Contacts of the strand formed by residues 190 - 197 (chain I) 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 I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154I CYS* 3.2 35.7 - - - +
155I GLN* 2.6 25.6 + - - +
158I VAL* 3.7 7.1 - - - +
184I GLU 3.9 2.0 - - - -
185I ILE* 4.7 1.6 - - - -
189I ASN* 1.3 70.1 - - - +
191I TRP* 1.3 63.9 + - - -
192I THR* 3.2 8.7 + - - +
384I LEU 3.8 2.4 - - - +
385I LEU* 4.5 6.1 - - - +
386I PRO* 4.5 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 191 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154I CYS* 3.8 0.9 - - - -
183I CYS* 3.4 2.8 - - - -
184I GLU* 2.7 60.4 + - + +
186I GLU* 2.8 36.0 + - + -
189I ASN* 4.3 6.6 - - + +
190I GLY* 1.3 71.4 - - - +
192I THR* 1.3 60.2 + - - +
193I VAL 3.5 3.3 + - - -
243I ARG* 3.7 24.0 - - - -
245I ARG* 3.6 47.6 - - + -
383I LYS* 3.2 51.6 - - + +
384I LEU 3.5 7.4 - - - -
385I LEU* 3.2 49.3 - - + +
390I ASP* 5.2 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 192 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153I ASP* 3.9 13.7 - - + -
154I CYS* 3.2 44.9 - - + +
170I ILE* 4.3 6.1 - - - +
181I VAL* 5.1 3.2 - - - +
190I GLY 3.6 4.5 - - - +
191I TRP* 1.3 70.8 - - - +
193I VAL* 1.3 64.5 + - - +
194I ILE* 3.5 2.9 + - - +
228I LEU* 5.3 0.7 - - - +
236I LEU* 3.3 24.1 - - + +
242I TYR* 4.7 4.0 - - + -
383I LYS* 4.4 0.2 - - - -
384I LEU* 2.9 45.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 193 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181I VAL* 5.0 2.1 - - - +
182I PHE* 3.2 43.7 + - + +
184I GLU* 4.6 8.5 - - + +
191I TRP 4.3 5.2 - - - +
192I THR* 1.3 71.7 + - - +
194I ILE* 1.3 62.0 + - - +
195I GLN 3.4 22.0 - - - +
222I LEU* 4.1 17.5 - - + -
226I PHE* 3.4 29.9 - - + -
228I LEU* 3.9 14.9 - - - +
381I THR* 4.4 7.6 - - - +
382I MET 4.0 4.7 - - - +
383I LYS* 4.1 11.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 194 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192I THR 4.1 2.5 - - - +
193I VAL* 1.3 76.4 - - - +
195I GLN* 1.3 63.1 + - + +
226I PHE* 3.8 3.0 - - - -
227I TRP* 3.9 8.3 - - + -
228I LEU* 2.9 48.1 + - + +
233I ILE* 3.1 55.2 - - + -
236I LEU* 4.4 7.6 - - + -
244I LEU* 6.2 0.2 - - + -
263I PHE* 5.6 3.1 - - + -
333I TRP* 6.4 0.2 - - + -
382I MET* 2.7 31.3 + - + +
384I LEU* 3.7 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 195 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193I VAL* 3.4 8.9 - - - +
194I ILE* 1.3 79.6 - - - +
196I HIS* 1.3 86.6 + - - +
197I ARG* 4.4 5.8 - - - +
204I PHE* 4.6 2.5 - - + -
226I PHE* 3.3 19.3 - - - +
227I TRP* 3.3 30.4 - - + -
342I LEU* 3.0 28.9 + - - +
343I ASN* 2.9 22.6 + - - +
380I THR* 3.0 25.1 - - - +
381I THR* 3.1 5.2 + - - -
382I MET* 2.9 34.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 196 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195I GLN* 1.3 84.2 - - - +
197I ARG* 1.3 80.8 + - - +
198I HIS* 2.9 36.6 + + + +
222I LEU* 3.7 37.8 + - + +
224I THR 3.3 13.7 + - - -
225I GLU* 3.2 23.6 - - - +
226I PHE* 3.2 28.2 + - + +
379I MET* 4.8 7.1 - - - +
380I THR 2.9 22.1 + - - -
381I THR* 3.6 17.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 197 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195I GLN* 3.8 2.2 + - - +
196I HIS* 1.3 87.6 + - - +
198I HIS* 1.3 60.7 + - - +
200I GLY* 5.1 1.4 - - - -
202I VAL 4.2 4.6 + - - -
204I PHE* 3.1 57.3 - - - +
225I GLU* 3.9 8.1 + - - -
342I LEU 3.2 22.8 + - - +
343I ASN* 3.5 4.8 - - - +
344I GLY 2.6 30.3 + - - -
345I LYS* 4.5 1.4 - - - +
346I TYR* 3.9 26.0 - - + +
365I ILE* 3.0 32.2 - - + +
378I LYS 4.4 0.4 - - - -
379I MET* 3.5 5.5 - - - -
380I THR* 2.8 43.5 + - - +
----------------------------------------------------------
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