Contacts of the helix formed by residues 279 - 294 (chain A) in PDB entry 4UC5
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 ARG 279 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A ASN 5.5 0.2 - - - +
273A SER* 3.8 20.9 - - - +
276A ASP* 2.8 35.8 + - + +
278A THR* 1.3 77.4 - - - +
280A GLN* 1.3 65.5 + - - +
281A MET 3.1 2.0 - - - -
282A GLU* 3.1 46.0 + - + +
283A VAL* 3.1 24.0 + - + +
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Residues in contact with GLN 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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268A CYS* 3.6 28.7 - - + +
269A SER* 3.6 22.4 + - - +
273A SER* 4.1 4.4 - - - -
276A ASP 3.8 0.8 + - - -
277A TYR* 3.1 27.4 + - - +
279A ARG* 1.3 77.7 - - - +
281A MET* 1.3 57.4 + - - +
283A VAL* 3.2 4.0 + - - +
284A ALA* 2.9 28.6 + - - +
303A VAL* 3.5 10.6 - - - +
304A GLU* 2.9 49.7 + - - +
325A ALA 4.2 2.4 + - - -
327A ILE* 3.8 19.4 - - + +
335A LEU* 4.6 8.5 - - + -
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Residues in contact with MET 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A TYR 4.5 0.2 + - - -
278A THR 4.1 11.9 + - - +
279A ARG 3.1 0.6 - - - -
280A GLN* 1.3 79.7 - - - +
282A GLU* 1.3 57.0 + - - +
284A ALA* 3.2 5.6 + - - +
285A GLN* 2.9 48.3 + - - +
327A ILE* 5.5 3.7 - - + +
331A ALA* 4.6 10.1 - - + +
334A GLU* 4.3 26.7 - - + +
335A LEU* 4.0 32.3 - - + +
338A LEU* 3.4 30.5 - - + -
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Residues in contact with GLU 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A TYR* 3.3 22.7 + - - +
272A ASN 5.8 0.2 - - - +
278A THR 4.5 1.5 + - - +
279A ARG* 3.1 56.0 + - - +
281A MET* 1.3 79.2 - - - +
283A VAL* 1.3 63.4 + - - +
285A GLN* 3.1 17.0 + - + +
286A ASP* 3.0 21.5 + - + +
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Residues in contact with VAL 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A TYR* 3.8 40.4 - - + +
266A ILE* 4.4 1.6 - - + -
267A ASP 4.5 0.9 - - - +
268A CYS* 3.7 34.8 - - + +
272A ASN 3.7 22.0 - - - +
279A ARG* 3.1 16.6 + - + +
280A GLN 3.2 6.3 + - - +
282A GLU* 1.3 79.2 - - + +
284A ALA* 1.3 64.9 + - - +
286A ASP* 3.1 3.8 + - - +
287A ILE* 2.9 39.7 + - + +
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Residues in contact with ALA 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A CYS* 4.1 10.9 - - - -
280A GLN 2.9 13.2 + - - +
281A MET* 3.5 8.7 - - - +
283A VAL* 1.3 76.9 - - - +
285A GLN* 1.3 56.8 + - - +
287A ILE* 3.1 9.0 + - - +
288A ALA* 2.9 28.1 + - - +
335A LEU* 3.8 33.2 - - + -
338A LEU* 4.2 9.4 - - + -
339A LEU* 3.8 11.4 - - + +
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Residues in contact with GLN 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A MET* 2.9 37.0 + - - +
282A GLU* 3.4 17.5 - - - +
283A VAL 3.1 0.4 - - - -
284A ALA* 1.3 71.9 - - - +
286A ASP* 1.3 66.3 + - - +
288A ALA* 3.2 5.0 + - - +
289A ALA* 3.0 22.7 + - - +
338A LEU* 3.7 23.0 - - + +
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Residues in contact with ASP 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A TYR* 3.6 28.3 - - + -
244A ASP* 3.8 13.8 - - - +
245A ALA 4.4 0.7 + - - -
282A GLU* 3.0 11.1 + - + +
283A VAL 3.5 7.4 - - - +
285A GLN* 1.3 75.6 - - - +
287A ILE* 1.3 62.7 + - - +
289A ALA* 3.3 9.4 + - - +
290A GLN* 3.0 51.3 + - - +
