Contacts of the helix formed by residues 237 - 256 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B LEU* 3.7 19.3 - - + -
235B SER* 3.3 16.0 + - - +
236B HIS* 1.3 79.7 - - - +
238B PRO* 1.3 78.4 - - + +
239B ASN* 4.3 2.0 - - + +
240B ALA* 2.8 12.5 + - - +
241B VAL* 3.1 9.9 + - - +
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Residues in contact with PRO 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A GLU* 4.2 18.0 - - + +
253A ASN* 4.9 4.0 - - - +
256A ARG* 3.6 40.4 - - - +
236B HIS 3.6 2.7 - - - +
237B ALA* 1.3 84.3 - - + +
239B ASN* 1.3 62.1 + - - +
241B VAL* 3.3 7.0 + - + +
242B LYS* 2.9 28.5 + - - +
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Residues in contact with ASN 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B GLU* 5.2 6.9 - - - +
157B LEU* 3.6 23.2 - - + +
160B SER* 3.4 24.8 + - - -
164B GLU* 5.6 3.2 - - - +
166B LEU* 3.6 23.2 - - + +
237B ALA* 3.2 2.4 - - + +
238B PRO* 1.3 78.3 - - - +
240B ALA* 1.3 60.0 + - - +
242B LYS* 4.2 11.9 + - - +
243B THR* 2.8 32.9 + - - -
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Residues in contact with ALA 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B LEU* 3.5 30.4 - - + +
221B PRO* 4.8 0.9 - - - +
224B ALA* 3.4 12.5 - - + +
235B SER* 3.5 37.5 - - - +
237B ALA 2.8 11.3 + - - +
239B ASN* 1.3 77.3 - - - +
241B VAL* 1.3 62.8 - - - +
243B THR* 3.4 6.2 + - - +
244B ALA* 3.2 16.8 + - - +
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Residues in contact with VAL 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A SER 3.3 24.7 - - - +
43A ALA* 3.7 19.3 - - - +
44A GLY* 4.0 10.1 - - - +
245A PHE* 4.0 8.4 - - + -
249A GLU* 6.1 1.3 - - + +
256A ARG* 5.3 1.8 - - - +
224B ALA* 3.6 28.7 - - - +
225B PRO* 4.0 10.2 - - + +
236B HIS 3.9 12.1 - - - +
237B ALA 3.1 12.0 + - - +
238B PRO* 3.6 10.3 - - + +
240B ALA* 1.3 77.6 - - - +
242B LYS* 1.3 62.0 + - - +
244B ALA* 3.3 5.7 + - - +
245B PHE* 3.2 19.1 + - - +
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Residues in contact with LYS 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A ASN* 4.7 8.5 + - - +
245A PHE* 3.7 16.6 - - + -
246A TYR* 3.7 31.3 + - - +
249A GLU* 2.8 42.3 + - - +
154B PRO* 5.6 2.0 - - + -
156B GLU* 5.3 7.1 + - - -
157B LEU* 3.9 18.6 - - + -
238B PRO 2.9 16.3 + - - +
239B ASN* 3.9 14.3 + - - +
241B VAL* 1.3 73.4 - - - +
243B THR* 1.3 66.3 + - - +
245B PHE* 3.2 2.1 + - - +
246B TYR* 3.0 48.1 + - + -
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Residues in contact with THR 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B PHE* 5.8 0.7 - - + -
153B PHE* 4.2 8.3 - - + -
157B LEU* 3.8 13.5 - - - +
161B LEU* 3.5 40.1 - - + +
166B LEU 6.1 0.4 - - - -
219B TRP* 3.7 33.9 - - + -
239B ASN 2.8 24.9 + - - -
240B ALA* 3.6 7.6 - - - +
242B LYS* 1.3 75.8 - - - +
244B ALA* 1.3 63.6 + - - +
246B TYR* 3.3 2.3 + - - +
247B LEU* 3.0 25.3 + - + +
