Contacts of the strand formed by residues 198 - 208 (chain K) in PDB entry 2AK4
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 GLU 198 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193K PRO* 3.8 2.1 - - - +
194K VAL* 3.1 26.9 + - + +
195K SER* 2.9 31.2 + - - +
197K HIS* 1.3 93.9 + - + +
199K ALA* 1.3 65.4 + - - +
248K VAL* 3.9 21.3 - - + +
249K VAL 3.2 11.6 - - - +
250K PRO* 4.3 10.6 - - + +
251K SER* 3.4 6.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 199 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191K HIS* 3.2 39.3 - - + +
192K HIS 3.5 9.0 - - - +
193K PRO* 4.0 3.8 - - + -
194K VAL* 4.0 2.4 - - - +
198K GLU* 1.3 78.4 - - - +
200K THR* 1.3 61.9 + - - +
247K VAL 3.7 0.2 - - - +
248K VAL* 3.5 4.4 - - - -
249K VAL* 2.7 46.9 + - + +
251K SER* 4.4 4.5 - - - +
254K GLU* 4.4 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 200 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190K THR 3.6 1.0 - - - +
191K HIS* 3.4 6.1 - - - -
192K HIS* 2.7 53.3 + - + +
193K PRO 4.7 0.4 + - - -
194K VAL* 4.5 12.5 - - - +
199K ALA* 1.3 71.2 - - - +
201K LEU* 1.3 66.1 + - - +
202K ARG* 3.9 29.7 + - - +
229K GLU* 5.5 0.9 - - - +
246K ALA* 4.0 17.0 - - + -
247K VAL 3.3 12.1 - - - +
248K VAL* 4.3 13.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 201 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189K VAL* 4.3 2.2 - - + -
190K THR 3.4 8.5 - - - +
191K HIS* 3.7 27.1 - - + -
199K ALA 3.7 0.4 + - - -
200K THR* 1.3 72.8 - - - +
202K ARG* 1.3 59.8 + - - +
217K TRP* 3.8 23.5 - - + -
246K ALA* 3.2 4.3 - - - +
247K VAL* 2.9 36.7 + - + -
249K VAL* 3.9 25.4 - - + -
254K GLU* 4.0 15.0 - - + +
257K TYR* 3.8 30.3 - - + +
274K TRP* 3.8 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 202 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188K HIS 3.8 0.9 - - - +
189K VAL* 3.2 5.9 - - - +
190K THR* 2.9 45.6 + - - +
192K HIS* 3.2 31.1 - - + -
200K THR* 3.9 18.2 - - + +
201K LEU* 1.3 73.7 - - - +
203K CYS* 1.3 62.3 + - - +
204K TRP* 3.6 18.5 + - - +
217K TRP* 4.2 2.5 - - - -
229K GLU* 4.2 8.5 + - - -
244K TRP* 3.4 56.6 - - + -
245K ALA 3.4 2.0 - - - +
246K ALA* 4.0 1.7 - - + +
98L ASP* 2.7 37.1 + - - +
99L MET* 4.0 18.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 203 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187K THR* 5.8 0.7 - - - -
188K HIS 3.8 3.1 - - - -
189K VAL* 4.4 9.9 - - - -
202K ARG* 1.3 71.6 - - - +
204K TRP* 1.3 66.5 + - - +
215K LEU* 3.7 7.1 - - + +
217K TRP* 3.7 13.1 - - + +
244K TRP* 3.1 7.2 - - - +
245K ALA* 2.6 40.2 + - + +
259K CYS* 2.0 50.5 - - - -
261K VAL* 4.5 11.0 - - - -
272K LEU* 5.3 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 204 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186K LYS 4.2 0.4 - - - -
187K THR* 3.2 27.7 - - - +
188K HIS* 2.9 51.6 + + + +
190K THR* 3.4 29.6 + - + +
192K HIS* 5.2 0.2 + - - -
202K ARG* 3.6 21.9 - - + +
203K CYS* 1.3 74.5 - - - +
205K ALA* 1.3 58.6 + - - +
206K LEU* 3.8 30.1 - - + -
215K LEU* 4.7 1.1 - - - -
234K ARG* 3.5 13.0 - - - -
242K GLN* 4.9 0.9 - - + -
243K LYS 3.9 5.4 - - - -
244K TRP* 3.5 24.7 - + + -
97L ARG 4.6 5.4 - - - -
98L ASP* 3.4 28.2 + - - +
99L MET 3.2 24.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 205 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185K PRO* 3.9 8.3 - - + -
186K LYS 3.6 3.8 - - - -
187K THR* 4.3 5.8 - - + -
203K CYS 4.1 0.2 + - - -
204K TRP* 1.3 72.6 - - - +
206K LEU* 1.3 63.6 + - - +
208K PHE* 3.3 21.8 - - + -
213K ILE* 3.9 17.3 - - + -
215K LEU* 3.9 16.1 - - + +
242K GLN* 3.4 1.9 - - - -
243K LYS 2.9 35.5 + - - +
261K VAL* 5.1 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 206 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185K PRO* 3.4 1.2 - - - +
186K LYS* 2.8 49.1 + - + +
188K HIS* 4.2 19.5 - - + +
204K TRP* 3.8 26.5 - - + -
205K ALA* 1.3 78.9 - - - +
207K GLY* 1.3 64.4 + - - +
208K PHE* 3.4 4.5 + - - -
241K PHE 3.8 2.2 - - - -
242K GLN* 3.7 35.9 - - + +
12L ARG 5.4 0.7 - - - +
13L HIS 6.4 0.2 - - - -
14L PRO* 3.8 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 207 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183K ASP* 3.8 14.9 - - - +
184K PRO 4.0 5.5 - - - +
186K LYS* 5.3 7.3 - - - +
206K LEU* 1.3 74.0 - - - +
208K PHE* 1.3 58.9 + - - +
236K ALA* 5.8 0.2 - - - +
240K THR* 3.4 32.1 + - - +
241K PHE 3.1 7.9 + - - -
242K GLN* 4.9 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 208 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183K ASP 3.2 13.9 - - - +
184K PRO 4.4 0.2 - - - -
185K PRO* 3.7 22.2 - - + -
205K ALA* 3.3 26.2 - - + -
207K GLY* 1.3 79.2 - - - +
209K TYR* 1.3 62.7 + - - +
210K PRO 3.3 19.5 - - - -
211K ALA 3.3 23.6 - - - -
213K ILE* 3.7 36.6 - - + -
233K THR* 4.2 2.2 - - + -
240K THR* 3.5 3.6 - - - -
241K PHE* 2.9 59.5 + - + -
242K GLN* 3.8 12.1 - - - -
243K LYS* 4.0 1.1 - - + -
263K HIS* 3.6 13.2 - + - +
----------------------------------------------------------
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