Contacts of the helix formed by residues 249 - 266 (chain B) in PDB entry 5J1T
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 ASN 249 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B PRO* 4.1 3.3 - - - +
248B LYS* 1.3 82.2 - - + +
250B PRO* 1.4 64.1 - - - +
251B ALA* 3.3 9.4 + - - +
252B LEU* 3.0 32.6 + - + +
253B GLU* 3.0 26.7 + - - +
285B LEU 3.0 26.4 + - - +
286B ASN* 3.6 21.2 + - - +
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Residues in contact with PRO 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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247B PRO* 3.9 25.1 - - + +
248B LYS 3.4 11.4 - - - +
249B ASN* 1.4 86.4 - - - +
251B ALA* 1.3 63.5 + - - +
253B GLU* 3.4 1.0 + - - +
254B ALA* 3.0 26.0 + - - +
322B SER* 4.1 8.5 - - - -
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Residues in contact with ALA 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ASN* 3.3 7.6 + - - +
250B PRO* 1.3 80.3 - - - +
252B LEU* 1.3 62.3 + - - +
254B ALA* 4.0 1.2 - - - +
255B PHE* 3.0 23.9 + - - +
285B LEU* 4.5 18.0 - - + +
319B TYR 4.9 6.6 - - - +
320B THR* 6.3 0.4 - - - -
321B SER* 5.0 1.0 - - - -
322B SER* 3.6 22.1 + - - +
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Residues in contact with LEU 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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249B ASN* 3.0 28.9 + - + +
251B ALA* 1.3 77.2 - - - +
253B GLU* 1.3 79.0 + - - +
255B PHE* 3.2 2.7 + - + +
256B LEU* 3.0 38.6 + - + +
282B GLN* 3.9 45.5 - - + +
285B LEU* 4.0 17.6 - - + +
286B ASN* 3.6 29.8 - - + +
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Residues in contact with GLU 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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247B PRO* 3.5 30.7 - - + -
248B LYS 5.4 0.2 - - - +
249B ASN* 3.0 18.0 + - - +
250B PRO 3.9 2.9 - - - +
252B LEU* 1.3 94.9 - - - +
254B ALA* 1.3 62.4 + - - +
256B LEU* 3.4 17.4 + - - +
257B ALA* 3.2 23.6 + - - +
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Residues in contact with ALA 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B PRO 3.0 15.9 + - - +
251B ALA 4.0 0.9 - - - +
253B GLU* 1.3 75.8 - - - +
255B PHE* 1.3 63.7 + - - +
257B ALA* 3.3 6.5 + - - +
258B GLN* 3.0 19.8 + - - +
321B SER* 3.3 11.1 - - - +
322B SER* 3.5 34.8 - - - +
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Residues in contact with PHE 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B ALA 3.0 18.4 + - - +
252B LEU* 3.2 5.4 + - + +
254B ALA* 1.3 77.2 - - - +
256B LEU* 1.3 81.8 + - + +
258B GLN 3.2 0.2 + - - -
259B PHE* 2.7 74.3 + + + +
278B ARG* 4.2 14.8 - - + -
281B LEU* 3.6 39.9 - - + -
282B GLN 4.2 2.0 - - - -
285B LEU* 3.5 26.2 - - + -
315B VAL 5.1 0.4 - - - -
318B ALA* 3.4 30.5 - - + +
319B TYR* 4.2 4.7 - - - +
321B SER* 3.3 10.0 - - - -
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Residues in contact with LEU 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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252B LEU* 3.0 35.0 + - + +
253B GLU* 3.8 22.7 - - - +
254B ALA 3.3 0.2 - - - -
255B PHE* 1.3 88.1 - - + +
257B ALA* 1.3 58.4 + - - +
259B PHE* 4.0 2.2 - - - +
260B SER* 3.0 30.1 + - - -
278B ARG* 3.8 31.4 - - + -
282B GLN* 3.5 27.6 - - + +
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Residues in contact with ALA 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 GLU 3.2 15.1 + - - +
254B ALA* 3.8 6.1 - - - +
255B PHE 3.2 0.2 - - - -
256B LEU* 1.3 80.6 - - - +
258B GLN* 1.3 60.2 + - - +
260B SER* 3.4 5.8 + - - -
261B GLN* 3.2 34.9 + - - +
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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
