Contacts of the helix formed by residues 233 - 246 (chain A) in PDB entry 1LI5
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 PRO 233 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206A HIS* 4.2 13.2 - - + +
229A ASP 5.2 0.2 - - - +
232A PHE* 1.3 123.3 - - + +
234A HIS* 1.3 60.9 + - + +
235A HIS 3.5 0.2 - - - -
236A GLU* 3.1 2.6 + - - -
237A ASN* 2.6 51.9 + - - +
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Residues in contact with HIS 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A CYS* 3.9 3.1 - - - +
205A TRP 4.2 5.9 + - - -
206A HIS* 3.1 41.5 + - + +
208A GLU* 5.7 2.9 - - + -
209A CYS* 4.4 3.8 - - + -
230A LEU* 3.2 33.0 - - + +
232A PHE 3.7 0.2 - - - -
233A PRO* 1.3 87.2 - - + +
235A HIS* 1.3 79.6 + + - +
237A ASN* 3.1 2.6 + - - +
238A GLU* 2.8 35.3 + - + +
963A ZN 2.0 37.0 - - - -
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Residues in contact with HIS 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A CYS* 3.1 35.0 - - - -
155A LEU* 3.3 14.4 - - + -
224A HIS* 3.5 8.7 - + - -
225A GLY 3.8 12.3 + - - -
226A GLY* 4.3 4.6 - - - -
230A LEU* 2.6 30.7 + - + +
231A MET 3.3 9.6 - - - +
234A HIS* 1.3 78.8 - + - +
236A GLU* 1.3 63.8 + - - +
238A GLU* 3.1 16.2 + - - +
239A ILE* 3.0 27.0 + - - +
254A TRP* 3.5 16.2 - + + -
256A HIS* 2.9 35.3 + + - -
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Residues in contact with GLU 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A TYR* 4.2 8.4 - - + -
153A GLY* 2.9 27.8 + - - +
154A VAL* 2.7 27.5 + - - +
155A LEU* 2.8 14.5 + - - +
156A SER* 2.7 39.0 + - - -
231A MET 3.0 10.2 + - - +
232A PHE* 3.7 25.8 - - + -
233A PRO 3.1 6.0 + - - +
235A HIS* 1.3 75.8 - - - +
237A ASN* 1.3 60.5 + - - +
239A ILE* 3.3 9.3 + - - +
240A ALA* 3.0 26.4 + - - +
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Residues in contact with ASN 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A TYR* 2.6 28.8 + - - -
181A PHE* 3.3 36.2 - - + +
206A HIS* 3.1 37.0 + - + -
233A PRO* 2.6 29.6 + - - +
234A HIS 3.6 3.1 - - - +
236A GLU* 1.3 72.5 - - - +
238A GLU* 1.3 58.7 + - - +
240A ALA* 3.3 6.8 + - - +
241A GLN* 2.8 35.8 + - - +
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Residues in contact with GLU 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A HIS* 4.1 9.2 - - + +
209A CYS* 3.4 17.9 - - + +
210A SER* 3.2 17.6 + - - +
224A HIS* 2.6 29.8 + - - -
234A HIS* 2.8 24.7 + - + +
235A HIS* 3.1 16.5 + - - +
237A ASN* 1.3 74.3 - - - +
239A ILE* 1.3 66.7 - - - +
241A GLN* 3.2 3.2 + - - -
242A SER* 2.8 24.1 + - - -
250A TYR* 3.0 16.2 + - + +
254A TRP* 4.8 1.1 - - + -
963A ZN 2.3 35.9 - - - -
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Residues in contact with ILE 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LEU* 4.9 3.1 - - + -
149A ASP* 5.9 0.2 - - - +
151A THR* 4.8 8.1 - - - +
154A VAL* 4.2 22.7 - - + -
155A LEU* 3.5 34.8 - - + -
235A HIS 3.0 13.5 + - - +
236A GLU* 3.4 8.3 - - - +
238A GLU* 1.3 74.8 - - - +
240A ALA* 1.3 65.2 + - - +
243A THR* 2.8 47.5 + - + +
