Contacts of the strand formed by residues 190 - 197 (chain L) in PDB entry 1LWU
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 GLY 190 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154L CYS* 3.2 36.1 - - - +
155L GLN* 2.6 25.8 + - - +
158L VAL* 3.7 6.5 - - - +
184L GLU 3.9 2.0 - - - -
185L ILE* 4.6 1.8 - - - -
189L ASN* 1.3 70.9 - - - +
191L TRP* 1.3 64.3 + - - -
192L THR* 3.2 8.0 + - - +
384L LEU 3.8 3.1 - - - +
385L LEU* 4.5 6.2 - - - +
386L PRO* 4.5 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 191 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154L CYS* 3.8 0.4 - - - -
183L CYS* 3.4 2.8 - - - -
184L GLU* 2.6 61.1 + - + +
186L GLU* 2.8 33.6 + - + -
189L ASN* 4.4 7.0 - - + +
190L GLY* 1.3 70.9 - - - +
192L THR* 1.3 62.1 + - - +
193L VAL 3.5 1.8 + - - -
243L ARG* 3.7 24.5 - - - -
245L ARG* 3.6 48.7 - - + -
383L LYS* 3.2 51.6 - - + +
384L LEU 3.5 7.9 - - - -
385L LEU* 3.2 48.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 192 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153L ASP* 3.9 13.2 - - + -
154L CYS* 3.1 44.4 - - + +
170L ILE* 4.3 6.3 - - - +
181L VAL* 5.1 3.1 - - - +
190L GLY 3.6 4.7 - - - +
191L TRP* 1.3 70.5 - - - +
193L VAL* 1.3 63.9 + - - +
194L ILE* 3.5 3.5 + - - +
228L LEU* 5.3 0.9 - - - +
236L LEU* 3.3 24.2 - - + +
242L TYR* 4.7 3.8 - - + -
383L LYS* 4.4 0.2 - - - -
384L LEU* 2.9 44.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 193 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181L VAL* 5.0 2.3 - - - +
182L PHE* 3.2 44.0 + - + +
184L GLU* 4.6 9.4 - - + +
191L TRP 4.3 4.9 - - - +
192L THR* 1.3 71.5 + - - +
194L ILE* 1.3 63.7 + - - +
195L GLN 3.4 22.2 - - - +
222L LEU* 4.1 15.7 - - + -
226L PHE* 3.5 29.7 - - + -
228L LEU* 3.9 15.1 - - - +
381L THR* 4.4 7.4 - - - +
382L MET 4.0 4.7 - - - +
383L LYS* 4.1 12.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 194 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192L THR 4.1 2.7 - - - +
193L VAL* 1.3 75.0 - - - +
195L GLN* 1.3 64.0 + - + +
226L PHE* 3.7 3.3 - - - -
227L TRP* 3.9 8.3 - - + -
228L LEU* 2.9 46.4 + - + +
233L ILE* 3.1 51.1 - - + -
236L LEU* 4.4 7.0 - - + -
263L PHE* 5.6 2.7 - - + -
333L TRP* 6.4 0.2 - - + -
382L MET* 2.7 32.1 + - + +
384L LEU* 3.7 38.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 195 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193L VAL* 3.4 9.0 - - - +
194L ILE* 1.3 79.7 - - - +
196L HIS* 1.3 87.9 + - - +
197L ARG* 4.4 5.0 - - - +
204L PHE* 4.6 2.2 - - + -
226L PHE* 3.3 18.8 - - - +
227L TRP* 3.3 30.8 - - + -
342L LEU* 2.9 30.8 + - - +
343L ASN* 2.9 23.1 + - - +
380L THR* 3.0 24.9 - - - +
381L THR* 3.1 4.3 + - - -
382L MET* 2.9 34.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 196 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195L GLN* 1.3 85.3 + - - +
197L ARG* 1.3 79.5 + - - +
198L HIS* 2.9 36.8 + + + +
222L LEU* 3.7 38.7 + - + +
224L THR 3.3 14.1 + - - -
225L GLU* 3.2 23.2 - - - +
226L PHE* 3.2 29.2 + - + +
379L MET* 4.8 6.7 - - - +
380L THR 2.8 22.1 + - - -
381L THR* 3.6 17.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 197 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195L GLN* 3.8 2.4 + - - +
196L HIS* 1.3 87.6 - - - +
198L HIS* 1.3 61.1 + - - +
200L GLY* 5.1 1.2 - - - -
202L VAL 4.2 4.9 + - - -
204L PHE* 3.1 56.7 - - - +
225L GLU* 3.9 8.5 + - - -
342L LEU 3.2 21.1 + - - +
343L ASN* 3.4 4.9 - - - +
344L GLY 2.6 29.9 + - - -
345L LYS* 4.5 1.6 - - - +
346L TYR* 3.9 23.9 - - + +
365L ILE* 3.0 32.9 - - + +
378L LYS 4.4 0.4 - - - -
379L MET* 3.5 5.9 - - - -
380L THR* 2.8 42.9 + - + +
----------------------------------------------------------
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