Contacts of the strand formed by residues 202 - 211 (chain B) in PDB entry 4X3G
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 HIS 202 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A LYS* 6.5 0.9 - - - -
199A TYR* 5.0 17.9 - - + +
196B GLN 4.1 0.2 - - - +
197B GLU* 3.5 12.2 - - - +
198B LYS 4.4 0.3 + - - -
199B TYR* 3.0 35.4 + - + +
200B ASP 3.3 12.6 + - - -
201B GLY* 1.4 81.0 - - - +
203B GLN* 1.3 61.4 + - - +
204B GLN* 5.6 2.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B PRO* 5.7 3.1 - - - +
174B GLY 5.7 0.9 - - - +
195B LYS* 3.5 35.8 + - + +
196B GLN 3.2 8.5 - - - +
197B GLU* 3.7 30.6 + - + +
201B GLY* 3.2 27.3 + - - -
202B HIS* 1.3 73.6 - - - +
204B GLN* 1.3 61.9 + - - +
205B PHE* 5.4 0.2 - - - -
260B ASP* 3.6 24.6 - - - +
261B THR* 3.4 29.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A LYS* 3.9 26.0 + - - +
204A GLN* 5.1 4.2 - - - +
260A ASP* 4.8 9.2 + - - +
194B GLU 3.6 1.4 - - - +
195B LYS* 3.5 2.4 - - - -
196B GLN* 2.8 41.7 + - + +
202B HIS* 4.3 2.4 + - + +
203B GLN* 1.3 77.6 - - - +
205B PHE* 1.3 62.5 + - - +
206B PHE* 3.8 24.6 - - + -
258B VAL* 3.5 26.5 - - - +
259B PHE 3.7 9.0 + - - +
260B ASP* 4.4 8.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B ILE* 3.4 44.0 - - + -
171B ASN* 5.7 1.6 - - - -
178B TRP* 4.1 10.1 - + - -
193B LEU* 3.9 20.0 - - + -
194B GLU 3.3 4.0 - - - -
195B LYS* 3.5 39.9 - - + -
203B GLN 5.6 0.2 - - - -
204B GLN* 1.3 75.5 - - - +
206B PHE* 1.3 62.9 + - - +
257B LEU 3.7 0.8 - - - +
258B VAL* 3.4 9.5 - - - +
259B PHE* 2.7 70.3 + + + +
260B ASP 4.0 6.7 - - - -
261B THR* 4.3 11.0 - - + -
264B ALA* 3.9 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B VAL* 3.8 1.7 - - - +
193B LEU* 3.4 4.4 - - - -
194B GLU* 2.9 44.5 + - + +
196B GLN* 3.3 33.4 - - + -
204B GLN* 3.8 42.6 - - + -
205B PHE* 1.3 73.6 - - - +
207B ALA* 1.3 59.6 + - - +
208B ILE* 4.2 2.9 + - - +
251B ILE* 3.5 45.1 - - + -
254B SER* 3.9 7.0 - - - -
256B CYS* 3.7 14.6 - - - -
257B LEU 3.3 4.9 - - - -
258B VAL* 3.6 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B PHE* 6.1 0.7 - - + -
192B VAL 3.4 7.2 - - - +
193B LEU* 4.1 14.8 - - + -
205B PHE 4.3 0.4 - - - -
206B PHE* 1.3 72.1 - - - +
208B ILE* 1.4 59.9 + - - +
225B LEU* 3.3 24.3 - - + +
256B CYS* 3.3 3.7 - - - +
257B LEU* 2.9 46.9 + - + +
259B PHE* 4.5 4.0 - - + -
275B ILE* 4.7 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B MET 3.9 0.9 - - - +
191B LEU* 3.9 1.0 - - - -
192B VAL* 3.0 39.3 + - + +
206B PHE 5.2 2.2 - - - +
207B ALA* 1.4 74.8 - - - +
209B VAL* 1.3 75.1 + - - +
223B TYR* 3.5 17.3 - - + +
225B LEU* 4.0 4.8 - - - +
241B ARG* 4.1 10.8 - - + +
247B ILE* 3.8 43.1 - - + +
250B ALA* 3.7 29.4 - - + -
251B ILE* 4.8 8.7 - - + +
255B ASP 3.8 6.1 - - - +
256B CYS* 3.7 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B PHE* 3.9 28.5 - - + -
190B MET 3.4 3.1 - - - -
191B LEU* 3.7 32.5 - - + -
208B ILE* 1.3 90.4 - - - +
210B GLN* 1.3 63.5 + - - +
223B TYR* 3.5 40.8 - - + -
225B LEU* 4.2 6.7 - - + -
240B PRO* 3.7 7.2 - - + +
241B ARG* 3.4 17.0 + - - +
277B VAL* 3.9 13.0 - - + -
279B ILE* 4.1 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B PRO* 4.2 16.2 + - - +
189B PHE* 3.2 11.2 - - - +
190B MET* 2.7 48.3 + - + +
192B VAL* 4.8 2.8 - - + +
209B VAL* 1.3 72.7 - - - +
211B LEU* 1.3 57.2 + - - +
240B PRO* 4.5 0.9 - - - -
241B ARG* 3.4 18.2 - - + +
243B ILE* 3.7 33.0 + - + +
246B GLY* 3.4 34.8 - - - -
247B ILE* 3.5 34.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B PHE* 3.5 30.7 - - + -
188B HIS 4.0 4.3 - - - +
189B PHE* 3.6 35.4 - - + -
210B GLN* 1.3 72.8 - - - +
212B ILE* 1.3 61.2 + - - +
213B GLY* 2.9 24.2 + - - +
214B THR 3.9 3.4 - - - +
217B GLN* 3.8 18.2 - - + +
218B ALA* 3.5 36.6 - - + +
221B PHE* 4.1 2.2 - - + -
240B PRO* 4.4 2.9 - - + +
241B ARG 2.7 15.8 + - - +
242B SER* 4.9 0.2 - - - -
243B ILE* 3.1 25.7 + - - +
----------------------------------------------------------
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