Contacts of the helix formed by residues 237 - 256 (chain D) in PDB entry 1L9X
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 ALA 237 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7C ALA 5.3 9.5 - - - +
164D GLU* 5.6 1.6 - - - +
166D LEU* 3.9 17.7 - - + -
235D SER* 3.3 15.9 + - - +
236D HIS* 1.3 82.1 - - - +
238D PRO* 1.3 76.1 - - + +
239D ASN* 4.4 1.8 - - + +
240D ALA* 2.9 12.3 + - - +
241D VAL* 3.1 8.3 + - - +
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Residues in contact with PRO 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C ALA 6.2 0.9 - - - +
249C GLU* 4.2 14.6 - - + +
253C ASN* 4.7 8.7 - - - +
256C ARG* 4.0 35.7 - - - +
236D HIS 3.6 3.1 - - - +
237D ALA* 1.3 86.6 - - + +
239D ASN* 1.3 61.0 + - - +
241D VAL* 3.2 8.7 + - + +
242D LYS* 2.9 28.4 + - - +
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Residues in contact with ASN 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157D LEU* 3.7 23.7 - - + +
160D SER* 3.3 22.5 + - - -
164D GLU* 3.5 15.7 + - - +
166D LEU* 3.6 23.5 - - + +
237D ALA* 3.2 2.2 - - + +
238D PRO* 1.3 77.6 - - - +
240D ALA* 1.3 59.9 + - - +
242D LYS* 3.8 13.4 + - - +
243D THR* 2.8 32.4 + - - -
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Residues in contact with ALA 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166D LEU* 3.5 31.8 - - + +
221D PRO* 4.8 0.5 - - - +
224D ALA* 3.4 12.6 - - + +
235D SER* 3.4 37.7 - - - +
237D ALA 2.9 10.7 + - - +
239D ASN* 1.3 76.5 - - - +
241D VAL* 1.3 64.3 + - - +
243D THR* 3.5 5.5 + - - +
244D ALA* 3.2 16.3 + - - +
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Residues in contact with VAL 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C SER 3.3 25.6 - - - +
43C ALA* 3.6 19.3 - - - +
44C GLY* 3.9 12.8 - - - +
245C PHE* 4.0 8.2 - - + -
249C GLU* 5.9 0.7 - - + +
256C ARG* 4.7 1.8 - - - +
224D ALA* 3.7 28.7 - - - +
225D PRO* 4.0 7.0 - - + +
236D HIS 3.9 11.7 - - - +
237D ALA 3.1 13.1 + - - +
238D PRO* 3.5 9.4 - - + +
240D ALA* 1.3 76.4 - - - +
242D LYS* 1.3 60.6 + - - +
244D ALA* 3.3 5.7 + - - +
245D PHE* 3.1 19.9 + - - +
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Residues in contact with LYS 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C ASN* 4.9 10.1 + - - +
245C PHE* 3.7 14.3 - - + -
246C TYR* 4.0 21.2 + - - +
249C GLU* 2.7 42.9 + - - +
154D PRO* 5.5 2.2 - - + -
157D LEU* 3.8 22.7 - - + -
238D PRO 2.9 15.5 + - - +
239D ASN* 4.0 14.5 + - - +
241D VAL* 1.3 77.2 - - - +
243D THR* 1.3 65.5 + - - +
245D PHE* 3.1 1.7 + - - +
246D TYR* 2.9 47.0 + - + -
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Residues in contact with THR 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D PHE* 5.9 0.2 - - + -
153D PHE* 4.1 8.5 - - + -
157D LEU* 3.8 12.6 - - - +
161D LEU* 3.5 40.2 - - + +
166D LEU* 5.9 0.9 - - - +
167D THR* 5.4 0.2 - - + -
219D TRP* 3.7 34.1 - - + -
239D ASN 2.8 22.0 + - - -
240D ALA* 3.6 7.2 - - - -
241D VAL 3.3 0.2 - - - -
242D LYS* 1.3 76.6 - - - +
244D ALA* 1.3 63.0 + - - +