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Residues in contact with ALA 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B TYR* 3.2 22.0 - - + -
221B PRO* 3.3 33.9 - - - +
225B PRO* 3.7 20.2 - - + -
240B ALA 3.2 7.7 + - - +
241B VAL 3.4 10.1 - - - +
242B LYS 3.2 0.4 - - - -
243B THR* 1.3 81.4 - - - +
245B PHE* 1.3 63.2 + - - +
247B LEU 3.3 0.2 + - - -
248B ALA* 3.0 19.4 + - - +
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Residues in contact with PHE 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A SER 5.8 0.2 - - - +
241A VAL* 4.0 10.5 - - + -
242A LYS* 3.7 39.0 - - + -
245A PHE* 3.7 53.8 - + + -
42B SER* 3.5 37.5 - - - +
43B ALA* 4.3 5.4 - - - -
225B PRO* 5.6 0.2 - - - +
241B VAL 3.2 2.6 + - - -
242B LYS 3.2 7.4 + - - +
244B ALA* 1.3 79.8 - - - +
246B TYR* 1.3 73.8 + + - +
248B ALA* 3.2 6.4 + - - +
249B GLU* 2.8 56.4 + - + +
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Residues in contact with TYR 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A PRO* 4.2 1.4 - - - +
242A LYS* 2.9 33.8 + - - -
246A TYR* 2.6 35.3 + + - -
152B ASN* 3.3 28.3 - - + -
153B PHE* 3.5 32.9 - + + -
154B PRO* 3.6 17.7 - - + +
157B LEU* 3.9 7.4 - - + -
242B LYS* 3.0 43.4 + - + +
245B PHE* 1.3 86.7 - + - +
247B LEU* 1.3 57.4 + - - +
249B GLU* 3.4 23.2 + - - +
250B PHE* 3.0 27.0 + - - +
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Residues in contact with LEU 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B TYR* 3.2 15.5 + - + +
107B TRP* 4.1 17.0 - - + -
149B MET* 3.7 35.0 - - + +
150B PHE* 4.3 4.0 - - + -
153B PHE* 3.6 23.1 - - + -
217B VAL* 4.5 2.0 - - + -
219B TRP* 3.4 37.7 - - + -
221B PRO* 4.0 17.3 - - + -
243B THR* 3.0 18.6 + - + +
244B ALA 3.9 1.6 - - - +
246B TYR* 1.3 74.3 - - - +
248B ALA* 1.3 66.2 + - - +
250B PHE* 3.3 5.5 + - + +
251B PHE* 3.2 22.7 + - - +
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Residues in contact with ALA 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B TYR* 3.4 46.1 + - + +
40B LEU* 4.9 3.4 - - - -
42B SER* 4.2 4.3 - - - +
43B ALA* 3.4 11.2 - - + -
244B ALA 3.0 17.2 + - - +
245B PHE 3.6 3.6 - - - +
247B LEU* 1.3 73.8 - - - +
249B GLU* 1.3 60.6 + - - +
251B PHE* 3.3 4.7 + - - +
252B VAL* 2.9 34.9 + - - +
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Residues in contact with GLU 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A PRO* 4.4 16.2 - - + +
242A LYS* 3.8 21.9 + - - +
43B ALA* 3.6 13.2 - - + +
152B ASN* 4.2 18.0 - - - +
245B PHE* 2.8 45.6 + - + +
246B TYR* 3.5 28.1 - - - +
248B ALA* 1.3 77.1 - - - +
250B PHE* 1.3 62.8 + - - +
252B VAL* 3.4 1.8 + - - +
253B ASN* 3.0 26.0 + - + +
256B ARG* 4.8 3.1 + - - +
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Residues in contact with PHE 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B TRP* 4.1 14.6 - + - -
148B ARG* 3.2 32.8 - - + -
149B MET* 3.6 30.1 - - + +
151B GLN* 5.9 0.2 - - + -
152B ASN* 6.2 3.4 - - + -
215B TYR* 3.4 57.9 - + - -
