Contacts of the helix formed by residues 255 - 272 (chain B) in PDB entry 4L1O
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 ILE 255 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218B VAL* 3.9 16.4 - - + +
219B ASP 3.9 21.8 - - - +
220B LYS* 4.0 27.6 - - + +
224B LEU* 4.2 17.0 - - + -
251B CYS* 4.0 7.4 - - + -
252B ASP* 3.4 18.4 - - + +
254B SER* 1.3 89.4 - - - +
256B GLN* 1.3 65.5 + - - +
257B ASN 3.4 2.5 - - - -
258B GLN* 3.3 19.1 + - - +
259B ILE* 3.0 39.0 + - + +
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Residues in contact with GLN 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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251B CYS* 4.0 14.8 - - - -
252B ASP 3.6 4.1 + - - +
253B PRO* 3.5 17.3 + - + +
255B ILE* 1.3 76.9 - - - +
257B ASN* 1.3 73.2 + - - +
259B ILE* 3.2 6.1 + - - +
260B VAL* 3.0 22.3 + - - +
321B THR* 3.2 22.7 - - + +
322B ASP* 2.9 52.3 + - - +
341B ILE* 3.8 24.8 - - + +
343B CYS* 3.4 14.0 - - - -
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Residues in contact with ASN 257 (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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253B PRO 4.9 4.3 + - - +
254B SER 5.4 0.8 + - - -
255B ILE 3.4 0.4 - - - -
256B GLN* 1.3 91.1 - - - +
258B GLN* 1.3 62.5 - - + +
260B VAL* 3.3 10.1 + - - +
261B GLU* 3.1 27.4 + - + +
321B THR* 5.4 3.6 - - - +
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Residues in contact with GLN 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B LEU* 3.9 22.6 - - + +
254B SER 3.3 24.7 + - - -
255B ILE* 3.3 17.3 + - - +
257B ASN* 1.3 76.6 - - + +
259B ILE* 1.3 58.8 + - - +
261B GLU* 3.3 6.9 + - - +
262B LYS* 2.9 48.2 + - - +
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Residues in contact with ILE 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B VAL* 3.9 24.7 - - + -
224B LEU* 4.4 12.8 - - + -
228B CYS* 3.7 23.5 - - - -
249B ILE* 3.9 15.9 - - + -
251B CYS* 3.8 35.4 - - + -
255B ILE* 3.0 20.1 + - + +
256B GLN* 3.2 8.0 + - - +
258B GLN* 1.3 74.3 - - - +
260B VAL* 1.3 58.9 + - - +
262B LYS* 5.0 0.2 - - - -
263B LEU* 2.8 52.1 + - + +
341B ILE* 4.3 8.3 - - + -
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Residues in contact with VAL 260 (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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256B GLN 3.0 19.6 + - - +
257B ASN* 3.5 11.2 - - - +
259B ILE* 1.3 77.1 - - - +
261B GLU* 1.3 64.9 + - - +
263B LEU* 3.7 7.6 - - - +
264B LYS* 2.9 46.9 + - + +
303B ALA* 3.9 20.0 - - + +
319B ILE* 4.1 10.7 - - + +
321B THR* 3.8 20.6 - - + -
341B ILE* 3.8 21.1 - - + -
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Residues in contact with GLU 261 (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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257B ASN* 3.1 18.4 + - + +
258B GLN* 3.7 9.0 - - - +
259B ILE 3.3 0.2 - - - -
260B VAL* 1.3 80.3 - - + +
262B LYS* 1.3 61.3 + - + +
264B LYS* 3.1 35.7 + - - +
265B LYS* 2.9 28.1 + - - +
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Residues in contact with LYS 262 (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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224B LEU* 3.5 34.5 - - + +
225B ASP* 3.0 40.3 + - - +
228B CYS* 3.6 20.1 - - + +
258B GLN* 2.9 41.9 + - - +
261B GLU* 1.3 76.7 - - + +
263B LEU* 1.3 64.9 + - - +
265B LYS* 3.7 12.4 - - - +
266B SER* 3.0 28.1 + - - -
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Residues in contact with LEU 263 (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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228B CYS* 3.4 30.5 - - + +
231B ILE* 4.1 12.8 - - + -
232B ALA* 3.9 17.0 - - + +
236B PHE* 5.3 1.6 - - + -
249B ILE* 4.0 4.5 - - + -
259B ILE* 2.8 47.5 + - + +
260B VAL* 3.7 0.4 - - - +
262B LYS* 1.3 73.9 - - - +
264B LYS* 1.3 56.3 + - - +
266B SER* 3.9 1.8 - - - -
267B LEU* 2.9 39.5 + - + +
319B ILE* 3.6 30.3 - - + -
339B LEU* 3.6 26.2 - - + -
341B ILE* 4.9 0.2 - - + -
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Residues in contact with LYS 264 (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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260B VAL* 2.9 37.5 + - + +
