Contacts of the helix formed by residues 276 - 287 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232A HIS* 4.0 25.7 + + - -
236A GLN* 5.2 5.0 + - - -
274A TYR* 3.4 27.2 - + + +
275A GLU* 1.3 86.0 + - + +
277A PHE* 1.3 58.7 + - - +
278A SER 3.3 2.9 - - - -
279A SER* 3.2 16.1 + - - +
280A CYS* 2.8 33.7 + - - -
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Residues in contact with PHE 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A PHE* 4.1 9.0 - + - -
271A LEU* 3.7 42.4 - - + +
272A THR 5.2 1.3 - - - +
274A TYR* 3.5 26.6 + - + +
275A GLU 3.5 0.6 - - - -
276A HIS* 1.3 77.6 - - - +
278A SER* 1.3 56.2 + - - +
280A CYS* 4.2 2.2 - - - -
281A LEU* 2.7 70.7 + - + +
306A PHE* 4.0 26.2 - + + -
312A LEU* 3.6 28.3 - - + -
315A MET* 3.6 30.3 - - + -
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Residues in contact with SER 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A TYR 5.1 0.2 + - - -
275A GLU 5.3 2.0 + - - -
276A HIS 3.3 1.0 - - - -
277A PHE* 1.3 81.5 - - - +
279A SER* 1.3 61.4 + - - +
282A HIS* 3.4 12.0 + - - +
315A MET* 5.6 5.6 - - - -
319A MET* 3.1 37.2 - - - +
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Residues in contact with SER 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A HIS* 3.2 21.1 + - - -
278A SER* 1.3 78.0 - - - +
280A CYS* 1.3 64.1 + - - +
282A HIS* 3.4 5.8 + - - +
283A GLN* 3.2 38.9 + - - +
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Residues in contact with CYS 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A GLN* 6.0 0.4 - - - -
239A PHE* 3.7 50.3 - - + -
243A ILE* 4.1 5.2 - - - +
274A TYR* 4.0 13.5 - - - -
276A HIS* 2.8 32.3 + - - +
277A PHE* 3.7 6.1 - - - +
279A SER* 1.3 72.3 - - - +
281A LEU* 1.3 61.1 + - - +
283A GLN* 3.3 13.2 + - - +
284A VAL* 2.9 33.6 + - - +
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Residues in contact with LEU 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A PHE* 5.8 0.7 - - - -
277A PHE* 2.7 45.0 + - + +
278A SER 4.1 1.3 - - - +
280A CYS* 1.3 73.2 - - - +
282A HIS* 1.3 57.7 + - - +
284A VAL* 3.2 7.0 + - + +
285A LEU* 2.9 29.3 + - + +
303A LEU* 3.8 28.3 - - + -
306A PHE* 3.9 23.1 - - + -
315A MET* 4.0 2.5 - - + -
316A LEU* 3.7 39.3 - - + +
319A MET* 3.8 24.2 - - + -
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Residues in contact with HIS 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A SER 3.4 16.2 + - - +
279A SER* 3.8 6.3 - - - +
280A CYS 3.3 0.8 - - - -
281A LEU* 1.3 78.0 - - - +
283A GLN* 1.3 61.7 + - + +
285A LEU* 3.6 8.1 + - + +
286A GLY* 3.3 16.1 + - - -
319A MET* 3.6 30.5 - - + +
336A LYS 6.0 1.8 + - - -
340A PRO* 5.4 12.1 - - + -
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Residues in contact with GLN 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A ILE* 3.5 38.2 - - + +
244A ASN* 5.0 5.0 + - - +
279A SER* 3.2 32.6 + - - +
280A CYS* 3.6 11.3 - - - +
282A HIS* 1.3 77.9 - - + +
284A VAL* 1.3 61.0 + - - +
286A GLY* 3.1 12.5 + - - +
287A LEU* 3.1 18.5 + - - +
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Residues in contact with VAL 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A PHE* 4.3 22.9 - - + -
242A LEU* 4.6 14.8 - - + -
243A ILE* 4.3 12.3 - - + -
280A CYS 2.9 23.5 + - - +
281A LEU* 3.2 8.3 + - + +
283A GLN* 1.3 73.5 - - - +
285A LEU* 1.3 64.1 + - - +
287A LEU* 3.2 24.0 + - + +
299A VAL* 3.6 24.6 - - + +
302A LEU* 4.6 14.6 - - + -
303A LEU* 4.3 20.2 - - + -
306A PHE* 5.0 3.6 - - + -
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Residues in contact with LEU 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A LEU* 2.9 13.0 + - + +
282A HIS* 3.7 11.0 - - + +
283A GLN 3.3 0.2 - - - -
284A VAL* 1.3 75.6 - - - +
286A GLY* 1.3 61.8 + - - +
288A LEU* 3.1 42.9 + - + +
289A ASN* 3.9 5.2 - - - +
303A LEU* 4.2 10.3 - - + -
316A LEU* 4.0 27.8 - - + -
319A MET* 3.7 39.0 - - + +
320A MET* 4.1 18.6 - - + -
340A PRO* 4.4 29.2 - - + +
343A ALA* 5.0 0.7 - - - +
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Residues in contact with GLY 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A HIS 3.3 7.4 + - - -
283A GLN* 3.1 12.2 + - - -
285A LEU* 1.3 77.2 - - - +
287A LEU* 1.3 61.1 + - - +
289A ASN* 3.3 26.0 + - - +
290A GLY 4.2 1.4 + - - -
339A GLU* 5.5 4.7 - - - -
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Residues in contact with LEU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A LEU* 3.5 28.5 - - + +
243A ILE* 4.2 22.0 - - + +
251A ARG* 3.3 48.6 + - - +
283A GLN 3.1 27.8 - - - +
284A VAL* 3.4 13.5 - - - +
285A LEU 3.2 0.8 - - - -
286A GLY* 1.3 76.3 - - - +
288A LEU* 1.3 62.2 + - - +
289A ASN 3.2 0.2 - - - -
290A GLY* 3.2 17.4 + - - +
296A SER* 4.1 6.4 + - - -
299A VAL* 3.8 19.3 - - + +
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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