Contacts of the strand formed by residues 189 - 201 (chain B) in PDB entry 4G7Z
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 ARG 189 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B GLU* 4.8 11.3 + - - -
185B ARG* 3.3 1.9 - - - -
186B LEU* 2.5 65.6 + - - +
188B GLN* 1.3 90.9 - - + +
190B THR* 1.3 57.8 + - - +
191B ASP 3.6 1.1 - - - -
192B LEU* 3.5 36.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B ASP* 3.7 10.1 - - - +
184B THR 3.4 13.7 + - - +
185B ARG* 3.0 47.8 + - - +
188B GLN 3.5 6.0 + - - -
189B ARG* 1.3 71.2 - - - +
191B ASP* 1.3 60.1 + - - +
192B LEU 3.5 1.6 - - - -
720D LEU 5.1 0.7 - - - +
721D VAL* 5.3 1.3 - - + -
722D GLU* 3.4 46.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ARG* 3.2 42.6 + - + +
183B ASP* 3.3 17.4 - - - +
189B ARG* 3.6 1.6 - - - +
190B THR* 1.3 78.8 - - - +
192B LEU* 1.3 72.8 + - + +
193B ASP* 3.7 8.0 + - - +
851C LYS* 5.8 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B PRO* 4.3 20.0 - - + -
28B LEU 3.6 11.0 - - - +
29B GLU* 3.9 21.3 - - - +
30B ARG* 4.9 3.4 - - + +
183B ASP* 3.6 4.2 - - - -
184B THR* 2.8 38.1 + - + +
186B LEU* 3.5 22.0 - - + +
189B ARG* 3.5 56.5 - - + +
191B ASP* 1.3 89.0 - - + +
193B ASP* 1.3 60.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B GLU* 4.1 1.2 - - - +
27B PRO* 3.6 6.8 - - - +
28B LEU* 2.8 56.0 + - + +
29B GLU 3.8 0.7 - - - +
30B ARG* 3.1 12.6 - - - +
31B GLY* 2.8 31.8 + - - -
33B GLY* 3.2 20.8 + - - +
34B VAL* 4.1 4.0 - - - +
181B VAL* 3.1 25.1 - - + +
182B GLU 3.8 3.6 - - - -
184B THR* 4.7 1.6 - - - -
191B ASP 4.0 3.2 - - - +
192B LEU* 1.3 73.7 - - - +
194B LYS* 1.3 58.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B VAL* 3.8 19.0 - - + +
26B GLU* 3.4 38.7 + - + +
180B GLN 3.8 1.6 - - - +
181B VAL* 3.5 7.1 - - - -
182B GLU* 3.0 62.7 + - + +
184B THR* 3.5 21.8 - - - +
193B ASP* 1.3 73.0 - - - +
195B LEU* 1.3 64.0 + - - +
196B THR* 4.0 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A PHE* 5.5 5.2 - - + -
23B PHE 3.2 2.1 - - - +
24B VAL* 3.2 8.6 - - - -
25B LEU* 3.1 47.9 + - + +
28B LEU* 4.1 19.5 - - + -
33B GLY* 3.6 25.1 - - - +
36B LEU* 4.1 15.5 - - + +
37B GLY* 4.4 5.6 - - - +
40B LEU* 6.1 1.3 - - + -
179B PHE* 3.6 31.2 - - + -
180B GLN 4.3 0.4 - - - +
181B VAL* 3.7 9.0 - - + +
194B LYS* 1.3 75.8 - - - +
196B THR* 1.3 66.7 + - - +
197B LEU* 5.2 6.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 196 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ARG* 5.4 0.4 - - - +
22B GLU* 3.9 22.4 - - + +
23B PHE 3.4 6.3 - - - +
24B VAL* 3.7 15.1 - - + +
179B PHE* 3.3 5.9 - - - +
180B GLN* 3.0 47.3 + - + +
182B GLU* 4.4 8.3 + - - -
194B LYS* 3.9 13.9 + - - -
195B LEU* 1.3 75.4 - - - +
197B LEU* 1.3 66.8 + - - +
198B ARG* 4.7 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A PHE* 6.5 0.4 - - + -
22B GLU* 3.2 6.6 - - - +
23B PHE* 2.9 43.9 + - + +
37B GLY 6.0 2.5 - - - +
40B LEU* 5.5 8.1 - - + -
44B LEU* 4.6 4.5 - - + -
177B VAL* 3.5 25.1 - - + -
178B ALA 3.3 15.3 - - - +
179B PHE* 3.6 13.0 - - + -
195B LEU* 5.2 7.0 - - + +
196B THR* 1.3 77.6 - - - +
198B ARG* 1.3 74.5 + - - +
199B ILE* 4.1 14.8 - - + -
211B LEU* 4.0 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B TYR* 3.5 25.3 + - + +
21B GLY 3.3 4.7 - - - -
22B GLU* 3.9 16.6 - - + +
176B ARG* 4.0 17.4 - - - +
177B VAL* 3.6 3.1 - - - -
178B ALA* 3.0 41.2 + - - +
180B GLN* 5.2 7.7 + - - -
196B THR* 4.7 8.3 - - + +
197B LEU* 1.3 78.2 - - - +
199B ILE* 1.3 65.4 + - - +
200B TRP* 3.6 32.1 - - + -
888D GLU* 4.1 17.6 + - - -
937D TYR* 4.6 11.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B TYR* 3.3 4.8 - - - -
21B GLY 3.1 29.3 + - - -
23B PHE* 4.0 17.0 - - + -
44B LEU* 3.5 31.9 - - + -
174B VAL* 4.0 22.9 - - + -
176B ARG 3.5 10.1 - - - +
177B VAL* 4.7 2.5 - - + -
197B LEU* 4.1 10.5 - - + -
198B ARG* 1.3 79.9 - - - +
200B TRP* 1.3 68.5 + - - +
201B THR* 4.9 1.3 - - - +
207B PRO* 3.6 35.4 - - + +
210B ALA* 5.1 1.6 - - + -
211B LEU* 4.1 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B GLU 3.2 10.3 - - - +
20B TYR* 3.2 36.5 - + + -
174B VAL* 3.5 6.4 - - - -
175B ARG* 2.8 32.2 + - + -
176B ARG* 3.1 81.9 + - + +
178B ALA 4.3 2.9 - - - -
198B ARG* 3.6 49.6 - - + -
199B ILE* 1.3 77.3 - - - +
201B THR* 1.3 61.5 + - - +
847D ASP* 5.5 2.0 - - - +
888D GLU* 5.0 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ARG 3.2 15.7 - - - -
19B GLU* 2.7 29.3 + - - +
173B PRO* 2.9 25.1 - - + +
174B VAL* 5.1 1.1 - - + +
175B ARG* 4.1 9.6 - - - +
199B ILE* 4.9 1.7 - - - +
200B TRP* 1.3 76.5 + - - +
202B ASP* 1.3 67.8 + - - +
203B GLY 3.0 5.6 - - - +
205B VAL* 2.9 31.0 - - + +
206B THR 3.8 0.6 - - - -
207B PRO* 3.2 30.0 - - - +
210B ALA* 5.5 3.6 - - + +
----------------------------------------------------------
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