Contacts of the helix formed by residues 268 - 281 (chain B) in PDB entry 1FUU
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 THR 268 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266B CYS* 3.8 1.1 - - - +
267B ASN* 1.3 88.4 - - + +
269B ARG* 1.3 63.6 + - - +
270B ARG* 4.0 7.0 + - - +
271B LYS* 3.3 27.0 + - - +
272B VAL* 3.2 21.8 + - - +
316B THR* 3.9 5.2 - - - -
335B ASP* 4.4 2.0 + - - +
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Residues in contact with ARG 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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268B THR* 1.3 71.1 - - - +
270B ARG* 1.3 70.7 + - - +
272B VAL* 3.1 13.6 + - - +
273B GLU* 3.2 29.1 + - - +
290B TYR* 3.5 47.6 - - + +
292B ASP* 2.8 31.0 + - - -
293B LEU* 5.3 0.4 - - - +
316B THR* 3.6 17.4 - - + +
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Residues in contact with ARG 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B THR* 3.4 6.8 + - - +
269B ARG* 1.3 83.4 - - - +
271B LYS* 1.3 56.8 + - - +
273B GLU* 2.9 29.4 + - + +
274B GLU* 2.9 47.8 + - + +
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Residues in contact with LYS 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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243B GLU* 3.1 29.7 + - - +
266B CYS* 3.6 21.8 - - + -
268B THR* 3.3 23.2 + - - +
269B ARG 3.3 0.2 - - - -
270B ARG* 1.3 78.1 - - - +
272B VAL* 1.3 63.2 + - - +
274B GLU* 3.7 23.1 + - + +
275B LEU* 3.0 27.0 + - - +
278B LYS* 5.4 5.3 - - - +
334B TYR* 3.7 24.0 - - + -
335B ASP* 3.7 15.3 - - - +
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Residues in contact with VAL 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B CYS* 3.7 17.0 - - + -
268B THR 3.2 17.3 - - - +
269B ARG 3.1 7.6 + - - +
271B LYS* 1.3 76.4 - - - +
273B GLU* 1.3 52.0 + - - +
275B LEU* 4.0 0.2 - - - +
276B THR* 2.4 39.0 + - - +
288B ALA* 4.6 1.1 - - + -
290B TYR* 3.5 23.8 - - + -
314B ILE* 3.3 39.4 - - + +
315B SER* 3.8 10.8 - - - +
316B THR* 3.5 21.1 - - + -
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Residues in contact with GLU 273 (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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269B ARG* 3.5 31.1 + - - +
270B ARG* 2.9 32.6 + - + +
272B VAL* 1.3 75.1 - - - +
274B GLU* 1.3 53.9 + - + +
275B LEU 3.2 1.3 - - - -
276B THR* 3.4 2.7 - - - -
277B THR* 2.6 46.1 + - - +
290B TYR* 3.1 38.7 + - + +
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Residues in contact with GLU 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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270B ARG* 2.9 32.3 + - + +
271B LYS* 3.7 34.5 + - + +
273B GLU* 1.3 75.6 - - + +
275B LEU* 1.3 55.2 + - - +
277B THR* 3.1 5.4 + - - -
278B LYS* 2.8 56.4 + - + +
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Residues in contact with LEU 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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247B TYR* 3.5 33.7 - - + -
250B LEU* 3.9 13.7 - - + -
264B ILE* 4.1 21.1 - - + -
266B CYS* 4.2 11.0 - - - -
271B LYS 3.0 14.6 + - - +
272B VAL 4.0 2.5 - - - +
274B GLU* 1.3 80.7 - - - +
276B THR* 1.3 60.5 + - - +
278B LYS* 3.6 7.9 - - - +
279B LEU* 2.9 35.0 + - + +
314B ILE* 3.5 32.8 - - + -
334B TYR* 3.8 26.0 - - + +
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Residues in contact with THR 276 (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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272B VAL 2.4 26.2 + - - -
273B GLU* 3.0 8.6 + - - -
275B LEU* 1.3 75.7 - - - +
277B THR* 1.3 58.8 + - - +
279B LEU* 3.7 1.2 - - - +
280B ARG* 2.9 70.3 + - - +
286B VAL* 3.5 15.0 - - + +
288B ALA* 3.4 26.2 - - + +
290B TYR* 4.7 2.0 - - - +
314B ILE* 3.8 11.7 - - - +
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Residues in contact with THR 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B GLU* 2.6 30.6 + - - +
274B GLU* 3.4 7.5 - - - -
276B THR* 1.3 70.8 - - - +
278B LYS* 1.3 69.5 + - + +
280B ARG* 2.9 7.8 + - - +
281B ASN* 2.8 45.5 + - - +
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Residues in contact with LYS 278 (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 TYR* 2.8 45.6 + - + +
271B LYS* 5.4 4.2 - - - +
274B GLU* 2.8 46.5 + - + +
275B LEU* 3.6 8.7 - - - +
277B THR* 1.3 77.3 - - + +
279B LEU* 1.3 60.6 + - - +
281B ASN* 3.4 14.1 + - - +
282B ASP* 3.5 14.9 - - - +
334B TYR* 3.7 22.6 + - - -
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Residues in contact with LEU 279 (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 TYR* 3.1 28.3 + - + +
250B LEU* 5.0 11.4 - - + -
251B THR* 5.3 4.3 - - - +
264B ILE* 5.3 0.2 - - + -
275B LEU* 2.9 34.8 + - + +
276B THR 3.7 3.6 - - - +
278B LYS* 1.3 77.5 - - - +
280B ARG* 1.3 59.1 + - - +
282B ASP* 3.2 8.9 + - - +
284B PHE* 2.9 55.2 + - + +
286B VAL* 4.3 8.7 - - + -
312B ILE* 4.4 21.5 - - + -
314B ILE* 3.5 27.4 - - + -
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Residues in contact with ARG 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B THR* 2.9 38.0 + - - +
277B THR* 2.9 5.8 + - - +
279B LEU* 1.3 71.6 - - - +
281B ASN* 1.3 62.3 + - - +
282B ASP 2.8 9.9 + - - -
283B LYS* 3.0 15.2 + - - +
284B PHE 3.7 11.2 - - - +
285B THR* 5.4 0.9 - - - -
286B VAL* 2.6 40.4 + - + +
287B SER* 4.2 1.2 - - - +
288B ALA* 3.9 16.6 - - - +
301B ILE* 6.3 1.0 - - - +
304B GLU* 5.9 0.8 + - - -
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Residues in contact with ASN 281 (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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277B THR* 2.8 36.7 + - - +
278B LYS* 3.6 10.7 - - - +
279B LEU 3.2 0.6 - - - -
280B ARG* 1.3 79.2 - - - +
282B ASP* 1.3 67.6 + - - +
283B LYS 3.6 0.4 - - - -
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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