Contacts of the helix formed by residues 249 - 263 (chain B) in PDB entry 5FQD
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 ASP 249 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192B SER* 5.9 1.4 - - - -
193B THR* 5.7 1.9 - - - +
227B TYR* 2.7 22.0 + - - -
231B LYS* 3.3 19.1 + - - -
232B PHE* 3.5 28.0 - - + -
245B TYR 3.3 1.5 + - - +
246B SER* 3.2 13.6 + - - +
247B LEU 3.6 0.4 - - - -
248B TYR* 1.4 75.7 - - - +
250B ALA* 1.4 54.1 + - - +
251B GLU* 3.1 16.1 - - - +
252B THR* 2.8 23.8 + - - +
253B LEU* 2.9 36.1 + - - +
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Residues in contact with ALA 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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249B ASP* 1.4 69.5 + - - +
251B GLU* 1.3 64.0 + - - +
253B LEU* 3.4 2.5 + - - +
254B MET* 2.8 40.8 + - + +
277B PRO* 3.7 31.0 - - + -
305B ILE* 3.6 29.4 - - + +
308B LEU* 4.0 7.6 - - + +
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Residues in contact with GLU 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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224B TRP* 3.7 9.8 - - + -
227B TYR* 3.4 26.0 - - + +
231B LYS* 3.2 14.5 + - - -
249B ASP* 3.1 18.9 - - - +
250B ALA* 1.3 81.2 + - - +
252B THR* 1.4 57.1 + - - +
254B MET* 3.5 17.3 + - + +
255B ASP* 2.9 28.6 + - - +
277B PRO* 6.3 0.2 - - - -
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Residues in contact with THR 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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841A ALA* 6.2 1.3 - - + -
224B TRP* 3.4 20.0 - - + -
227B TYR* 3.4 16.3 - - + -
232B PHE* 5.0 0.2 - - - -
246B SER* 3.8 30.9 + - - +
249B ASP* 2.8 25.1 + - - +
251B GLU* 1.4 72.5 - - - +
253B LEU* 1.3 59.3 + - - +
255B ASP* 3.2 4.4 + - + +
256B ARG* 3.0 44.1 + - + +
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Residues in contact with LEU 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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246B SER 4.5 1.1 - - - +
247B LEU* 3.4 25.6 - - - +
249B ASP 2.9 26.2 + - - +
250B ALA* 3.7 5.6 - - - +
252B THR* 1.3 75.5 - - - +
254B MET* 1.4 55.9 + - - +
256B ARG* 3.2 28.4 + - - +
257B ILE* 3.0 33.9 + - - +
305B ILE* 3.9 24.7 - - + +
308B LEU* 4.1 17.0 - - + -
309B ARG* 3.6 30.1 - - + +
312B LEU* 3.7 14.2 - - + +
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Residues in contact with MET 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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250B ALA* 2.8 36.1 + - + +
251B GLU* 3.7 17.9 - - + +
253B LEU* 1.4 71.0 - - - +
255B ASP* 1.4 59.4 + - - +
257B ILE* 3.3 1.2 + - - -
258B LYS* 2.9 39.6 + - - +
274B PRO 4.7 0.9 - - - +
275B SER* 3.9 17.5 - - - +
277B PRO* 3.7 37.7 - - + -
280B PHE* 3.5 45.8 - - + -
308B LEU* 3.9 11.0 - - + -
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Residues in contact with ASP 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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224B TRP* 3.5 41.9 + - + -
251B GLU 2.9 18.2 + - - +
252B THR* 3.2 5.6 + - - +
254B MET* 1.4 72.8 - - - +
256B ARG* 1.3 64.8 + - + +
258B LYS* 3.8 14.9 + - + +
259B LYS* 3.3 37.5 + - - +
262B ARG* 4.4 14.4 + - - -
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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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841A ALA* 3.6 26.3 - - - +
