Contacts of the strand formed by residues 198 - 207 (chain D) in PDB entry 4BEI
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 ALA 198 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164D LEU* 4.3 19.7 - - + -
192D ASN* 3.4 21.7 - - + +
194D ARG* 3.5 26.9 - - - +
197D GLU* 1.3 76.0 - - - +
199D ASN* 1.3 62.3 + - - +
200D VAL* 3.9 2.8 + - + +
222D TRP 3.5 2.6 - - - +
223D VAL* 3.6 1.6 - - - +
224D ILE* 2.9 36.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 199 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194D ARG* 4.8 2.2 - - - +
197D GLU* 3.9 23.5 + - - +
198D ALA* 1.3 74.1 - - - +
200D VAL* 1.3 64.9 + - - +
222D TRP 3.5 3.5 - - - +
223D VAL* 3.3 28.7 - - - +
255D ASP* 3.5 7.1 + - - +
256D ILE* 2.9 44.5 + - + +
257D VAL* 4.6 19.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 200 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161D LEU* 4.6 0.7 - - + -
164D LEU* 3.2 31.6 - - + -
190D LEU* 4.6 9.2 - - + -
198D ALA* 4.7 3.4 - - + +
199D ASN* 1.3 82.5 - - - +
201D GLU* 1.3 60.5 + - - +
202D PHE* 5.2 2.0 - - + -
220D GLU 3.9 0.3 - - - +
221D LYS* 3.5 2.3 - - - -
222D TRP* 2.8 57.9 + - + +
224D ILE* 4.1 16.6 - - + -
253D VAL* 3.9 16.6 - - + -
254D VAL 3.1 11.7 - - - +
255D ASP* 4.3 7.6 - - + -
256D ILE* 3.5 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 201 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C ALA* 5.3 2.8 - - - +
121C PRO* 3.9 4.7 - - - +
123C TYR* 2.6 48.1 + - + +
124C MET* 3.5 9.5 - - - +
200D VAL* 1.3 74.5 - - - +
202D PHE* 1.3 64.8 + - - +
203D TRP* 3.7 21.4 - - + -
219D ARG* 3.8 30.1 + - + +
220D GLU 3.2 15.0 - - - +
221D LYS* 4.0 15.2 + - + +
252D GLN 4.1 0.2 - - - +
253D VAL* 3.4 4.0 - - - +
254D VAL* 2.8 35.3 + - + +
256D ILE* 3.8 4.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 202 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168D ILE* 4.5 3.8 - - + -
188D VAL* 4.0 24.9 - - + -
190D LEU* 4.3 18.4 - - + -
200D VAL* 5.2 3.1 - - + -
201D GLU* 1.3 76.6 - - - +
203D TRP* 1.3 76.3 + - - +
204D MET* 3.8 37.2 - - + -
217D ASN* 3.7 27.8 - - - -
218D ALA 3.4 2.3 - - - +
219D ARG* 3.5 0.5 - - - -
220D GLU* 2.8 45.7 + - + +
222D TRP* 5.3 2.9 - + + -
230D TYR* 4.2 24.5 - + - -
232D LYS* 4.6 1.3 - - - -
251D ALA* 4.5 8.5 - - + -
252D GLN 3.4 14.1 - - - +
253D VAL* 3.8 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 203 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C ILE* 5.1 1.3 - - + -
87C TYR 2.7 27.6 + - - -
88C PHE* 3.5 28.7 - + + -
89C PRO* 3.9 4.0 - - + -
124C MET* 3.5 22.7 - - + -
201D GLU* 3.7 25.8 - - + -
202D PHE* 1.3 93.7 - - - +
204D MET* 1.3 74.1 + - - +
205D THR* 4.7 1.3 - - + -
217D ASN* 3.4 15.0 - - - +
218D ALA 4.0 1.8 - - - +
219D ARG* 3.6 26.0 - - + -
250D ASN 5.5 0.2 - - - -
252D GLN* 2.8 67.3 + - + +
254D VAL* 3.3 31.2 - - + -
261D ARG* 4.5 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 204 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C PRO* 4.0 1.6 - - - +
168D ILE* 4.3 15.5 - - + -
186D PHE* 4.5 13.5 - - + -
188D VAL* 4.2 13.2 - - - -
202D PHE* 3.8 22.4 - - + -
203D TRP* 1.3 82.9 - - - +
205D THR* 1.3 70.6 + - - +
216D VAL* 2.9 21.2 + - + -
217D ASN* 2.9 45.3 + - + +
234D ARG* 4.5 7.6 - - - -
249D ILE* 4.0 26.0 - - + -
250D ASN 3.2 5.4 - - - +
251D ALA* 3.7 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 205 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C SER* 5.7 0.4 - - - +
87C TYR* 3.8 30.0 - - - +
88C PHE* 4.0 3.6 - - - -
89C PRO* 4.0 25.4 - - + -
203D TRP* 4.7 0.8 - - + -
204D MET* 1.3 79.9 - - - +
206D ALA* 1.3 57.2 + - - +
207D VAL* 3.9 9.5 - - - +
213D ILE* 3.9 22.0 - - + -
214D ILE 3.2 11.7 - - - +
215D PRO* 4.7 1.8 - - + -
216D VAL* 3.7 6.9 - - - +
248D THR 3.7 0.2 - - - +
249D ILE* 3.6 3.5 - - - +
250D ASN* 2.7 43.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 206 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D THR* 1.3 73.0 - - - +
207D VAL* 1.3 63.4 + - - +
208D GLY 3.6 2.4 + - - -
212D LEU 3.7 0.3 - - - +
213D ILE* 3.7 0.5 - - - -
214D ILE* 2.7 44.9 + - + +
216D VAL* 3.7 12.1 - - + -
236D ILE* 4.0 10.8 - - + -
247D TYR* 4.5 12.0 - - + -
248D THR 3.5 4.7 - - - -
249D ILE* 3.5 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 207 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C TYR* 3.8 37.7 - - + -
1272C O4B 4.2 14.1 - - - +
205D THR* 3.9 13.5 - - - +
206D ALA* 1.3 72.1 - - - +
208D GLY* 1.3 61.9 + - - +
212D LEU 3.5 10.1 - - - +
213D ILE* 4.5 4.3 - - + +
246D GLU 3.8 1.2 - - - +
247D TYR* 3.5 1.0 - - - -
248D THR* 2.7 50.6 + - - +
250D ASN* 4.9 2.2 - - + -
1272D O4B 4.0 33.7 - - - +
----------------------------------------------------------
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