Contacts of the helix formed by residues 263 - 276 (chain B) in PDB entry 4LT6
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 263 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30B PRO* 3.8 28.8 - - + +
34B ASP* 4.4 9.2 - - + +
35B HIS* 4.9 9.4 - - + +
38B THR* 3.7 15.5 - - + +
218B THR* 4.7 3.8 - - - -
261B ASN 3.7 1.2 + - - -
262B ALA* 1.3 76.1 - - - +
264B ALA* 1.3 68.3 + - - +
265B SER* 4.1 7.2 - - - +
266B THR* 2.9 17.9 + - - +
267B LEU* 2.9 10.8 + - - +
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Residues in contact with ALA 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B THR* 3.8 9.5 + - + +
41B LEU* 4.8 3.8 - - + -
218B THR* 4.3 12.7 - - + +
221B LEU* 3.6 42.8 - - + -
222B THR* 3.7 16.3 + - - +
262B ALA 4.0 0.6 + - - -
263B ALA* 1.3 72.1 - - - +
265B SER* 1.3 61.8 + - - +
267B LEU* 3.1 6.6 + - - +
268B VAL* 2.9 28.5 + - - +
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Residues in contact with SER 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ASP* 3.2 16.8 + - - -
37B TYR* 3.8 8.0 - - - +
38B THR* 2.9 37.6 + - - -
41B LEU* 4.5 3.6 - - - +
263B ALA* 4.1 3.8 - - - +
264B ALA* 1.3 78.2 - - - +
266B THR* 1.3 68.0 + - - +
268B VAL 3.6 0.7 + - - -
269B HIS* 3.4 15.9 + - - +
351B LEU* 4.3 5.5 - - - +
357B TRP* 3.7 33.9 - - - -
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Residues in contact with THR 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B PRO* 5.6 1.0 - - - +
34B ASP* 3.5 30.8 - - - +
262B ALA* 3.2 19.8 - - - +
263B ALA* 2.9 21.2 + - - +
265B SER* 1.3 79.9 + - - +
267B LEU* 1.3 55.1 + - - +
269B HIS* 3.0 4.2 + - + +
270B LYS* 2.7 47.6 + - - +
351B LEU* 3.9 21.8 - - + -
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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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218B THR* 3.7 30.5 - - - +
222B THR* 3.2 30.1 - - + +
255B THR* 3.7 21.9 - - + +
256B CYS* 3.9 19.3 - - - -
259B TYR* 3.3 35.2 - - + +
260B PRO 6.3 0.2 - - - -
262B ALA* 3.7 16.4 - - + +
263B ALA 2.9 12.3 + - - +
264B ALA* 3.4 4.0 - - - +
266B THR* 1.3 76.4 + - - +
268B VAL* 1.3 56.6 + - - +
270B LYS* 3.2 2.4 + - + +
271B PHE* 2.7 30.7 + - - +
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Residues in contact with VAL 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LEU* 3.9 12.1 - - + -
222B THR* 3.9 16.4 - - + +
225B ALA* 3.6 30.5 - - + -
226B VAL* 5.0 6.1 - - + -
264B ALA 2.9 21.3 + - - +
265B SER 3.9 5.6 - - - +
266B THR 3.3 0.2 - - - -
267B LEU* 1.3 71.5 - - - +
269B HIS* 1.3 65.0 + - - +
271B PHE* 3.1 21.3 - - - +
272B PHE* 3.3 30.5 - - + -
347B THR* 4.4 1.3 - - + -
357B TRP* 4.2 19.3 - - + -
360B LEU* 4.2 8.3 - - + -
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Residues in contact with HIS 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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265B SER 3.4 4.0 + - - +
266B THR* 3.0 8.8 + - + +
268B VAL* 1.3 80.4 - - - +
270B LYS* 1.3 80.6 + - + +
272B PHE* 3.2 5.5 + - - +
273B LEU* 3.0 25.3 + - + +
344B LEU* 3.8 23.7 - - + +
347B THR* 2.7 36.9 + - - +
348B ASP* 3.7 31.9 + - - -
351B LEU* 3.7 30.5 - - + -
357B TRP* 5.2 0.6 - - + -
