Contacts of the helix formed by residues 276 - 287 (chain B) in PDB entry 5UFL
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 HIS 276 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232B HIS* 4.0 26.4 + + - -
236B GLN* 5.2 4.4 + - + -
274B TYR* 3.4 27.5 - + + +
275B GLU* 1.3 87.8 + - + +
277B PHE* 1.3 58.9 + - - +
278B SER* 3.3 3.4 - - - -
279B SER* 3.2 16.0 + - - +
280B CYS* 2.8 33.5 + - - -
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Residues in contact with PHE 277 (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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239B PHE* 4.1 9.0 - + - -
271B LEU* 3.6 43.3 - - + +
272B THR 5.2 1.3 - - - +
274B TYR* 3.5 27.3 + - + +
275B GLU 3.5 0.8 - - - -
276B HIS* 1.3 77.4 - - - +
278B SER* 1.3 58.3 + - - +
280B CYS* 3.7 3.3 - - - +
281B LEU* 2.7 70.6 + - + +
306B PHE* 4.0 25.1 - + - -
312B LEU* 3.6 29.4 - - + -
315B MET* 3.6 30.1 - - + -
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Residues in contact with SER 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B GLU 5.3 2.0 + - - -
276B HIS 3.3 0.6 - - - -
277B PHE* 1.3 82.5 - - - +
279B SER* 1.3 61.3 + - - +
282B HIS* 3.4 11.1 + - - +
315B MET* 6.1 3.1 - - - -
319B MET* 3.2 38.0 - - - +
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Residues in contact with SER 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B HIS* 3.2 20.9 + - - +
278B SER* 1.3 78.0 - - - +
280B CYS* 1.3 64.3 + - - +
282B HIS* 3.4 5.8 + - - +
283B GLN* 3.2 38.8 + - - +
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Residues in contact with CYS 280 (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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236B GLN* 6.0 0.2 - - - -
239B PHE* 3.7 51.4 - - + -
243B ILE* 4.1 5.7 - - - +
274B TYR* 4.0 12.8 - - - -
276B HIS* 2.8 32.9 + - - +
277B PHE* 3.7 5.4 - - - +
279B SER* 1.3 70.4 - - - +
281B LEU* 1.3 60.9 + - - +
283B GLN* 3.3 13.1 + - - +
284B VAL* 2.9 34.0 + - - +
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Residues in contact with LEU 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B PHE* 5.8 0.9 - - - -
277B PHE* 2.7 47.5 + - + +
278B SER 4.1 1.3 - - - +
280B CYS* 1.3 72.4 - - - +
282B HIS* 1.3 57.9 + - - +
284B VAL* 3.2 7.4 + - + +
285B LEU* 2.9 29.2 + - + +
303B LEU* 3.8 27.4 - - + -
306B PHE* 3.9 23.3 - - + -
315B MET* 4.0 2.0 - - + -
316B LEU* 3.7 39.0 - - + +
319B MET* 3.8 24.2 - - + -
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Residues in contact with HIS 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B SER 3.4 16.2 + - - +
279B SER* 3.8 6.7 - - - +
280B CYS 3.3 0.8 - - - -
281B LEU* 1.3 78.0 - - - +
283B GLN* 1.3 62.4 + - + +
285B LEU* 3.6 10.7 + - + +
286B GLY* 3.3 15.8 + - - -
319B MET* 3.6 30.9 - - + +
340B PRO* 5.5 8.3 - - + -
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Residues in contact with GLN 283 (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 ILE* 3.5 39.7 - - + +
244B ASN* 5.1 3.8 + - - +
279B SER* 3.2 33.2 + - - +
280B CYS* 3.6 10.7 - - - +
282B HIS* 1.3 77.2 - - + +
284B VAL* 1.3 64.6 + - - +
286B GLY* 3.1 13.2 + - - -
287B LEU* 3.1 19.0 + - - +
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Residues in contact with VAL 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B PHE* 4.3 23.1 - - + -
242B LEU* 4.5 15.9 - - + -
243B ILE* 4.4 11.9 - - + -
280B CYS 2.9 23.9 + - - +
281B LEU* 3.2 9.2 + - + +
283B GLN* 1.3 73.7 - - - +
285B LEU* 1.3 63.6 + - - +
287B LEU* 3.2 24.2 + - + +
299B VAL* 3.6 24.3 - - + +
302B LEU* 4.6 15.0 - - + -
303B LEU* 4.3 18.6 - - + -
306B PHE* 5.0 2.9 - - + -
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Residues in contact with LEU 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B LEU* 2.9 14.6 + - + +
282B HIS* 3.7 11.9 - - + +
283B GLN 3.3 0.2 - - - -
284B VAL* 1.3 74.3 - - - +
286B GLY* 1.3 62.5 + - - +
288B LEU* 3.1 43.1 + - + +
289B ASN* 3.9 5.2 - - - +
303B LEU* 4.2 9.6 - - + -
316B LEU* 4.0 26.2 - - + -
319B MET* 3.7 41.1 - - + +
320B MET* 4.1 18.4 - - + -
340B PRO* 4.5 26.6 - - + +
343B ALA* 5.1 0.7 - - - +
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Residues in contact with GLY 286 (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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282B HIS 3.3 8.0 + - - -
283B GLN* 3.1 11.7 + - - -
285B LEU* 1.3 78.5 - - - +
287B LEU* 1.3 61.4 + - - +
289B ASN* 3.3 26.0 + - - +
290B GLY 4.2 1.4 + - - -
339B GLU* 5.6 3.6 - - - -
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Residues in contact with LEU 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B LEU* 3.5 26.7 - - + +
243B ILE* 4.5 19.1 - - + +
251B ARG* 3.3 48.3 + - - +
283B GLN 3.1 28.0 - - - +
284B VAL* 3.2 13.2 + - - +
285B LEU 3.2 1.0 - - - -
286B GLY* 1.3 75.0 - - - +
288B LEU* 1.3 61.5 + - - +
289B ASN 3.2 0.2 - - - -
290B GLY* 3.2 17.4 + - - +
296B SER* 4.2 6.6 + - - -
299B VAL* 3.8 22.2 - - + +
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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