Contacts of the helix formed by residues 196 - 211 (chain B) in PDB entry 2AX1
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 SER 196 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B TYR* 1.3 75.6 - - - +
197B PRO* 1.3 76.9 - - - +
198B GLY* 3.6 4.0 + - - -
199B GLN* 3.0 37.1 + - - +
200B ARG* 2.9 18.8 + - - +
466B LEU* 4.4 13.8 + - - -
551B PHE* 3.6 29.5 - - - +
1002B 5EE 4.6 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B SER* 1.3 87.8 - - - +
198B GLY* 1.3 61.8 + - - +
200B ARG* 3.3 3.5 + - + +
201B VAL* 3.1 24.1 + - - +
384B LEU* 4.7 15.8 - - + +
414B MET* 3.6 52.9 - - + +
466B LEU* 5.0 4.7 - - + -
467B HIS* 3.8 15.5 - - + -
551B PHE* 3.9 18.2 - - + -
1002B 5EE 3.6 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B SER* 3.2 5.0 + - - -
197B PRO* 1.3 80.9 - - - +
199B GLN* 1.3 60.3 + - - +
201B VAL* 2.9 25.4 - - - +
202B GLU* 3.1 12.0 + - - +
466B LEU 4.4 13.9 + - - -
467B HIS* 4.7 6.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B GLN 3.6 7.6 - - - +
195B TYR* 3.5 23.4 - - + -
196B SER* 3.0 36.6 + - - +
198B GLY* 1.3 74.6 - - - +
200B ARG* 1.3 60.9 + - - +
202B GLU* 3.6 16.9 - - - +
203B PHE* 3.0 29.3 + - - +
551B PHE* 5.1 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B GLY* 4.7 4.2 + - - -
195B TYR* 3.7 17.2 - - + +
196B SER 2.9 16.2 + - - +
197B PRO* 3.5 6.1 - - + +
198B GLY 3.3 0.4 - - - -
199B GLN* 1.3 78.7 - - - +
201B VAL* 1.3 62.1 + - - +
203B PHE* 3.3 4.4 + - - +
204B LEU* 3.0 34.3 + - + +
314B LEU* 3.4 33.6 + - + +
316B ASN* 2.9 35.3 + - - +
319B ASP* 4.4 2.0 + - - -
321B VAL* 4.6 2.0 - - - +
365B SER* 2.9 32.5 + - - -
366B CYS* 3.7 16.2 - - - +
368B SER* 5.7 0.2 - - - -
384B LEU* 3.8 21.4 - - + +
448B TYR* 5.4 0.2 - - - -
1002B 5EE 3.8 26.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B PRO 3.1 15.7 + - - +
198B GLY* 2.9 27.4 - - - +
200B ARG* 1.3 73.8 - - - +
202B GLU* 1.3 65.5 + - - +
204B LEU* 3.3 8.3 + - - +
205B VAL* 2.9 30.9 + - + +
370B VAL* 4.1 12.6 - - + -
382B TYR* 3.5 46.2 - - + +
383B TYR* 4.0 14.1 - - - +
384B LEU* 4.7 6.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B GLY 3.1 16.8 + - - +
199B GLN* 3.6 19.1 - - - +
201B VAL* 1.3 79.4 - - - +
203B PHE* 1.3 55.7 + - - +
205B VAL* 4.0 2.8 - - - +
206B ASN* 2.9 55.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B SER* 3.5 37.7 - - - -
195B TYR* 3.5 28.7 - + + -
199B GLN 3.0 17.4 + - - +
200B ARG* 3.7 4.7 - - - +
201B VAL 3.3 0.2 - - - -
202B GLU* 1.3 77.8 - - - +
204B LEU* 1.3 59.4 + - + +
206B ASN* 4.2 4.6 - - + +
207B THR* 2.6 48.9 + - - -
312B THR* 3.8 26.0 - - + -
313B MET 4.2 6.5 - - - -
314B LEU* 4.0 32.3 - - + -
323B ILE* 6.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B ARG* 3.0 42.5 + - + +
201B VAL 3.3 2.9 + - - +
203B PHE* 1.3 80.2 - - + +
205B VAL* 1.3 59.4 + - - +
207B THR* 3.4 4.3 + - - -
208B TRP* 2.9 30.5 + - - +
314B LEU* 3.7 23.8 - - + -
321B VAL* 4.4 14.8 - - + -
323B ILE* 4.0 22.3 - - + +
360B LEU* 4.1 11.6 - - + +
365B SER* 4.6 9.0 - - - +
370B VAL* 4.1 25.6 - - + -
384B LEU* 4.8 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B VAL* 2.9 35.7 + - + +
202B GLU* 4.0 3.4 - - - +
204B LEU* 1.3 76.3 - - - +
206B ASN* 1.3 60.3 + - - +
208B TRP* 3.2 2.3 + - + +
209B LYS* 2.9 60.5 + - + +
360B LEU* 3.8 23.3 - - + -
370B VAL* 4.1 3.6 - - + -
382B TYR* 4.0 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B GLU* 2.9 41.9 + - - +
203B PHE* 4.2 4.4 - - + +
205B VAL* 1.3 80.2 - - - +
207B THR* 1.3 62.9 + - - +
209B LYS* 3.5 11.9 + - - +
210B SER* 3.0 25.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B PHE* 2.6 46.2 + - + -
204B LEU* 3.6 4.0 - - - -
205B VAL 3.2 0.2 - - - -
206B ASN* 1.3 77.7 - - - +
208B TRP* 1.3 62.7 + - - +
210B SER* 2.7 23.5 + - - +
211B LYS* 3.4 11.6 - - - +
312B THR* 3.5 35.8 - - + +
323B ILE* 3.8 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B LEU 2.9 17.5 + - - +
205B VAL 3.2 4.9 + - - +
207B THR* 1.3 77.3 - - - +
209B LYS* 1.3 66.7 + - + +
210B SER 3.3 0.9 + - - -
211B LYS* 3.3 12.3 + - - +
214B PRO* 3.5 45.8 - - + +
215B MET 3.9 5.2 - - - -
216B GLY* 3.8 13.5 - - - -
323B ILE* 3.6 23.3 - - + +
357B GLU 3.6 21.3 - - - -
358B TYR 3.4 22.1 + - - -
359B ASP* 3.8 3.5 - - - +
360B LEU* 3.4 53.1 - - + +
363B ILE* 3.8 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B VAL* 2.9 41.5 + - + +
206B ASN* 3.9 11.9 + - - +
208B TRP* 1.3 81.9 - - + +
210B SER* 1.3 60.6 + - - +
211B LYS 3.3 8.1 + - - +
382B TYR* 4.2 22.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ASN 3.0 14.7 + - - -
207B THR* 2.7 23.1 + - - +
208B TRP 3.2 0.2 - - - -
209B LYS* 1.3 76.0 - - - +
211B LYS* 1.3 73.3 + - - +
212B LYS 4.0 0.5 + - - -
310B ASP* 5.0 3.1 + - - +
325B GLU* 4.4 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B THR* 3.4 24.2 - - - +
208B TRP 3.3 9.3 + - - +
209B LYS 3.3 9.3 - - - +
210B SER* 1.3 87.4 + - - +
212B LYS* 1.3 66.2 + - - +
214B PRO* 3.7 22.6 - - + +
310B ASP* 2.8 42.8 + - - +
312B THR* 2.7 26.6 + - - -
323B ILE* 3.5 27.4 - - + -
324B CYS 3.7 15.7 - - - +
325B GLU* 3.3 12.3 - - + +
----------------------------------------------------------
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