261B GLU* 3.1 32.9 + - - +
263B LEU* 1.3 76.3 - - - +
265B LYS* 1.3 57.5 + - - +
267B LEU* 3.3 8.4 + - - +
268B LYS* 2.9 51.9 + - - +
303B ALA 4.4 7.2 + - - +
304B TYR* 3.7 43.3 + - + -
319B ILE* 4.3 2.4 - - + +
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Residues in contact with LYS 265 (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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225B ASP* 4.3 21.1 + - - +
229B ARG* 5.8 4.0 - - - +
261B GLU 2.9 17.2 + - - +
262B LYS* 3.7 12.8 - - - +
263B LEU 3.3 0.2 - - - -
264B LYS* 1.3 75.2 - - - +
266B SER* 1.3 67.0 + - - +
268B LYS* 3.2 13.9 + - - +
269B GLU* 3.1 52.8 + - + +
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Residues in contact with SER 266 (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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225B ASP 4.8 1.0 + - - -
228B CYS 4.5 0.2 - - - -
229B ARG* 3.3 42.1 + - - +
232B ALA* 4.2 6.7 - - - -
262B LYS 3.0 16.7 + - - -
263B LEU 3.9 2.9 - - - -
265B LYS* 1.3 81.4 + - - +
267B LEU* 1.3 57.7 + - - +
269B GLU* 3.2 12.4 + - - +
270B PHE* 2.9 46.7 + - - -
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Residues in contact with LEU 267 (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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232B ALA* 4.5 5.8 - - + -
236B PHE* 3.6 46.9 - - + -
263B LEU* 2.9 27.1 + - + +
264B LYS 3.6 4.5 - - - +
266B SER* 1.3 75.8 - - - +
268B LYS* 1.3 58.2 + - - +
270B PHE* 4.3 7.9 - - + -
271B TYR* 3.0 53.6 + - + +
272B GLY 4.0 2.2 + - - +
304B TYR* 4.1 25.6 - - + +
317B PRO* 3.9 23.3 - - + -
319B ILE* 4.3 7.9 - - + -
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Residues in contact with LYS 268 (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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264B LYS* 2.9 35.9 + - - +
265B LYS* 3.4 13.7 - - - +
267B LEU* 1.3 73.9 - - - +
269B GLU* 1.3 62.1 + - + +
272B GLY* 2.8 39.9 + - - +
273B GLU* 3.3 37.7 + - - +
304B TYR* 3.8 33.8 + - - +
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Residues in contact with GLU 269 (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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443A PRO 4.5 0.7 - - - -
444A PRO* 3.6 18.4 - - - +
229B ARG* 4.4 20.0 + - - -
265B LYS* 3.1 47.6 + - + +
266B SER* 3.6 16.0 + - - +
268B LYS* 1.3 76.9 - - + +
270B PHE* 1.3 68.9 + - + +
272B GLY 4.6 0.9 + - - -
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Residues in contact with PHE 270 (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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442A TYR* 3.7 32.1 - + + -
443A PRO* 3.3 46.4 - - + +
444A PRO* 3.7 12.0 - - - +
229B ARG* 3.6 35.9 - - + -
232B ALA* 3.8 12.8 - - + -
233B TRP* 3.6 27.1 - - - -
266B SER* 2.9 26.4 + - - +
267B LEU* 3.8 4.3 - - + +
268B LYS 3.3 0.2 - - - -
269B GLU* 1.3 83.0 - - + +
271B TYR* 1.3 89.5 + + + +
278B SER* 4.4 3.1 + - - -
280B ASP* 4.8 0.3 - - - +
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Residues in contact with TYR 271 (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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443A PRO* 3.8 21.6 - - + +
233B TRP* 5.2 2.3 + - - -
236B PHE* 3.3 28.0 + - + +
237B MET* 4.1 5.0 + - - +
267B LEU* 3.0 36.2 + - + +
270B PHE* 1.3 97.7 - + + +
272B GLY* 1.3 62.7 + - - +
274B ASP 3.6 4.5 - - - +
275B ALA* 3.6 31.6 - - + -
277B LYS 5.4 0.2 - - - -
278B SER* 3.6 29.6 - - - -
280B ASP* 3.7 23.7 + - + -
281B TYR* 3.8 28.7 - + + -
317B PRO* 4.6 3.4 - - + -
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Residues in contact with GLY 272 (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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267B LEU 4.1 1.7 - - - +
268B LYS* 2.8 38.9 + - - +
269B GLU 4.6 0.8 + - - -
270B PHE 3.8 0.8 - - - -
271B TYR* 1.3 75.6 - - - +
273B GLU* 1.3 66.8 + - - +
274B ASP 3.3 2.2 - - - -
275B ALA* 4.2 3.1 + - - +
304B TYR* 4.9 2.6 + - - -
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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