Contacts of the helix formed by residues 272 - 283 (chain A) in PDB entry 1UA4
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 272 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A ASP* 6.4 0.9 - - - -
237A LEU 3.6 20.4 + - - +
238A THR* 3.3 11.6 - - + +
239A LYS* 2.8 36.2 + - - +
270A THR* 3.4 3.6 - - + +
271A PRO* 1.3 79.5 - - + +
273A GLU* 1.3 57.2 + - - +
274A LYS* 2.9 35.3 + - - +
275A VAL* 3.0 12.1 + - + +
276A ARG* 2.9 27.4 + - - +
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Residues in contact with GLU 273 (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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271A PRO 3.1 3.8 + - - +
272A ASP* 1.3 73.0 + - - +
274A LYS* 1.3 61.3 + - - +
276A ARG* 3.4 32.7 + - - +
277A GLU* 3.1 24.5 + - - +
301A GLU* 4.0 16.1 - - - +
302A ILE* 4.1 16.0 - - + +
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Residues in contact with LYS 274 (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 LYS* 3.9 27.6 - - + -
242A TYR* 3.6 24.8 + - + -
272A ASP* 2.9 11.5 + - - +
273A GLU* 1.3 78.5 - - - +
275A VAL* 1.3 58.1 + - - +
277A GLU* 3.2 18.4 + - + +
278A GLU* 2.9 56.0 + - + +
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Residues in contact with VAL 275 (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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234A LEU 3.7 22.9 - - - +
237A LEU* 3.3 29.8 - - + +
238A THR* 3.3 28.9 - - - +
239A LYS* 3.8 1.6 - - - +
242A TYR* 3.9 11.4 - - + -
246A PHE* 4.2 15.3 - - + -
270A THR* 4.1 7.9 - - + -
272A ASP* 3.0 12.2 + - + +
274A LYS* 1.3 72.9 - - - +
276A ARG* 1.3 67.2 - - - +
278A GLU* 3.0 8.6 + - - +
279A ILE* 2.9 24.9 + - + +
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Residues in contact with ARG 276 (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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267A PHE* 4.1 22.3 - - + -
269A PHE* 6.1 1.6 - - - -
270A THR* 2.9 34.6 + - + +
271A PRO* 3.3 20.2 + - - +
272A ASP 2.9 12.0 + - - +
273A GLU* 3.6 21.0 - - - +
274A LYS 3.3 0.2 - - - -
275A VAL* 1.3 77.1 - - - +
277A GLU* 1.3 61.1 + - - +
279A ILE* 3.4 7.8 + - - +
280A LEU* 3.3 24.8 + - - +
298A SER* 2.8 61.7 + - - -
299A ILE* 4.3 2.0 - - + +
301A GLU* 2.9 24.0 + - - -
302A ILE* 3.6 23.0 - - + +
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Residues in contact with GLU 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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273A GLU 3.1 13.4 + - - +
274A LYS* 3.4 20.2 + - + +
275A VAL 3.1 0.2 - - - -
276A ARG* 1.3 75.3 - - - +
278A GLU* 1.3 70.8 + - - +
280A LEU* 3.2 10.9 + - + +
281A ASN* 3.0 34.9 + - - +
302A ILE* 3.8 24.3 - - + +
333A LYS* 6.5 1.3 - - - -
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Residues in contact with GLU 278 (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 TYR* 3.5 32.3 - - + -
246A PHE* 3.7 23.5 - - + -
274A LYS* 2.9 47.5 + - - +
275A VAL* 3.0 8.0 + - - +
277A GLU* 1.3 77.4 - - - +
279A ILE* 1.3 65.7 + - - +
281A ASN* 3.2 33.0 + - - +
282A VAL* 3.4 15.6 + - - +
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Residues in contact with ILE 279 (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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234A LEU* 3.9 28.9 - - + -
235A GLN* 4.6 0.9 - - + +
246A PHE* 3.8 15.9 - - + -
265A LEU* 3.6 31.4 - - + -
267A PHE* 3.6 22.7 - - + -
270A THR* 4.0 22.9 - - + +
275A VAL* 2.9 26.0 + - + +
276A ARG* 3.5 6.7 - - - +
277A GLU 3.2 0.2 - - - -
278A GLU* 1.3 77.6 - - - +
280A LEU* 1.3 62.4 + - - +
282A VAL* 3.1 15.2 + - + +
283A LEU* 3.1 19.8 + - + +
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Residues in contact with LEU 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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267A PHE* 4.2 15.0 - - + -
276A ARG 3.3 10.5 + - - +
277A GLU* 3.2 11.1 + - + +
279A ILE* 1.3 79.9 - - - +
281A ASN* 1.3 64.4 + - - +
283A LEU* 3.1 23.3 + - + -
284A GLY 4.5 0.3 + - - -
299A ILE* 4.0 21.3 - - + -
302A ILE* 3.5 29.8 - - + -
303A LEU* 4.1 17.7 - - + -
330A LEU* 3.8 27.6 - - + -
333A LYS* 5.3 10.3 - - + -
334A THR* 3.4 22.8 - - + +
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Residues in contact with ASN 281 (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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277A GLU* 3.0 31.8 + - - +
278A GLU* 3.4 36.4 + - - +
279A ILE 3.2 0.4 - - - -
280A LEU* 1.3 78.8 - - - +
282A VAL* 1.3 62.1 + - + +
283A LEU 3.5 0.2 - - - -
284A GLY 4.9 1.7 + - - -
333A LYS* 5.0 11.4 + - - -
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Residues in contact with VAL 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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234A LEU* 5.3 5.4 - - + -
246A PHE* 4.4 13.7 - - + -
249A VAL* 6.3 1.3 - - + -
250A LYS* 4.1 32.3 - - + +
253A LEU* 5.1 3.1 - - + -
278A GLU 3.6 12.3 - - - +
279A ILE* 3.1 20.2 - - + +
281A ASN* 1.3 81.7 - - + +
283A LEU* 1.3 64.5 + - - +
284A GLY 3.1 3.1 - - - -
285A MET* 3.0 36.2 + - - +
286A PHE* 3.5 17.3 - - + -
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Residues in contact with LEU 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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265A LEU* 3.7 27.4 - - + -
267A PHE* 4.8 5.4 - - + -
279A ILE* 3.1 14.6 + - + +
280A LEU* 3.1 23.5 + - + +
282A VAL* 1.3 72.4 - - - +
284A GLY* 1.3 56.9 + - - +
285A MET 3.0 5.6 - - - -
286A PHE* 2.9 45.4 + - + +
289A VAL* 4.1 27.1 - - + -
330A LEU* 4.0 29.8 - - + -
334A THR* 3.7 16.8 - - + +
336A VAL* 4.0 8.8 - - + +
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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