246D TYR* 3.3 2.4 + - - +
247D LEU* 2.9 25.6 + - + +
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Residues in contact with ALA 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D TYR* 3.2 22.4 - - + -
221D PRO* 3.2 35.9 - - - +
225D PRO* 3.7 18.4 - - + -
240D ALA 3.2 7.9 + - - +
241D VAL 3.4 9.6 - - - +
242D LYS 3.2 0.4 - - - -
243D THR* 1.3 79.7 - - - +
245D PHE* 1.3 63.4 + - - +
247D LEU 3.3 0.2 + - - -
248D ALA* 3.0 19.9 + - - +
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Residues in contact with PHE 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C VAL* 4.1 9.4 - - + -
242C LYS* 3.7 38.6 - - + -
245C PHE* 3.6 53.4 - + + -
42D SER* 3.4 40.4 - - - +
43D ALA* 4.3 4.3 - - - -
225D PRO* 5.6 0.2 - - - +
241D VAL 3.1 3.2 + - - +
242D LYS 3.1 7.4 + - - +
244D ALA* 1.3 79.3 - - - +
246D TYR* 1.3 71.3 + + - +
248D ALA* 3.2 4.3 + - - +
249D GLU* 2.8 57.0 + - + +
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Residues in contact with TYR 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C PRO* 4.1 1.0 - - - +
242C LYS* 2.9 32.0 + - - -
246C TYR* 2.5 34.3 + + - -
152D ASN* 3.3 33.0 - - + -
153D PHE* 3.5 30.3 - + + -
154D PRO* 3.6 17.1 - - + +
157D LEU* 3.9 8.5 - - + -
242D LYS* 2.9 45.4 + - + +
243D THR 3.9 0.2 - - - +
245D PHE* 1.3 86.8 - + - +
247D LEU* 1.3 56.7 + - - +
249D GLU* 3.6 21.2 - - - +
250D PHE* 2.9 27.5 + - - +
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Residues in contact with LEU 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D TYR* 3.3 14.7 + - + +
107D TRP* 4.1 17.5 - - + -
149D MET* 3.6 35.4 - - + +
150D PHE* 4.4 4.5 - - + -
153D PHE* 3.6 22.2 - - + -
217D VAL* 4.6 1.6 - - + -
219D TRP* 3.3 39.3 - - + -
221D PRO* 4.0 15.5 - - + -
243D THR* 2.9 18.3 + - + +
244D ALA* 3.9 1.3 - - - +
246D TYR* 1.3 72.8 - - - +
248D ALA* 1.3 66.9 + - - +
250D PHE* 3.3 5.9 + - + +
251D PHE* 3.1 23.4 + - - +
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Residues in contact with ALA 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D TYR* 3.4 47.5 + - + +
40D LEU* 4.9 2.7 - - - -
42D SER* 4.3 4.3 - - - +
43D ALA* 3.5 10.1 - - + -
244D ALA 3.0 17.4 + - - +
245D PHE* 3.6 3.6 - - - +
247D LEU* 1.3 75.4 - - - +
249D GLU* 1.3 58.2 + - - +
251D PHE* 3.3 5.1 + - - +
252D VAL* 2.9 34.6 + - - +
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Residues in contact with GLU 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C PRO* 4.3 16.0 - - + +
241C VAL* 6.4 0.4 - - + -
242C LYS* 3.7 27.2 + - - +
43D ALA* 3.6 12.3 - - + +
152D ASN* 4.4 15.7 - - - +
245D PHE* 2.8 40.3 + - + +
246D TYR* 3.6 29.7 - - - +
248D ALA* 1.3 76.7 - - - +
250D PHE* 1.3 63.3 + - - +
252D VAL* 3.8 1.3 - - - +
253D ASN* 2.9 27.3 + - + +
256D ARG* 4.5 5.0 + - - +
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Residues in contact with PHE 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D TRP* 4.1 8.5 - + - -
148D ARG* 3.2 32.8 - - + -
149D MET* 3.6 37.2 - - + +
152D ASN* 6.1 3.8 - - + -
215D TYR* 3.4 54.5 - + - -
246D TYR 2.9 17.9 + - - +
