Contacts of the helix formed by residues 272 - 283 (chain A) in PDB entry 6UPR
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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192A ARG* 4.6 9.5 + - - -
196A LYS* 2.8 31.0 + - - -
234A SER* 4.4 9.0 - - - -
237A PHE* 3.7 15.7 - - + -
238A SER* 2.8 39.2 + - - +
239A VAL* 3.7 3.8 - - - -
268A PRO 4.8 2.4 - - - +
271A ASN* 1.3 76.9 - - - +
273A PHE* 1.3 58.7 + - - +
274A LEU 3.4 2.5 - - - -
275A LYS* 3.1 24.7 + - + +
276A LEU* 2.8 28.2 + - - +
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Residues in contact with PHE 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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53A LEU* 3.6 22.4 - - + -
56A SER* 3.5 42.6 - - - -
57A LEU* 3.8 26.2 - - + -
239A VAL* 3.9 9.6 - - + +
240A VAL 4.0 2.2 - - - +
254A ARG* 3.7 15.7 - - - -
265A VAL* 3.4 30.7 + - + +
266A GLU* 4.7 1.6 - - + -
271A ASN* 3.2 22.2 + - - +
272A ASP* 1.3 76.6 - - - +
274A LEU* 1.3 78.6 + - + +
276A LEU* 3.1 4.0 + - + +
277A ARG* 2.8 40.4 + - - +
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Residues in contact with LEU 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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265A VAL 4.8 0.4 + - - -
266A GLU* 3.3 54.1 - - + +
268A PRO* 4.4 19.7 - - + -
271A ASN 5.1 0.8 + - - -
272A ASP 3.4 0.2 - - - -
273A PHE* 1.3 95.8 - - + +
275A LYS* 1.3 59.9 + - + +
277A ARG* 3.9 8.0 - - - +
278A THR* 2.8 39.5 + - - +
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Residues in contact with LYS 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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230A LEU* 3.3 31.2 - - + +
231A LEU* 3.5 29.1 - - + +
234A SER* 3.2 33.7 + - - +
237A PHE* 3.8 13.4 - - + -
268A PRO* 4.9 22.2 + - + +
272A ASP* 3.1 24.0 + - - +
274A LEU* 1.3 79.1 - - + +
276A LEU* 1.3 58.2 + - - +
278A THR* 4.6 1.3 - - - -
279A MET* 3.1 27.2 + - - +
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Residues in contact with LEU 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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53A LEU* 3.8 30.3 - - + -
57A LEU* 4.8 9.4 - - + -
150A PHE* 3.9 27.4 - - + -
178A VAL* 4.3 7.4 - - + -
180A VAL* 4.4 9.2 - - + -
237A PHE* 3.6 27.7 - - + -
239A VAL* 4.0 17.5 - - + -
272A ASP 2.8 13.4 + - - +
273A PHE* 3.6 6.7 - - - +
275A LYS* 1.3 75.6 - - - +
277A ARG* 1.3 66.8 + - - +
279A MET* 3.2 17.8 + - + +
280A LEU* 3.0 21.0 + - - +
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Residues in contact with ARG 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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56A SER 5.5 0.2 - - - -
57A LEU* 3.1 46.7 + - + +
58A PHE* 4.5 14.4 - - + +
273A PHE* 2.8 38.0 + - + +
274A LEU* 3.9 10.1 - - + +
276A LEU* 1.3 73.5 - - - +
278A THR* 1.3 62.8 + - - +
280A LEU* 3.3 5.6 + - + +
281A ILE* 3.1 55.4 + - + +
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Residues in contact with THR 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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227A GLN* 3.5 39.3 - - + +
231A LEU* 4.3 8.1 - - + -
274A LEU* 2.8 27.0 + - - +
275A LYS* 4.2 4.5 - - - -
277A ARG* 1.3 74.8 - - - +
279A MET* 1.3 55.1 + - - +
281A ILE* 4.6 5.2 - - - +
282A THR* 2.6 43.0 + - + +
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Residues in contact with MET 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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150A PHE* 4.8 4.3 - - + -
178A VAL* 4.1 18.8 - - + -
211A TYR* 4.5 17.0 - - - -
213A LEU* 3.9 36.1 - - + -
231A LEU* 3.9 11.2 - - + +
237A PHE* 3.8 20.2 - - + -
275A LYS 3.1 21.0 + - - +
276A LEU* 3.2 28.7 + - + +
278A THR* 1.3 78.1 - - - +
280A LEU* 1.3 74.9 + - + +
282A THR* 4.0 1.6 - - - -
283A HIS* 3.1 34.3 + - + +
287A LEU* 5.2 4.3 - - + -
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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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38A PHE* 4.1 19.3 - - + -
40A LEU* 4.8 9.6 - - + -
57A LEU* 4.7 10.5 - - + -
58A PHE* 4.1 24.0 - - + -
97A LEU* 6.1 0.4 - - + -
148A CYS* 4.8 2.0 - - - -
150A PHE* 4.4 28.7 - - + -
276A LEU* 3.0 14.4 + - + +
277A ARG* 3.8 6.3 - - + +
278A THR 3.3 0.4 - - - -
279A MET* 1.3 85.8 - - + +
281A ILE* 1.3 59.1 + - - +
283A HIS 3.7 0.2 - - - -
284A MET* 3.0 54.8 + - + +
287A LEU* 4.0 21.5 - - + -
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Residues in contact with ILE 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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58A PHE* 4.8 17.5 - - + -
277A ARG* 3.1 60.3 + - + +
278A THR* 4.1 4.9 - - - +
280A LEU* 1.3 79.2 - - + +
282A THR* 1.3 70.7 + - + +
283A HIS 3.3 0.7 + - - -
284A MET* 3.5 21.2 + - - +
285A GLN 5.2 0.2 + - - -
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Residues in contact with THR 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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224A PHE* 5.0 13.8 - - + -
227A GLN* 4.1 20.7 + - - +
231A LEU* 4.7 0.7 - - - +
278A THR* 2.6 30.8 + - + +
279A MET* 4.0 0.3 - - - -
281A ILE* 1.3 83.4 - - + +
283A HIS* 1.3 80.4 + - - +
284A MET 3.6 0.4 + - - -
285A GLN* 5.3 1.4 + - - +
286A ASP 5.7 0.2 + - - -
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Residues in contact with HIS 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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211A TYR* 3.8 16.1 + - + +
213A LEU* 3.8 21.7 - - + +
214A PRO* 3.4 39.0 - - + +
224A PHE* 5.2 14.0 - + - -
227A GLN* 5.9 0.4 + - - -
228A THR* 5.3 6.8 + - + +
231A LEU* 4.5 5.6 - - + +
279A MET* 3.1 33.1 + - + +
280A LEU 3.7 2.0 - - - -
282A THR* 1.3 103.0 + - - +
284A MET* 1.3 64.6 + - - +
285A GLN 3.3 2.2 - - - -
286A ASP* 3.3 8.6 + - - +
287A LEU* 2.9 29.3 + - + +
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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