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Residues in contact with LYS 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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26B SER* 5.4 3.0 - - - -
255B THR* 3.9 5.4 - - + -
259B TYR* 3.4 66.2 + - + +
262B ALA* 5.7 0.9 - - + -
266B THR* 2.7 33.0 + - - +
267B LEU* 3.8 4.9 - - - +
269B HIS* 1.3 81.0 + - + +
271B PHE* 1.3 59.6 + - - +
273B LEU* 3.3 21.3 - - + +
274B VAL* 2.8 34.7 + - - +
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Residues in contact with PHE 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B THR* 5.2 1.8 - - + -
226B VAL* 3.5 33.9 - - + -
229B TRP* 4.3 2.0 - + - -
248B TRP* 3.8 16.6 - + - -
251B LEU* 3.6 28.7 - - + -
252B VAL* 3.9 21.1 - - + -
255B THR* 3.3 30.4 - - + +
267B LEU 2.7 13.3 + - - +
268B VAL* 3.1 13.5 - - - +
270B LYS* 1.3 76.5 - - - +
272B PHE* 1.3 85.5 + + - +
275B PHE* 3.1 33.2 + + - +
340B PHE* 3.8 22.9 - + - -
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Residues in contact with PHE 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B VAL* 5.8 1.8 - - + -
229B TRP* 3.3 60.3 - + + -
268B VAL* 3.3 39.5 + - + -
269B HIS 3.2 6.0 + - - +
271B PHE* 1.3 86.6 - + - +
273B LEU* 1.3 65.0 + - - +
275B PHE* 5.4 0.2 - - - +
276B SER* 2.9 32.1 + - - +
340B PHE* 3.5 24.2 - + - +
343B GLY* 3.9 4.9 - - - -
344B LEU* 3.5 25.5 - - - +
347B THR* 3.6 25.1 - - + -
360B LEU* 4.1 9.9 - - + -
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Residues in contact with LEU 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B TYR* 4.1 9.4 - - - +
269B HIS* 3.0 22.4 + - - +
270B LYS* 3.0 39.9 + - + +
272B PHE* 1.3 79.8 - - - +
274B VAL* 1.3 63.6 + - + +
276B SER* 3.7 7.3 + - - -
277B LYS* 4.1 25.4 + - + +
344B LEU* 3.7 22.8 - - + +
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Residues in contact with VAL 274 (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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25B ILE* 5.0 3.4 - - + -
255B THR* 5.0 5.4 - - + +
258B LEU* 3.7 32.8 - - + -
259B TYR* 4.1 19.7 - - + +
270B LYS 2.8 22.5 + - - +
271B PHE* 4.0 2.7 - - - +
273B LEU* 1.3 75.3 - - + +
275B PHE* 1.3 75.4 + - + +
277B LYS* 3.3 5.9 + - - +
278B TRP* 3.2 46.4 + - + +
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Residues in contact with PHE 275 (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 LEU* 3.3 57.9 - - + -
254B ARG* 3.9 20.9 - - + -
255B THR* 3.5 11.0 - - - -
271B PHE* 3.1 31.3 + + - +
274B VAL* 1.3 82.8 - - + +
276B SER* 1.3 62.1 + - - +
277B LYS 3.2 2.0 + - - -
278B TRP* 3.7 44.9 + + + +
280B TRP* 4.4 12.1 + + - -
284B VAL* 3.8 10.3 - - + -
337B VAL* 5.7 1.4 - - - +
340B PHE* 3.5 36.9 - - + -
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Residues in contact with SER 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B PHE 2.9 24.4 + - - -
273B LEU 3.7 5.0 + - - -
275B PHE* 1.3 77.1 - - - +
277B LYS* 1.3 69.2 + - - +
278B TRP 3.6 0.4 - - - -
337B VAL* 4.7 7.0 - - - +
340B PHE* 3.8 31.0 - - - +
341B LYS* 3.8 34.4 - - - +
344B LEU* 3.9 15.9 - - - +
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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