Contacts of the strand formed by residues 190 - 198 (chain B) in PDB entry 1MS4
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 LEU 190 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B ILE* 4.0 13.2 - - + -
102B LYS* 3.6 35.4 - - + -
107B TYR* 3.7 29.2 - - + -
183B ILE 3.8 3.6 - - - -
184B VAL* 4.1 12.6 - - + -
188B GLY 3.5 2.4 + - - +
189B ASN* 1.3 72.8 - - - +
191B VAL* 1.3 58.4 + - - +
192B TYR 4.2 0.2 - - - -
209B TYR* 3.1 8.5 - - - +
210B SER 2.9 34.2 + - - +
213B GLU* 3.7 11.2 - - - +
214B GLY* 3.5 33.7 - - - +
217B TRP* 3.8 18.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B ILE* 3.7 1.8 - - - +
182B ALA* 3.2 20.3 - - - +
183B ILE* 2.9 27.8 + - + +
185B ALA* 3.8 22.9 - - + +
189B ASN 3.8 11.9 - - - +
190B LEU* 1.3 78.4 - - - +
192B TYR* 1.3 64.2 + - - +
193B PRO* 3.9 3.7 - - + +
207B ILE* 3.9 30.3 - - + -
208B PHE 3.8 2.2 - - - -
209B TYR* 4.3 0.7 - - - -
233B ALA* 5.7 2.9 - - + -
240B LEU* 4.1 20.9 - - + -
259B MET* 4.2 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B THR* 3.1 45.7 + - + -
100B ILE* 3.5 23.6 - - + -
107B TYR* 2.9 35.4 + - + +
109B LEU* 3.4 30.7 + - + -
133B LEU* 3.9 5.1 - - + +
177B GLY* 5.5 0.4 - - - -
182B ALA* 3.8 6.5 - - + -
191B VAL* 1.3 74.4 - - - +
193B PRO* 1.3 67.6 - - - +
194B VAL* 4.1 15.0 - - + -
207B ILE* 3.7 0.9 - - - -
208B PHE* 2.8 46.3 + + + +
217B TRP* 3.4 39.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B THR* 5.2 3.3 - - + +
177B GLY* 4.0 1.0 - - - -
178B GLY 3.3 18.8 + - - +
182B ALA* 3.8 20.0 - - + -
183B ILE* 6.4 0.2 - - + -
191B VAL* 3.9 4.0 - - + +
192B TYR* 1.3 86.5 - - + +
194B VAL* 1.3 61.4 + - - +
206B LYS 3.3 8.7 - - - +
207B ILE* 4.5 7.0 - - + -
231B PRO* 3.7 35.3 - - + +
232B VAL* 4.2 0.4 - - - -
233B ALA* 3.7 36.6 - - + +
242B ILE* 4.5 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B LEU* 4.4 1.8 - - + -
175B PHE* 3.9 17.9 - - + -
176B LEU 3.4 13.0 - - - +
177B GLY* 4.2 6.1 - - - -
192B TYR* 3.8 7.4 - - + +
193B PRO* 1.3 79.3 - - - +
195B GLN* 1.3 61.3 + - - +
196B VAL* 4.0 9.6 - - + -
205B SER* 3.1 6.1 - - - -
206B LYS 2.7 44.5 + - - +
208B PHE* 3.6 30.3 - - + -
219B PHE* 3.8 28.7 - - + -
231B PRO* 3.4 6.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ASP* 3.8 16.0 + - - -
119B TYR* 5.5 1.8 + - - -
120B TRP* 3.5 29.8 + - + +
175B PHE* 3.1 4.7 - - - +
176B LEU* 2.9 43.2 + - + +
177B GLY 3.2 18.3 + - - +
178B GLY 4.7 0.6 - - - -
194B VAL* 1.3 73.9 - - - +
196B VAL* 1.3 59.8 + - - +
203B VAL* 4.4 6.5 - - + -
204B PHE 3.6 5.8 - - - +
205B SER* 4.5 0.2 - - - +
228B CYS 4.9 0.2 - - - +
229B SER* 3.3 15.2 - - - -
230B GLU* 3.1 41.5 + - - +
231B PRO* 3.9 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 196 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B TRP* 4.1 1.8 - - - -
163B PHE* 3.8 22.9 - - + -
167B MET* 4.4 6.5 - - + -
172B THR* 4.6 1.6 - - + -
174B GLN 3.4 13.2 - - - +
175B PHE* 4.0 3.4 - - + -
194B VAL* 4.0 16.2 - - + +
195B GLN* 1.3 78.1 - - - +
197B THR* 1.3 69.8 + - - +
203B VAL* 3.3 5.5 - - - +
204B PHE* 2.8 60.3 + - + +
206B LYS* 3.9 24.0 - - + -
219B PHE* 4.5 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B TRP* 3.5 26.4 - - + +
121B THR* 4.1 28.0 - - + +
123B HIS 6.1 0.2 - - - -
172B THR* 3.6 3.5 - - - -
173B ASN* 2.7 37.5 + - - +
174B GLN* 2.9 37.6 + - - +
196B VAL* 1.3 79.2 - - - +
198B ASN* 1.3 60.1 + - - +
201B LYS* 5.0 3.6 - - - -
202B GLN 3.2 13.7 - - - +
203B VAL* 4.8 1.8 - - - -
204B PHE* 4.3 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B HIS 5.6 0.2 - - - +
170B MET* 3.4 35.5 - - + +
171B HIS 3.1 18.2 - - - +
172B THR* 4.2 1.3 - - + +
173B ASN* 4.0 10.0 + - - +
197B THR* 1.3 75.2 - - - +
199B LYS* 1.3 56.5 + - - +
200B LYS* 2.8 23.1 + - - +
201B LYS* 2.7 24.9 + - - +
202B GLN* 2.9 50.6 + - - +
204B PHE* 4.1 7.6 - - + -
226B PHE* 3.9 2.6 - - - -
----------------------------------------------------------
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