250A TYR* 3.9 12.1 - - + -
254A TRP* 3.6 34.8 - - + +
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Residues in contact with ALA 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A PHE* 3.7 17.4 - - + -
149A ASP* 3.7 23.8 - - - +
152A TYR* 3.8 15.5 - - + -
181A PHE* 4.2 3.4 - - + -
236A GLU 3.0 14.0 + - - +
237A ASN* 3.3 13.2 - - - +
239A ILE* 1.3 78.9 - - - +
241A GLN* 1.3 63.4 + - - +
243A THR* 4.3 1.6 - - - -
244A CYS* 3.1 27.5 + - - +
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Residues in contact with GLN 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A LEU* 4.1 3.3 - - + +
128A LEU* 3.6 11.1 - - + +
144A PHE* 4.0 9.9 - - + -
181A PHE* 3.6 20.7 - - + -
182A VAL 5.2 0.6 + - - -
183A LEU* 3.5 25.0 - - + +
206A HIS* 2.9 23.9 - - - +
207A ILE* 3.2 33.5 - - + +
210A SER* 3.0 23.2 + - - +
237A ASN 2.8 26.5 + - - +
238A GLU* 3.7 3.5 - - - +
240A ALA* 1.3 73.4 - - - +
242A SER* 1.3 59.9 + - - +
245A ALA* 3.1 30.3 + - - +
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Residues in contact with SER 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A LEU* 5.7 0.4 - - - -
210A SER* 3.0 26.9 + - - -
238A GLU 2.8 16.5 + - - -
241A GLN* 1.3 72.5 - - - +
243A THR* 1.3 60.1 + - - +
245A ALA* 3.3 0.6 + - - -
246A HIS* 3.1 49.5 + - - +
250A TYR* 3.3 42.6 - - - -
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Residues in contact with THR 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A ASP* 4.6 0.3 + - - -
151A THR* 4.3 10.9 + - - +
239A ILE* 2.8 44.2 + - + +
240A ALA* 3.8 3.6 + - - -
242A SER* 1.3 72.4 - - - +
244A CYS* 1.3 65.1 + - - +
246A HIS 3.0 20.3 - - - +
248A GLY 4.5 15.1 - - - +
250A TYR* 3.8 25.6 - - + +
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Residues in contact with CYS 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A LEU* 3.9 9.5 - - + +
131A LYS* 3.6 12.3 - - - +
133A HIS* 3.3 48.5 + - + -
144A PHE* 3.9 7.0 - - + -
149A ASP* 3.1 39.9 - - - -
150A PRO* 5.5 0.9 - - - -
240A ALA 3.1 20.1 + - - +
243A THR* 1.3 82.8 + - - +
245A ALA* 1.3 59.0 + - - +
246A HIS 3.6 0.9 - - - -
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Residues in contact with ALA 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A LEU* 3.8 20.2 - - + +
127A GLN* 4.6 13.6 - - + +
128A LEU* 3.7 15.0 - - + -
131A LYS* 3.7 21.3 - - - +
241A GLN 3.1 21.1 + - - +
242A SER 3.3 2.0 + - - +
244A CYS* 1.3 79.8 - - - +
246A HIS* 1.3 73.4 + - + +
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Residues in contact with HIS 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A LEU* 4.9 12.2 - - + +
131A LYS* 5.1 5.6 - - - +
210A SER 5.1 0.2 + - - -
214A CYS* 4.0 19.7 - - + +
219A ASN* 3.5 54.1 + - + +
242A SER* 3.1 36.1 + - - +
243A THR* 3.0 19.1 - - - +
244A CYS 4.6 0.5 - - - -
245A ALA* 1.3 95.2 + - + +
247A ASP* 1.2 72.4 + - - +
248A GLY 3.6 3.3 + - - +
249A GLN 5.9 0.7 - - - +
250A TYR* 5.7 0.7 - + - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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