247D LEU* 3.6 5.6 - - - +
249D GLU* 1.3 78.0 + - - +
251D PHE* 1.3 66.8 + - - +
253D ASN* 3.2 9.1 + - + +
254D GLU* 3.0 41.4 + - + +
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Residues in contact with PHE 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ILE* 3.8 28.5 - - + -
39D TYR* 5.6 2.2 - + + +
40D LEU* 3.7 23.8 - - + -
68D GLY 4.6 0.7 - - - -
69D ILE 3.4 31.0 - - - -
70D LEU* 4.2 7.6 - - + -
105D PRO* 3.7 37.5 - - + -
106D VAL 4.3 0.4 - - - -
107D TRP* 3.6 44.4 - + + -
215D TYR* 4.9 3.6 - + - -
247D LEU 3.1 14.2 + - - +
248D ALA* 3.3 4.9 + - - +
250D PHE* 1.3 85.5 - - - +
252D VAL* 1.3 61.5 + - - +
254D GLU* 3.0 8.7 + - + +
255D ALA* 3.0 18.4 + - - +
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Residues in contact with VAL 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D PRO* 3.6 20.2 - - + -
12D ILE* 3.9 9.9 - - + -
40D LEU* 4.0 9.2 - - + +
43D ALA* 3.4 30.7 - - + +
44D GLY 4.2 0.2 - - - +
45D ALA* 3.7 23.3 - - + -
248D ALA 2.9 20.3 + - - +
249D GLU 4.0 2.0 - - - +
251D PHE* 1.3 76.6 - - - +
253D ASN* 1.3 62.4 + - - +
255D ALA* 3.0 8.9 + - - +
256D ARG* 3.0 42.0 + - - +
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Residues in contact with ASN 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C PRO* 4.3 23.2 - - - +
152D ASN* 5.6 6.2 + - - +
249D GLU* 2.9 22.7 + - + +
250D PHE* 3.2 8.3 + - + +
252D VAL* 1.3 76.9 - - - +
254D GLU* 1.3 63.8 + - - +
256D ARG* 3.2 30.3 + - - +
257D LYS* 3.6 23.2 + - - +
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Residues in contact with GLU 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D TYR* 2.6 32.2 + - + -
105D PRO* 3.7 20.3 - - + +
148D ARG* 4.2 1.9 + - - -
215D TYR* 2.5 31.4 + - + +
250D PHE* 3.0 45.6 + - + +
251D PHE* 3.2 9.6 - - - +
253D ASN* 1.3 79.8 - - - +
255D ALA* 1.3 57.9 + - - +
257D LYS* 2.8 58.8 + - - +
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Residues in contact with ALA 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D LYS* 5.2 0.2 - - - +
10D PRO* 4.2 6.8 - - + +
12D ILE* 4.0 22.7 - - + -
67D ASN* 3.4 50.1 + - + +
105D PRO* 3.8 6.5 - - + -
251D PHE 3.0 11.9 + - - +
252D VAL 3.0 9.2 + - - +
254D GLU* 1.3 73.5 - - - +
256D ARG* 1.3 59.2 + - - +
257D LYS 3.1 7.1 + - - -
258D ASN* 3.5 10.7 + - - +
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Residues in contact with ARG 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236C HIS 3.9 19.4 + - - -
238C PRO* 4.0 33.6 - - - +
241C VAL* 4.5 4.9 - - - +
8D LYS* 3.0 46.7 + - + +
10D PRO* 4.0 24.1 - - + +
43D ALA 3.3 22.2 + - - -
44D GLY* 4.0 10.9 + - - -
249D GLU* 4.5 5.5 + - - +
252D VAL* 3.0 37.3 + - - +
253D ASN* 3.4 33.2 - - - +
254D GLU 3.1 1.0 - - - -
255D ALA* 1.3 75.8 - - - +
257D LYS* 1.3 56.2 + - - +
258D ASN 3.3 2.7 - - - -
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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
------------------------------------------------------------
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