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Residues in contact with ILE 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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243A TYR* 5.1 2.5 - - + +
266A ILE* 3.6 43.5 - - + -
268A CYS* 4.0 14.8 - - - -
283A VAL* 2.9 29.5 + - + +
284A ALA* 3.1 8.3 + - - +
286A ASP* 1.3 77.3 - - + +
288A ALA* 1.3 55.1 + - - +
290A GLN* 3.3 13.8 + - - +
291A LEU* 3.0 40.6 + - + +
298A ILE* 4.3 18.2 - - + -
301A VAL* 4.2 23.3 - - + -
339A LEU* 4.5 4.0 - - + -
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Residues in contact with ALA 288 (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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284A ALA 2.9 12.7 + - - +
285A GLN 3.2 9.4 + - - +
287A ILE* 1.3 73.2 - - - +
289A ALA* 1.3 58.6 + - - +
291A LEU* 3.1 7.3 + - - +
292A GLU* 2.9 29.6 + - - +
338A LEU* 4.1 26.7 - - + +
339A LEU* 4.5 3.9 - - + +
342A ALA* 3.7 26.1 - - + +
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Residues in contact with ALA 289 (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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285A GLN 3.0 13.6 + - - +
286A ASP* 3.5 13.0 - - - +
288A ALA* 1.3 74.5 - - - +
290A GLN* 1.3 63.7 + - + +
292A GLU* 3.2 7.6 + - - +
293A GLN* 3.0 25.4 + - - +
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Residues in contact with GLN 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A TYR 2.9 25.7 + - - -
245A ALA* 3.5 29.4 - - + +
248A VAL* 3.6 15.8 - - - +
286A ASP* 3.0 36.5 + - - +
287A ILE* 3.3 16.0 + - - +
289A ALA* 1.3 76.0 - - - +
291A LEU* 1.3 55.3 + - - +
293A GLN* 4.0 4.2 - - - +
294A ASP* 2.7 31.0 + - - +
295A GLY* 2.9 14.3 + - - +
298A ILE* 3.5 24.8 - - + +
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Residues in contact with LEU 291 (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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56A LEU* 4.3 16.8 - - + -
287A ILE* 3.0 31.1 + - + +
288A ALA* 3.1 8.5 + - - +
290A GLN* 1.3 74.6 - - - +
292A GLU* 1.3 62.8 + - - +
294A ASP 4.3 3.4 - - - -
295A GLY* 3.9 8.7 - - - +
298A ILE* 4.4 15.7 - - + -
339A LEU* 4.8 5.4 - - + +
342A ALA* 4.2 18.6 - - + +
343A ASN* 4.1 23.1 - - + +
346A ARG* 3.4 49.0 - - + +
349A ARG* 3.4 21.0 + - - -
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Residues in contact with GLU 292 (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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288A ALA 2.9 12.5 + - - +
289A ALA* 3.2 11.2 + - - +
291A LEU* 1.3 75.0 - - - +
293A GLN* 1.3 57.7 + - - +
342A ALA* 4.7 8.7 + - + -
345A LYS* 5.1 17.9 - - + +
349A ARG* 2.7 22.5 + - - +
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Residues in contact with GLN 293 (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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289A ALA 3.0 15.9 + - - +
290A GLN* 4.0 4.7 - - - +
292A GLU* 1.3 78.3 - - - +
294A ASP* 1.3 63.5 + - + +
349A ARG* 4.3 5.7 + - - -
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Residues in contact with ASP 294 (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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290A GLN 2.7 11.2 + - - +
291A LEU 3.9 0.5 - - - +
292A GLU 3.8 1.0 - - - -
293A GLN* 1.3 77.5 - - + +
295A GLY* 1.3 66.1 + - - +
296A GLY* 3.1 14.1 + - - -
346A ARG* 3.7 8.3 - - - -
349A ARG* 3.0 23.9 + - - +
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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