246B TYR 3.0 14.2 + - - +
247B LEU* 3.6 8.5 - - - +
248B ALA 3.2 0.2 - - - -
249B GLU* 1.3 78.6 - - - +
251B PHE* 1.3 65.5 + - - +
253B ASN* 3.2 11.5 + - - +
254B GLU* 3.0 39.8 + - + +
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Residues in contact with PHE 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ILE* 3.7 32.1 - - + -
39B TYR* 5.6 2.2 - + + +
40B LEU* 3.6 25.1 - - + -
68B GLY 4.6 0.7 - - - -
69B ILE 3.4 27.8 - - - -
70B LEU* 4.2 7.2 - - + -
105B PRO* 3.8 33.9 - - + -
106B VAL 4.2 0.2 - - - -
107B TRP* 3.6 46.4 - + + -
215B TYR* 5.0 3.8 - + - -
247B LEU 3.2 13.5 + - - +
248B ALA* 3.8 4.3 - - - +
250B PHE* 1.3 83.6 - - - +
252B VAL* 1.3 61.8 + - - +
254B GLU* 3.0 16.0 + - + +
255B ALA* 3.1 11.6 + - - +
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Residues in contact with VAL 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B PRO* 3.8 25.1 - - + -
12B ILE* 4.0 13.0 - - + -
40B LEU* 3.9 10.1 - - + +
43B ALA* 3.4 34.8 - - + +
44B GLY 3.9 0.9 - - - +
45B ALA* 3.7 24.7 - - + -
248B ALA 2.9 21.4 + - - +
249B GLU 4.0 2.5 - - - +
251B PHE* 1.3 76.5 - - - +
253B ASN* 1.3 61.7 + - - +
255B ALA* 3.0 11.8 + - - +
256B ARG* 3.1 24.2 + - - +
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Residues in contact with ASN 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A PRO* 4.8 7.0 - - + +
152B ASN* 5.6 4.1 + - - -
249B GLU* 3.0 21.6 + - + +
250B PHE* 3.5 9.2 + - - +
252B VAL* 1.3 77.1 - - - +
254B GLU* 1.3 65.8 + - - +
256B ARG* 3.2 41.7 + - - +
257B LYS* 3.7 25.7 - - - +
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Residues in contact with GLU 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B TYR* 2.5 33.5 + - + +
105B PRO* 3.6 20.3 - - + +
148B ARG* 5.2 1.5 + - - -
215B TYR* 2.5 31.7 + - + +
250B PHE* 3.0 45.2 + - + +
251B PHE* 3.0 11.3 + - - +
253B ASN* 1.3 81.2 + - - +
255B ALA* 1.3 60.6 + - - +
257B LYS* 2.8 52.3 + - - +
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Residues in contact with ALA 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LYS* 5.5 0.2 - - - +
10B PRO* 4.2 6.6 - - + +
12B ILE* 4.0 21.5 - - + -
67B ASN* 3.3 50.3 + - + +
105B PRO* 3.7 7.1 - - + +
251B PHE 3.1 10.9 + - - +
252B VAL 3.0 10.4 + - - +
254B GLU* 1.3 75.9 - - - +
256B ARG* 1.3 59.9 + - - +
257B LYS 3.1 2.4 + - - -
258B ASN* 3.5 9.6 + - - +
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Residues in contact with ARG 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A HIS 3.9 19.0 + - - -
238A PRO* 3.6 36.5 - - - +
241A VAL* 4.8 2.8 - - - +
8B LYS* 3.0 50.3 + - + +
10B PRO* 4.1 23.2 - - + +
43B ALA 3.7 21.2 + - - -
44B GLY 4.3 5.9 + - - -
249B GLU* 4.8 3.8 + - - +
252B VAL* 3.4 18.5 - - - +
253B ASN* 3.4 43.1 + - - +
254B GLU 3.1 1.2 - - - -
255B ALA* 1.3 75.0 - - - +
257B LYS* 1.3 57.9 + - - +
258B ASN 3.3 4.3 - - - -
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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