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254B ALA 3.0 7.7 + - - +
257B ALA* 1.3 73.7 - - - +
259B PHE* 1.3 66.5 + - - +
261B GLN* 3.1 14.4 + - + +
262B LEU* 3.0 28.8 + - + +
314B HIS* 4.9 3.8 + - - -
317B ASP* 4.1 15.8 + - - +
318B ALA* 3.5 29.4 - - + +
321B SER* 3.2 40.3 + - - +
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Residues in contact with PHE 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B PHE* 2.7 52.4 + + + +
256B LEU* 4.0 3.6 - - - +
258B GLN* 1.3 72.9 - - - +
260B SER* 1.3 63.7 + - - +
262B LEU* 3.2 31.2 + - + +
263B GLU* 3.7 4.0 + - - +
273B LEU* 4.5 3.6 - - + -
274B TRP* 3.5 55.7 - + + -
277B GLY* 4.0 8.3 - - - -
278B ARG* 3.6 34.1 - - + -
281B LEU* 4.8 2.7 - - + -
298B PHE* 5.9 1.8 - + - -
315B VAL* 4.1 28.9 - - + -
318B ALA* 4.7 2.4 - - + +
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Residues in contact with SER 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 LEU 3.0 19.8 + - - -
257B ALA* 3.6 7.2 - - - -
259B PHE* 1.3 79.8 - - - +
261B GLN* 1.3 62.2 + - - +
263B GLU* 3.2 27.1 + - - +
264B ASP* 4.1 5.4 + - - +
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Residues in contact with GLN 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 ALA* 3.2 20.5 + - - +
258B GLN* 3.1 16.2 + - + +
260B SER* 1.3 78.0 - - - +
262B LEU* 1.3 62.7 + - - +
264B ASP* 3.2 22.3 + - - +
265B LYS* 3.6 28.3 + - - +
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Residues in contact with LEU 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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258B GLN* 3.0 21.3 + - + +
259B PHE* 3.4 26.7 - - + +
260B SER 3.1 0.6 - - - -
261B GLN* 1.3 75.9 - - - +
263B GLU* 1.3 64.8 + - - +
265B LYS* 3.0 23.4 + - - +
266B PHE* 3.0 29.1 + - + +
274B TRP* 4.0 10.1 - - + -
311B LEU* 4.7 3.6 - - + -
314B HIS* 3.7 53.4 - - + +
315B VAL* 4.0 23.3 - - + -
318B ALA* 4.6 3.4 - - + -
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Residues in contact with GLU 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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259B PHE 3.7 3.1 + - - +
260B SER* 3.2 21.0 + - - +
262B LEU* 1.3 78.4 - - - +
264B ASP* 1.3 65.3 + - - +
266B PHE 3.4 19.2 + - - +
267B PRO* 3.7 4.3 - - - +
274B TRP* 3.3 59.1 - - + +
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Residues in contact with ASP 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 SER 4.7 6.2 - - - +
261B GLN* 3.2 15.4 + - - +
262B LEU 3.1 1.0 - - - -
263B GLU* 1.3 84.2 - - - +
265B LYS* 1.3 60.7 + - + +
266B PHE 3.6 0.2 + - - -
267B PRO* 3.9 10.1 - - - +
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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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261B GLN* 3.7 28.3 + - - +
262B LEU* 3.0 23.4 + - + +
264B ASP* 1.3 78.1 - - + +
266B PHE* 1.4 71.3 + - + +
267B PRO* 3.4 8.9 - - - +
314B HIS* 5.0 4.0 - - - -
460B VAL* 4.3 2.8 - - - +
463B ILE* 4.2 11.6 - - - +
470B PHE* 3.5 43.5 - - + +
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Residues in contact with PHE 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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262B LEU* 3.0 35.7 + - + +
263B GLU* 3.4 8.2 - - - +
265B LYS* 1.4 78.3 - - + +
267B PRO* 1.3 68.4 - - - +
269B GLN* 3.4 19.0 + - + +
274B TRP* 3.6 17.4 + - + -
307B THR* 3.9 17.0 - - + -
310B CYS* 3.7 20.9 - - + -
311B LEU* 3.5 56.1 - - + -
314B HIS* 4.2 2.9 - + - -
460B VAL* 3.9 3.6 - - + -
463B ILE* 3.5 24.7 - - + -
470B PHE* 4.0 19.7 - + - -
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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
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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