Contacts of the helix formed by residues 229 - 240 (chain A) in PDB entry 1L1G
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 TYR 229 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A HIS* 3.7 36.8 - + - -
92A TYR* 3.2 39.8 + + - -
94A ILE* 3.8 29.4 - - + -
171A SER* 4.1 17.9 - - - -
224A THR* 3.3 29.4 - - + +
225A ARG 3.1 24.2 - - - -
226A VAL 2.8 8.3 + - - +
228A ALA* 1.3 92.9 - - + +
230A ILE* 1.3 63.7 + - - +
231A SER 3.3 3.1 - - - -
232A TRP* 3.2 11.6 + - + -
233A ILE* 2.9 27.8 + - + +
285A BR 4.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A LEU* 4.1 24.2 - - + -
115A PRO 3.4 21.5 - - - +
116A ARG* 5.9 0.2 - - - -
117A ALA* 3.7 39.3 - - + +
226A VAL* 3.6 22.7 - - + +
227A SER* 3.9 5.2 - - - +
229A TYR* 1.3 77.8 - - - +
231A SER* 1.3 64.7 + - - +
233A ILE* 3.7 3.9 - - + +
234A ASN* 2.9 45.1 + - - +
285A BR 3.4 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A TYR 3.3 0.2 - - - -
230A ILE* 1.3 80.1 - - - +
232A TRP* 1.3 54.8 + - - +
234A ASN* 3.4 7.8 + - - +
235A ASN* 2.7 48.2 + - - +
285A BR 3.3 16.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A VAL* 3.7 22.6 - - + +
79A VAL 4.0 2.9 - - - -
80A HIS* 3.7 46.4 - + + +
81A PRO* 3.6 19.3 - - + +
94A ILE* 3.9 30.1 - - + -
95A ALA* 4.2 3.4 - - - -
96A LEU* 3.7 29.6 - - + -
229A TYR* 3.2 20.0 + - + +
231A SER* 1.3 78.9 - - - +
233A ILE* 1.3 84.1 + - + +
235A ASN* 3.2 11.1 + - + +
236A VAL* 2.9 44.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ILE* 3.7 14.8 - - + -
36A ARG* 5.5 1.3 - - - +
41A MET* 3.9 19.1 - - - -
94A ILE* 4.2 2.7 - - + -
96A LEU* 3.8 14.1 - - + -
114A LEU* 3.9 27.1 - - + -
226A VAL* 4.3 6.1 - - + -
229A TYR* 2.9 33.4 + - + +
230A ILE* 3.7 5.6 - - - +
232A TRP* 1.3 90.5 - - + +
234A ASN* 1.3 70.2 + - - +
236A VAL* 3.2 3.3 + - - +
237A ILE* 3.0 44.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ARG* 4.1 17.9 + - - +
230A ILE* 2.9 37.3 + - - +
231A SER* 3.7 6.9 - - - +
233A ILE* 1.3 81.2 - - - +
235A ASN* 1.3 64.5 + - - +
237A ILE* 4.0 4.5 - - - +
238A ALA* 3.0 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A SER* 2.7 37.7 + - - +
232A TRP* 3.5 9.5 - - + +
234A ASN* 1.3 73.5 - - - +
236A VAL* 1.3 64.3 + - + +
238A ALA* 3.8 5.3 - - - +
239A SER* 3.0 26.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A TRP* 3.9 15.0 - - + -
78A VAL* 3.9 22.4 - - + -
96A LEU* 3.6 22.7 - - + -
232A TRP* 2.9 53.4 + - + +
233A ILE 3.2 0.4 + - - -
235A ASN* 1.3 78.0 - - + +
237A ILE* 1.3 63.2 + - - +
239A SER* 3.2 5.3 + - - -
240A ASN* 2.7 42.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ILE* 3.9 16.2 - - + -
36A ARG* 3.9 39.3 - - + +
39A TRP* 3.9 40.1 + - + +
96A LEU* 4.4 7.0 - - + -
233A ILE* 3.0 40.4 + - + +
234A ASN* 4.1 3.8 - - - +
236A VAL* 1.3 75.6 - - - +
238A ALA* 1.3 58.5 + - - +
240A ASN* 3.0 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A ASN 3.0 18.9 + - - +
235A ASN* 3.8 5.8 - - - +
237A ILE* 1.3 79.2 - - - +
239A SER* 1.3 57.7 + - - +
240A ASN* 4.1 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ASN 3.0 16.4 + - - -
236A VAL* 3.2 4.4 + - - -
238A ALA* 1.3 77.3 - - - +
240A ASN* 1.3 80.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ASN* 5.5 0.9 + - - -
39A TRP* 3.4 25.3 + - + -
76A LYS* 2.8 33.6 - - - +
78A VAL* 4.4 4.0 - - - +
98A ARG* 3.1 39.5 + - - +
236A VAL* 2.7 37.4 + - - +
237A ILE 3.0 15.1 - - - +
238A ALA 4.1 3.3 - - - +
239A SER* 1.3 99.4 + - - +
----------------------------------------------------------
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