Contacts of the strand formed by residues 198 - 208 (chain J) in PDB entry 3MGO
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 J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193J ALA* 3.8 3.1 - - - +
194J VAL* 3.3 35.7 + - + +
195J SER* 3.4 17.9 + - - +
196J ASP 3.6 0.8 - - - -
197J HIS* 1.3 89.4 - - + +
199J ALA* 1.3 64.0 + - - +
248J VAL* 3.6 26.1 - - + +
249J VAL 3.4 5.6 - - - -
250J PRO* 4.4 14.4 - - + +
251J SER* 4.1 3.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 199 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191J HIS* 3.3 39.3 - - + +
192J HIS 3.2 11.0 - - - +
193J ALA* 4.1 2.9 - - + +
194J VAL* 4.1 4.5 - - - +
198J GLU* 1.3 78.0 - - - +
200J THR* 1.3 62.5 + - - +
201J LEU 3.7 0.5 + - - -
248J VAL* 3.5 3.9 - - - -
249J VAL* 2.8 39.0 + - + +
251J SER* 5.9 1.6 - - - +
254J GLU* 4.3 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 200 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190J THR* 3.4 2.3 + - - +
191J HIS* 3.4 6.5 - - - -
192J HIS* 2.6 40.1 + - - +
194J VAL* 3.2 22.8 - - - +
199J ALA* 1.3 71.8 - - - +
201J LEU* 1.3 64.4 + - - +
202J ARG* 3.9 32.9 - - - +
246J ALA* 4.1 15.7 - - + -
247J VAL 3.8 7.0 - - - +
248J VAL* 4.6 9.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 201 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189J MET* 4.3 5.4 - - - -
190J THR 3.5 11.9 - - - +
191J HIS* 3.5 30.3 - - + -
199J ALA 3.7 0.6 + - - -
200J THR* 1.3 72.1 - - - +
202J ARG* 1.3 59.9 - - - +
217J TRP* 3.8 23.7 - - + -
245J ALA 3.8 0.9 - - - +
246J ALA* 3.2 2.4 - - - -
247J VAL* 2.9 49.3 + - + +
249J VAL* 3.8 22.9 - - + -
254J GLU* 4.2 19.1 - - + +
257J TYR* 4.5 0.9 - - + -
274J TRP* 3.9 34.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 202 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189J MET* 3.3 8.1 - - - -
190J THR* 3.0 48.5 + - - +
192J HIS* 5.0 4.9 + - - -
200J THR* 3.9 23.4 + - + +
201J LEU* 1.3 73.8 - - - +
203J CYS* 1.3 61.7 + - - +
204J TRP* 3.4 30.2 - - + +
229J GLU* 5.1 1.8 + - - -
244J TRP* 3.2 54.1 - - + -
245J ALA 3.6 2.7 - - - -
246J ALA* 3.9 5.5 - - + +
98K ASP* 3.1 30.2 + - - +
99K MET* 3.3 30.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 203 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188J HIS 3.8 4.0 - - - -
189J MET* 4.5 4.9 - - + -
202J ARG* 1.3 71.5 - - - +
204J TRP* 1.3 66.4 + - - +
215J LEU* 4.1 5.3 - - + +
217J TRP* 3.6 16.0 - - + +
244J TRP* 3.1 8.3 - - - +
245J ALA* 2.9 36.2 + - + +
259J CYS* 2.0 48.9 - - - -
261J VAL* 4.5 4.9 - - - -
272J LEU* 4.0 20.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 204 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186J LYS 4.3 0.4 - - - -
187J THR* 3.1 30.4 - - - +
188J HIS* 2.8 50.0 + + + +
190J THR* 3.6 17.3 + - + +
202J ARG* 3.4 39.2 - - + +
203J CYS* 1.3 76.9 - - - +
205J ALA* 1.3 60.4 + - - +
206J LEU* 3.8 30.5 - - + -
215J LEU* 5.1 0.9 - - - -
234J ARG* 3.5 18.8 - - - -
242J GLN* 5.0 0.9 - - + -
243J LYS 3.9 4.5 - - - -
244J TRP* 3.5 22.7 - + + -
97K ARG 4.9 3.4 - - - -
98K ASP* 3.3 26.7 + - - -
99K MET* 3.6 21.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 205 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185J PRO* 4.0 8.5 - - + -
186J LYS 3.6 3.6 - - - -
187J THR* 4.4 4.5 - - + -
204J TRP* 1.3 75.1 - - - +
206J LEU* 1.3 65.8 + - - +
208J PHE* 3.4 21.1 - - + -
213J ILE* 4.0 17.7 - - + -
215J LEU* 4.2 15.0 - - + -
242J GLN* 3.4 0.5 - - - -
243J LYS* 3.0 34.2 + - + +
261J VAL* 5.0 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 206 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185J PRO* 3.4 1.2 - - - +
186J LYS* 2.8 46.6 + - + +
188J HIS* 4.2 24.7 - - + +
204J TRP* 3.8 26.2 - - + -
205J ALA* 1.3 85.8 - - - +
207J SER* 1.3 73.8 + - - +
208J PHE* 3.2 4.6 + - - -
241J PHE 3.9 2.2 - - - -
242J GLN* 3.6 31.4 - - + +
12K ARG 6.1 0.4 - - - +
14K PRO* 4.5 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 207 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183J ASP* 3.5 17.8 - - - +
184J ALA 4.0 5.8 - - - +
186J LYS* 4.2 21.8 + - - +
206J LEU* 1.3 79.8 - - - +
208J PHE* 1.3 57.2 + - - +
238J ASP* 5.3 2.4 + - - -
240J THR* 3.5 29.8 + - - +
241J PHE 3.3 6.9 + - - -
242J GLN* 4.9 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 208 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183J ASP 3.1 13.0 - - - +
185J PRO* 3.6 25.1 - - + -
205J ALA* 3.4 37.5 - - + -
207J SER* 1.3 78.7 - - - +
209J TYR* 1.3 64.3 + - - +
210J PRO 3.2 18.8 - - - -
211J ALA 3.4 23.1 - - - -
213J ILE* 3.9 21.1 - - + -
233J THR* 4.0 2.5 - - + -
240J THR* 3.6 2.6 - - - -
241J PHE* 3.0 68.9 + - + -
242J GLN* 3.7 12.8 - - - -
243J LYS* 4.0 0.7 - - + -
263J HIS* 3.6 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