72.7 - - - +
402B PHE* 1.3 53.2 + - - +
403B GLN* 2.8 38.1 + - - +
404B ALA* 3.0 27.2 + - + +
405B ILE* 3.0 15.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 402 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B ARG* 2.4 51.4 + - + -
401B ASP* 1.3 66.1 + - - +
403B GLN* 1.3 56.0 + - - +
405B ILE* 4.0 8.0 - - - +
406B SER* 3.0 29.6 + - - -
414B VAL* 3.5 26.7 - - + +
417B VAL* 4.1 6.0 - - + +
418B LYS* 4.1 31.9 - - + -
421B PHE* 3.6 44.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 403 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A ARG* 5.8 1.3 - - - +
401B ASP* 2.8 12.9 + - - +
402B PHE* 1.3 76.8 - - - +
404B ALA* 1.3 55.7 + - - +
406B SER* 3.2 5.9 + - - -
407B ASP* 2.8 62.9 + - - +
414B VAL* 3.5 29.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 404 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A ARG* 3.0 42.3 - - - +
398B TYR* 3.7 19.1 - - + -
401B ASP* 3.0 16.8 + - - +
403B GLN* 1.3 75.4 - - - +
405B ILE* 1.3 59.7 + - - +
407B ASP* 2.6 26.5 + - - +
408B VAL* 2.8 18.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 405 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B ALA* 5.2 2.9 - - + +
394B ALA* 3.8 19.1 - - + +
395B ILE* 3.6 43.7 - - + +
398B TYR* 4.1 15.0 - - + -
399B GLY 4.6 6.7 - - - +
400B ARG 5.4 0.4 - - - -
401B ASP 3.0 16.0 + - - +
402B PHE* 4.0 5.4 - - - +
404B ALA* 1.3 78.8 - - - +
406B SER* 1.3 64.1 + - - +
408B VAL* 3.3 3.1 + - - +
409B ILE* 3.2 44.3 + - + +
417B VAL* 3.7 21.3 - - + -
421B PHE* 4.2 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 406 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B PHE 3.0 21.1 + - - -
403B GLN* 3.3 7.9 + - - -
404B ALA 3.1 0.2 - - - -
405B ILE* 1.3 78.2 - - - +
407B ASP* 1.3 66.8 + - - +
409B ILE* 4.0 2.8 - - - +
410B GLY* 3.0 21.1 + - - -
412B LYS 2.8 28.8 + - - +
413B SER* 4.5 0.3 - - - -
414B VAL* 4.1 21.2 + - - +
417B VAL* 4.3 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 407 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A ARG* 4.0 25.2 + - + +
403B GLN* 2.8 54.7 + - - +
404B ALA* 2.6 15.3 + - - +
406B SER* 1.3 75.0 + - - +
408B VAL* 1.3 61.4 + - - +
410B GLY* 3.5 10.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 408 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A PHE* 4.5 18.4 - - + -
481A LYS* 3.2 47.8 - - + +
482A SER* 4.3 14.4 - - - +
485A ARG* 4.0 26.2 - - + -
390B LEU* 4.7 5.8 - - + +
394B ALA* 4.8 7.6 - - + -
398B TYR* 4.9 11.9 - - + -
404B ALA 2.8 19.8 + - - +
405B ILE* 3.7 8.5 - - - +
406B SER 3.1 0.2 - - - -
407B ASP* 1.3 75.8 - - - +
409B ILE* 1.3 68.5 + - + +
410B GLY* 2.9 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 409 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A LYS* 5.0 5.9 - - - +
377B GLN* 4.5 2.6 + - - -
383B TRP* 4.1 16.4 - - + -
387B GLU* 3.8 37.9 - - + +
390B LEU* 4.5 14.6 - - + +
391B ALA* 3.6 39.5 - - + +
394B ALA* 5.1 0.7 - - + -
405B ILE* 3.2 29.6 + - + +
406B SER 4.3 2.5 - - - +
408B VAL* 1.3 76.3 - - + +
410B GLY* 1.3 56.0 + - - +
411B ASN* 3.0 12.5 + - - +
412B LYS* 4.3 20.2 - - + -
417B VAL* 5.3 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 410 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A LYS* 5.7 2.7 - - - -
375B VAL* 6.3 0.9 - - - -
377B GLN* 3.2 32.5 + - - +
406B SER 3.0 12.3 + - - +
407B ASP* 3.7 13.8 - - - -
408B VAL 2.9 5.2 - - - -
409B ILE* 1.3 75.6 - - - +
411B ASN* 1.3 54.0 + - - +
412B LYS 3.7 3.1 + - - -
----------------------------------------------------------
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