Contacts of the strand formed by residues 236 - 242 (chain A) in PDB entry 4LIR
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 ILE 236 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A GLY 3.7 16.6 - - - +
181A PHE* 4.2 5.4 - - + -
182A PRO* 4.3 9.2 - - + -
185A SER* 3.5 34.1 - - - +
188A TYR* 4.8 9.0 - - + -
189A ILE* 4.5 11.0 - - + -
230A ARG 3.7 0.2 - - - +
231A ILE* 3.4 3.4 - - - +
232A PHE* 2.8 43.7 + - + +
235A SER* 1.3 92.1 - - - +
237A MSE 1.3 58.9 + - - +
238A ILE* 3.6 31.2 + - + -
209B ASN* 3.4 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A GLY 3.8 7.4 - - - +
229A GLY 3.4 17.9 - - - +
230A ARG 3.3 5.2 - - - +
231A ILE* 3.7 23.8 - - + +
235A SER 4.0 0.6 + - - -
236A ILE* 1.3 69.8 - - - +
238A ILE* 1.3 60.6 + - - +
239A GLY 4.3 0.2 + - - -
177B THR* 3.8 8.5 - - + -
179B PHE* 3.4 50.8 - - + -
209B ASN* 2.8 26.5 + - - +
210B TRP* 3.6 43.3 - - + +
212B HIS* 5.4 1.3 - - + -
241B LYS* 3.5 28.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A VAL* 3.9 2.7 - - + -
179A PHE 3.4 14.6 - - - +
181A PHE* 3.7 26.7 - - + +
189A ILE* 3.9 15.9 - - + -
193A PHE* 3.7 31.2 - - + -
227A LYS 3.7 3.9 - - - +
229A GLY* 2.8 31.2 + - - -
230A ARG 2.9 6.7 + - - -
232A PHE* 3.6 29.4 - - + -
236A ILE* 3.7 25.6 - - + -
237A MSE 1.3 73.0 - - - +
239A GLY* 1.3 65.9 + - - +
240A VAL* 3.8 4.0 - - + -
179B PHE* 3.6 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A VAL* 3.4 2.4 - - - -
179A PHE* 2.8 59.3 + - - +
228A ASP* 3.3 10.1 - - - -
238A ILE* 1.3 74.5 - - - +
240A VAL* 1.3 64.1 - - - +
179B PHE* 3.5 11.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A VAL* 4.1 18.6 - - + -
177A THR 3.4 8.7 - - - +
178A VAL* 4.2 9.2 - - + -
179A PHE* 3.7 0.6 - - - -
193A PHE* 3.7 24.0 - - + -
224A ALA 3.4 35.7 - - - +
225A LEU* 3.8 13.9 - - + +
227A LYS 4.0 0.4 - - - -
228A ASP* 2.8 42.5 + - + +
238A ILE* 3.8 5.2 - - + -
239A GLY* 1.3 79.3 - - - +
241A LYS* 1.3 63.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A VAL* 3.5 3.3 - - - +
177A THR* 2.8 50.6 + - - +
179A PHE* 3.7 21.1 - - + -
225A LEU* 3.6 7.2 - - - -
240A VAL* 1.3 74.9 - - - +
242A PRO* 1.4 80.5 - - + +
244A ILE* 4.3 24.3 - - + +
228B ASP* 5.5 5.4 - - - +
229B GLY* 3.2 31.5 + - - -
231B ILE* 6.1 0.2 - - - +
237B MSE 3.8 23.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A TRP 4.1 8.3 - - - +
176A VAL* 5.0 0.4 - - + -
225A LEU* 3.6 22.6 - - + -
241A LYS* 1.4 98.6 - - + +
243A CYS* 1.3 67.4 + - - +
244A ILE* 3.5 14.4 + - + +
----------------------------------------------------------
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