Contacts of the helix formed by residues 232 - 248 (chain A) in PDB entry 1LHP
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 232 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A TYR 3.9 11.7 - - - -
19A VAL* 4.2 5.8 - - - +
23A ALA* 3.9 3.8 - - - +
120A ARG 5.5 0.6 + - - -
231A VAL* 1.3 79.0 - - - +
233A THR* 1.3 63.6 + - - +
234A GLY 3.2 3.8 - - - +
235A ASP* 3.1 23.3 + - - +
236A LEU* 3.0 22.5 + - - +
291A LEU* 4.3 4.9 - - - +
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Residues in contact with THR 233 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230A PHE* 3.6 36.4 + - + -
231A VAL 3.4 0.2 - - - -
232A GLY* 1.3 77.0 + - - +
234A GLY* 1.3 59.5 + - - +
236A LEU* 4.4 1.1 - - - -
237A PHE* 2.9 31.1 + - - +
263A MET* 3.5 19.7 - - + +
267A LEU* 3.9 24.7 - - + -
291A LEU* 4.4 7.0 - - + -
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Residues in contact with GLY 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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113A ASP* 3.9 16.2 - - - +
119A GLN* 5.8 3.4 - - - -
148A THR* 5.3 0.3 + - - -
186A THR* 6.4 2.2 - - - -
232A GLY 3.2 0.8 - - - -
233A THR* 1.3 81.6 + - - +
235A ASP* 1.3 64.1 + - - +
237A PHE* 3.6 6.7 + - - +
238A ALA* 3.2 23.4 + - - +
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Residues in contact with ASP 235 (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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11A GLN* 3.8 14.7 + - - +
19A VAL* 3.3 14.9 - - - +
20A GLY* 2.8 40.8 + - - +
23A ALA* 3.9 9.0 - - + -
24A ALA* 4.4 4.0 - - - +
81A LEU* 5.8 0.5 - - - +
83A GLY* 5.1 1.9 - - - -
84A TYR* 4.9 13.4 + - - +
113A ASP* 4.6 7.3 - - - +
115A VAL* 5.5 1.9 - - - +
232A GLY* 3.1 13.6 + - - +
234A GLY* 1.3 78.4 - - - +
236A LEU* 1.3 63.5 + - - +
238A ALA* 3.6 4.1 + - - +
239A ALA* 3.3 22.7 + - - +
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Residues in contact with LEU 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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23A ALA* 3.7 16.5 - - + +
27A PRO* 3.6 30.7 - - + -
232A GLY 3.0 12.6 + - - +
233A THR 3.3 6.9 + - - +
235A ASP* 1.3 73.8 - - - +
237A PHE* 1.3 67.2 + - - +
239A ALA* 3.4 2.5 + - - +
240A MET* 3.1 43.7 + - + +
263A MET* 3.3 25.1 - - + -
266A VAL* 4.2 22.2 - - + -
291A LEU* 4.2 8.1 - - + -
293A MET* 4.1 20.0 - - + -
300A ILE* 5.4 2.0 - - + -
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Residues in contact with PHE 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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148A THR* 4.3 5.6 - - + -
184A VAL* 4.1 18.6 - - + -
186A THR* 3.6 33.7 - - + -
221A MET* 5.9 1.3 - - + -
233A THR 2.9 18.4 + - - +
234A GLY* 3.7 7.9 - - - +
236A LEU* 1.3 78.4 - - - +
238A ALA* 1.3 62.1 + - - +
240A MET* 3.2 0.7 + - - -
241A LEU* 2.9 52.5 + - + +
256A CYS* 5.5 4.3 - - - -
259A THR* 3.8 28.0 - - + +
260A VAL* 4.2 21.1 - - + -
263A MET* 4.0 22.4 - - + -
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Residues in contact with ALA 238 (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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81A LEU* 4.4 17.9 - - + -
111A VAL* 4.2 11.5 - - + +
113A ASP* 4.7 10.1 - - + -
148A THR* 4.3 22.2 - - + +
234A GLY 3.2 14.0 + - - +
235A ASP* 4.0 5.2 - - - +
236A LEU 3.4 0.2 - - - -
237A PHE* 1.3 84.1 - - - +
239A ALA* 1.3 62.9 + - - +
241A LEU* 3.4 6.0 + - - +
242A LEU* 3.1 22.5 + - - +
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Residues in contact with ALA 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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23A ALA 4.8 0.9 - - - +
24A ALA* 3.7 37.7 - - + +
27A PRO* 5.1 3.4 - - + -
28A LEU* 3.4 18.8 - - + +
81A LEU* 4.3 11.5 - - + +
235A ASP 3.3 16.0 + - - +
236A LEU* 3.7 4.3 - - - +
238A ALA* 1.3 77.4 - - - +
240A MET* 1.3 64.3 + - + +
242A LEU* 3.3 7.6 - - - +
243A ALA 3.3 15.1 + - - -
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Residues in contact with MET 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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27A PRO* 4.2 12.6 - - + -