842A GLU* 4.9 14.1 + - - +
246B SER 5.3 0.6 + - - -
247B LEU* 3.5 29.1 - - - +
252B THR* 3.0 30.1 + - + +
253B LEU* 3.2 28.4 + - - +
255B ASP* 1.3 75.4 - - - +
257B ILE* 1.4 63.2 + - - +
259B LYS* 3.4 33.4 + - - +
260B GLN* 3.7 5.7 + - - +
309B ARG* 5.8 0.6 - - - +
312B LEU* 3.6 39.0 - - + +
316B ASN* 4.5 10.7 - - - +
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Residues in contact with ILE 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 LEU 3.0 20.4 + - - +
254B MET 3.3 0.6 + - - +
256B ARG* 1.4 72.6 - - - +
258B LYS* 1.4 55.7 + - - +
259B LYS 3.1 1.6 - - - -
260B GLN* 2.8 27.6 + - - +
261B LEU* 2.9 19.2 + - + +
280B PHE* 3.6 23.8 - - + -
284B VAL* 3.7 16.2 - - + -
308B LEU* 3.6 51.4 - - + +
311B GLU* 4.1 7.6 - - - +
312B LEU* 3.5 18.6 - - + -
315B MET* 3.8 22.2 - - + -
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Residues in contact with LYS 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 MET* 2.9 30.3 + - - +
255B ASP* 3.8 18.1 + - - +
257B ILE* 1.4 72.2 - - - +
259B LYS* 1.3 55.5 + - - +
261B LEU* 3.2 9.6 + - - +
262B ARG* 2.9 54.9 + - - +
269B LYS* 3.7 28.6 - - + +
273B LEU* 3.8 22.6 - - + +
274B PRO 5.3 3.1 - - - -
280B PHE* 3.9 17.7 - - + -
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Residues in contact with LYS 259 (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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839A GLU 5.8 2.4 + - - -
255B ASP* 3.3 30.3 + - - +
256B ARG* 3.5 27.2 - - - +
257B ILE 3.1 1.0 + - - -
258B LYS* 1.3 77.0 - - - +
260B GLN* 1.3 57.0 + - - +
262B ARG* 3.6 24.2 + - - +
263B GLU* 3.6 21.3 + - - +
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Residues in contact with GLN 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 ARG 3.7 7.2 + - - +
257B ILE* 2.8 9.3 + - - +
259B LYS* 1.3 73.6 - - - +
261B LEU* 1.3 64.2 + - - +
262B ARG 3.3 1.6 - - - -
263B GLU* 3.2 28.9 - - - +
264B TRP* 3.4 36.1 + - + -
312B LEU* 5.8 2.5 - - + -
315B MET* 3.5 50.9 + - + +
316B ASN* 4.5 6.7 + - - -
334B LYS* 4.0 17.2 - - - +
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Residues in contact with LEU 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 ILE* 2.9 35.7 + - + +
258B LYS* 3.7 7.2 - - - +
260B GLN* 1.3 75.4 - - - +
262B ARG* 1.4 57.6 + - - +
264B TRP* 3.2 35.2 + - + +
265B ASP* 3.0 29.3 + - - +
273B LEU* 3.7 39.7 - - + -
280B PHE* 4.1 9.0 - - + -
284B VAL* 4.1 17.5 - - + -
287B CYS* 5.1 7.6 - - - -
315B MET* 5.3 2.2 - - - -
345B PRO* 5.9 0.4 - - + -
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Residues in contact with ARG 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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255B ASP* 4.4 10.1 + - - -
258B LYS* 2.9 43.9 + - - +
259B LYS* 3.6 41.9 - - - +
260B GLN 3.3 0.2 - - - -
261B LEU* 1.4 73.1 - - - +
263B GLU* 1.4 61.9 + - - +
264B TRP 3.1 0.4 - - - -
265B ASP 2.9 21.7 - - - +
266B GLU* 3.2 17.5 - - - +
267B ASN 4.9 9.9 - - - +
268B LEU* 5.9 3.9 - - - +
269B LYS* 4.2 18.2 - - + +
273B LEU* 6.2 2.9 - - + -
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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 LYS 3.6 13.4 + - - +
260B GLN* 3.2 27.1 + - - +
262B ARG* 1.4 78.1 - - - +
264B TRP* 1.4 60.5 + - + +
266B GLU* 5.0 2.5 - - - +
335B ASN* 5.8 4.0 + - - +
337B ILE 4.6 2.9 - - - +
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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