Contacts of the strand formed by residues 166 - 170 (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 166 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145L LYS 5.3 2.9 - - - -
164L ASP 3.5 2.8 + - - -
165L SER* 1.3 74.6 - - - +
167L LEU* 1.3 63.4 + - - -
168L TYR* 3.3 11.3 - - - -
182L PHE* 3.4 15.7 - - - -
183L CYS 2.7 37.9 + - - -
220L PRO* 4.2 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 167 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224K VAL* 4.1 19.3 - - + -
142L THR* 4.6 3.8 - - + +
145L LYS 4.1 6.6 + - - +
146L ILE* 3.7 26.0 - - + -
147L SER 3.3 21.1 + - - -
166L GLY* 1.3 69.4 - - - -
168L TYR* 1.3 72.1 + - - +
180L LEU* 3.9 14.8 - - + -
181L VAL 3.4 11.4 - - - +
182L PHE* 4.2 11.2 - - + -
218L LEU* 3.7 15.5 - - + -
219L ALA* 3.0 49.1 - - - +
220L PRO* 4.3 9.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 168 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146L ILE* 4.6 3.4 - - - -
147L SER* 3.2 36.1 - - - -
149L ILE* 3.7 16.3 - - + +
157L VAL* 3.4 32.1 - - + -
162L GLY* 4.3 4.0 - - - -
163L LYS 4.0 5.0 + - - -
164L ASP* 2.5 35.9 + - - +
166L GLY* 3.3 24.9 - - - -
167L LEU* 1.3 89.7 - - - +
169L TYR* 1.3 64.2 + - - +
170L ILE* 4.7 0.4 - - + -
180L LEU* 3.4 8.2 - - - -
181L VAL* 2.9 34.7 + - - +
183L CYS* 3.7 28.0 - - + -
185L ILE* 3.9 7.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 169 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247K TYR* 4.2 17.0 - - - +
255K GLU* 5.6 4.9 - - - -
256K PRO* 3.8 37.6 + - + +
146L ILE* 3.9 20.0 - - + +
147L SER 4.9 4.4 + - - +
149L ILE 3.8 3.7 + - - +
150L THR* 2.8 38.4 - - + +
168L TYR* 1.3 76.2 - - - +
170L ILE* 1.3 63.0 + - - +
178L PRO* 4.0 22.0 - - + -
179L PHE* 3.1 22.4 - - - -
180L LEU* 3.6 37.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 170 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150L THR* 3.9 1.1 - - - -
151L GLY 3.3 12.6 - - - +
152L LYS 4.3 1.6 - - - +
153L ASP* 4.1 30.5 - - - -
154L CYS* 4.2 2.9 - - - +
157L VAL* 4.1 11.4 - - + -
168L TYR 4.4 1.1 - - - +
169L TYR* 1.3 79.7 - - - +
171L LYS* 1.3 60.7 + - - +
172L PRO* 3.8 4.8 - - + +
178L PRO* 3.4 2.5 - - - +
179L PHE* 2.9 51.4 + - + +
181L VAL* 3.4 41.5 - - + -
183L CYS* 4.5 1.3 - - - -
192L THR* 4.3 4.7 - - - +
236L LEU* 4.3 16.8 - - + -
----------------------------------------------------------
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