31A LEU* 4.8 5.6 - - + -
236A LEU* 3.1 39.8 + - + +
237A PHE 4.0 1.8 - - - +
239A ALA* 1.3 73.7 - - - +
241A LEU* 1.3 66.4 + - - +
243A ALA* 3.2 7.5 + - - +
244A TRP* 3.0 38.2 + - + -
259A THR* 3.9 17.7 - - + +
262A ALA* 3.7 32.3 - - + -
263A MET* 3.6 32.1 - - - +
266A VAL* 5.8 0.4 - - + -
300A ILE* 4.2 24.0 - - + -
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Residues in contact with LEU 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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111A VAL* 5.9 0.7 - - + -
146A ILE* 4.1 18.8 - - + -
148A THR* 3.9 26.9 - - + -
182A THR* 5.5 0.9 - - + -
184A VAL* 4.1 15.5 - - + -
237A PHE* 2.9 25.8 + - + +
238A ALA 3.7 5.4 - - - +
239A ALA 3.3 0.2 - - - -
240A MET* 1.3 73.3 - - - +
242A LEU* 1.3 59.8 + - - +
245A THR* 2.8 58.6 + - + +
252A LEU* 4.9 2.0 - - + -
255A ALA* 4.7 5.4 - - + +
256A CYS* 4.2 24.0 - - - -
259A THR* 3.6 21.9 + - + +
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Residues in contact with LEU 242 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A VAL* 4.1 25.1 - - + -
28A LEU* 4.3 9.2 - - + -
33A PHE* 4.0 21.5 - - + -
79A TYR* 3.6 39.5 + - + -
80A VAL 5.0 0.2 - - - +
81A LEU* 4.3 20.6 - - + -
111A VAL* 3.9 26.2 - - + +
146A ILE* 5.4 1.1 - - - -
238A ALA 3.1 13.6 + - - +
239A ALA 3.3 10.3 - - - +
241A LEU* 1.3 77.0 - - - +
243A ALA* 1.3 65.0 + - - +
245A THR* 3.1 17.0 + - - -
246A HIS* 3.2 10.7 + - - +
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Residues in contact with ALA 243 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A LEU* 4.1 5.2 - - + -
31A LEU* 3.4 32.8 - - + -
33A PHE* 3.7 28.7 - - + -
239A ALA 3.3 7.7 + - - +
240A MET 3.2 7.5 + - - +
242A LEU* 1.3 80.5 - - - +
244A TRP* 1.3 64.7 + - + +
246A HIS* 3.3 6.8 + - - +
247A LYS* 3.2 20.1 + - - +
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Residues in contact with TRP 244 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A LEU* 4.0 20.3 - - + +
240A MET* 3.0 35.7 + - + +
241A LEU 4.2 0.4 - - - +
243A ALA* 1.3 73.9 - - + +
245A THR* 1.3 61.6 + - - +
246A HIS 3.1 1.6 - - - -
247A LYS* 3.2 16.7 + - + +
248A HIS* 2.9 40.9 + + + +
255A ALA* 3.7 23.9 - - + +
258A LYS* 3.6 51.3 + - + +
259A THR* 3.3 24.1 - - - +
262A ALA* 5.2 2.4 - - - +
300A ILE 3.9 21.4 + - - -
301A GLU 3.9 16.8 - - - -
302A SER* 5.4 0.2 - - - -
303A PRO* 4.0 13.3 - - + +
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Residues in contact with THR 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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79A TYR* 5.1 2.9 + - - -
146A ILE* 3.7 25.3 - - + +
182A THR* 5.3 3.6 - - + -
205A GLN* 5.8 5.4 - - - +
241A LEU* 2.8 54.1 + - + +
242A LEU* 3.1 9.5 + - - -
244A TRP* 1.3 73.1 - - - +
246A HIS* 1.3 56.8 + - - +
248A HIS 4.2 3.8 - - - +
249A PRO* 3.0 32.8 - - - +
252A LEU* 4.5 12.3 - - + -
255A ALA* 3.9 14.6 - - + -
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Residues in contact with HIS 246 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A CYS* 3.3 29.9 - - - -
33A PHE* 3.8 24.0 - + + -
79A TYR* 3.1 31.3 + + + +
242A LEU 3.2 10.7 + - - +
243A ALA 3.4 8.3 - - - +
244A TRP 3.1 0.6 - - - -
245A THR* 1.3 80.4 + - - +
247A LYS* 1.3 70.0 + - + +
249A PRO* 3.6 11.2 - - - +
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Residues in contact with LYS 247 (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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243A ALA 3.2 11.5 + - - +
244A TRP* 3.2 21.5 + - + +
246A HIS* 1.3 89.7 + - + +
248A HIS* 1.3 82.0 + - + +
249A PRO* 3.4 6.7 - - - +
258A LYS* 5.5 0.4 - - - +
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Residues in contact with HIS 248 (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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244A TRP* 2.9 25.2 + + - +
245A THR* 3.2 11.4 - - - +
247A LYS* 1.3 100.1 + - + +
249A PRO* 1.3 65.7 - - - +
250A ASN 3.2 2.7 - - - -
251A ASN* 3.1 36.1 + - + +
254A VAL* 3.7 27.7 - - + +
255A ALA* 4.5 6.1 - - + +
258A LYS* 3.2 30.3 + - + -
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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