Contacts of the helix formed by residues 292 - 303 (chain D) in PDB entry 2AXV
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 PRO 292 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B ILE* 3.3 24.4 - - + -
252B ASP* 3.4 21.8 - - - +
255B LEU* 5.9 1.1 - - + -
254D TYR* 3.5 10.5 - - + +
258D VAL* 4.2 18.4 - - + -
280D LEU* 4.9 0.2 - - + -
291D PRO* 1.3 94.2 - - + +
293D LYS* 1.3 59.3 + - - +
294D GLU* 3.1 22.2 - - + +
295D VAL* 2.9 34.4 + - + +
296D THR* 3.1 8.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 293 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B ASP* 3.2 17.0 + - - +
291D PRO 3.5 1.4 + - - -
292D PRO* 1.3 72.0 - - - +
294D GLU* 1.3 65.5 + - - +
296D THR* 3.6 9.0 - - - +
297D MET* 2.9 29.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 294 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B ASP* 4.1 12.9 - - - +
258D VAL* 5.8 3.8 - - + -
292D PRO* 3.4 22.3 - - + +
293D LYS* 1.3 78.9 - - - +
295D VAL* 1.3 59.6 + - + +
297D MET* 3.1 19.3 - - - +
298D TYR* 3.0 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 295 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258D VAL* 4.5 15.3 - - + -
261D ILE* 5.5 9.0 - - + -
277D VAL* 3.5 26.0 - - + +
280D LEU* 4.1 13.0 - - + -
281D THR* 4.0 9.9 - - - +
291D PRO* 3.6 29.2 - - + -
292D PRO* 2.9 31.5 + - + +
294D GLU* 1.3 73.9 - - + +
296D THR* 1.3 63.9 + - - +
297D MET 3.3 1.8 - - - -
298D TYR* 3.1 10.1 + - + +
299D TYR* 3.0 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 296 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281D THR* 3.8 17.0 - - + +
291D PRO* 3.7 34.6 + - + -
292D PRO 3.1 13.2 + - - -
293D LYS* 3.6 12.0 + - - +
295D VAL* 1.3 74.3 - - - +
297D MET* 1.3 60.1 + - - +
298D TYR 3.2 0.4 - - - -
299D TYR* 3.7 9.8 - - + +
300D GLU* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 297 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293D LYS* 2.9 17.5 + - + +
294D GLU* 3.1 21.3 - - - +
296D THR* 1.3 78.7 - - - +
298D TYR* 1.3 94.6 + - + +
300D GLU* 3.4 18.0 + - - +
301D ASN* 3.2 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 298 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262D ASN* 5.7 1.3 - - - -
265D LYS* 3.0 42.9 + - + +
273D HIS* 3.8 24.0 - + - -
277D VAL* 4.1 6.1 - - + -
294D GLU* 3.0 33.7 - - + -
295D VAL* 3.1 12.5 + - + +
297D MET* 1.3 103.8 - - + +
299D TYR* 1.3 56.0 + - - +
301D ASN* 2.9 19.1 - - - +
302D TYR* 2.7 49.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 299 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277D VAL* 3.8 9.8 - - + +
278D GLU* 4.2 25.1 - - + -
281D THR* 3.7 40.2 - - + +
282D LYS* 5.4 7.6 - - + -
295D VAL 3.0 13.0 + - - +
296D THR* 3.3 12.5 + - + +
298D TYR* 1.3 75.3 - - - +
300D GLU* 1.3 71.6 + - - +
301D ASN 3.3 0.5 + - - -
302D TYR* 4.0 4.9 - - - +
303D VAL* 3.1 39.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 300 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296D THR 2.9 18.6 + - - +
297D MET* 3.4 10.7 - - - +
298D TYR 3.4 0.4 - - - -
299D TYR* 1.3 83.6 - - - +
301D ASN* 1.3 81.6 + - - +
303D VAL* 3.5 19.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 301 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297D MET* 3.2 22.8 + - - +
298D TYR* 2.9 25.3 - - - +
300D GLU* 1.3 88.8 + - - +
302D TYR* 1.3 73.2 + - - +
303D VAL 3.0 14.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 302 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270D GLU* 4.8 8.7 + - + +
273D HIS* 3.1 27.7 + + - +
274D ARG* 2.9 89.2 + - + +
277D VAL* 4.1 14.8 - - + -
278D GLU* 4.4 7.6 - - + +
298D TYR* 2.7 44.8 + + + +
299D TYR* 3.4 6.7 + - + +
301D ASN* 1.3 86.9 + - - +
303D VAL* 1.3 58.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 303 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274D ARG* 5.2 2.0 - - - +
299D TYR* 3.1 44.7 + - + +
300D GLU* 3.5 19.5 - - - +
301D ASN* 3.0 19.1 - - - +
302D TYR* 1.3 78.3 - - - +
----------------------------------------------------------
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