Contacts of the helix formed by residues 233 - 247 (chain A) in PDB entry 1UMZ
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 233 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231A ASP 3.8 1.2 + - - -
232A LEU* 1.3 75.3 - - - +
234A ALA* 1.3 64.3 + - - +
235A PHE* 3.1 13.3 + - - +
236A GLN* 2.9 39.5 + - - +
237A TYR* 3.0 20.2 + - - -
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Residues in contact with ALA 234 (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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233A ASP* 1.3 74.9 - - - +
235A PHE* 1.3 62.7 + - - +
237A TYR* 3.4 9.7 + - - +
238A ARG* 3.1 44.6 + - + +
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Residues in contact with PHE 235 (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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233A ASP* 3.1 12.6 + - - +
234A ALA* 1.3 77.8 - - - +
236A GLN* 1.3 69.1 + - + +
238A ARG* 3.2 32.1 + - + +
239A ARG* 3.2 75.8 + - + +
17B PRO 5.2 4.9 - - - -
18B THR* 4.9 7.6 - - - -
21B PHE* 3.9 21.8 - + - -
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Residues in contact with GLN 236 (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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142A LEU* 5.3 6.6 - - - +
145A ASP 5.5 3.5 - - - +
147A PRO* 3.7 26.6 - - + +
231A ASP 4.7 1.0 + - - -
232A LEU* 3.3 28.7 - - + +
233A ASP* 2.9 47.4 + - - +
235A PHE* 1.3 85.1 - - + +
237A TYR* 1.3 56.7 + - - +
239A ARG* 3.5 10.0 + - - +
240A LEU* 3.0 26.7 + - - +
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Residues in contact with TYR 237 (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 VAL* 4.9 4.9 - - + +
152A LYS* 3.9 11.4 - - - -
231A ASP* 2.5 30.8 + - - -
232A LEU* 3.1 40.4 + - + +
233A ASP 3.0 23.9 + - - -
234A ALA* 3.8 10.8 - - - +
235A PHE 3.3 0.2 - - - -
236A GLN* 1.3 73.9 - - - +
238A ARG* 1.3 61.9 + - + +
240A LEU* 3.6 16.7 - - + +
241A SER* 3.0 27.4 + - - -
268A ARG 4.6 3.2 + - - -
269A ASP* 4.9 1.7 - - - -
270A ARG* 3.4 63.8 + - + +
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Residues in contact with ARG 238 (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 ALA* 3.1 41.5 + - - +
235A PHE* 3.5 43.2 - - + +
237A TYR* 1.3 74.5 - - + +
239A ARG* 1.3 66.2 + - + +
241A SER* 3.2 7.0 + - - -
242A TRP* 3.1 22.5 + - - +
46B GLN* 4.8 20.6 + - - +
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Residues in contact with ARG 239 (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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145A ASP* 3.2 58.5 + - - +
146A VAL* 4.2 22.3 - - + +
147A PRO* 4.3 5.9 - - + +
235A PHE* 3.2 58.7 + - + +
236A GLN* 3.7 10.0 - - - +
238A ARG* 1.3 77.4 - - + +
240A LEU* 1.3 60.5 + - - +
242A TRP* 3.3 9.6 + - - +
243A VAL* 3.2 26.0 + - - +
18B THR 4.8 6.7 - - - +
19B TRP* 4.1 17.6 - - + +
20B ALA 6.1 0.4 - - - +
21B PHE* 4.0 21.0 - - - -
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Residues in contact with LEU 240 (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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147A PRO* 3.6 16.5 + - + +
148A ILE* 3.4 35.9 - - - +
149A ARG* 3.6 4.7 - - - +
150A VAL* 3.8 27.1 - - + +
232A LEU* 4.4 1.8 - - + -
236A GLN 3.0 16.3 + - - +
237A TYR* 3.6 23.3 - - + +
239A ARG* 1.3 77.2 - - - +
241A SER* 1.3 62.2 + - - +
243A VAL* 3.2 5.3 + - - +
244A ARG* 3.0 41.6 + - + +
269A ASP 3.8 17.0 - - - +
270A ARG* 4.5 7.0 - - + +
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Residues in contact with SER 241 (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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237A TYR 3.0 17.9 + - - -
238A ARG* 3.2 8.2 + - - -
240A LEU* 1.3 76.7 - - - +
242A TRP* 1.3 57.8 + - - +
244A ARG* 3.3 8.8 + - - +
245A GLN* 2.8 44.0 + - - +
270A ARG 5.8 0.7 - - - -
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Residues in contact with TRP 242 (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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238A ARG 3.1 12.4 + - - +
239A ARG* 3.4 9.9 - - - +
241A SER* 1.3 75.3 - - - +
243A VAL* 1.3 59.9 + - - +
245A GLN* 4.4 5.8 - - + +
246A LYS* 2.8 74.9 + - + +
247A TYR* 4.0 12.3 + + - -
18B THR* 6.4 2.9 - - + -
19B TRP* 3.3 60.9 - + + +
174B TRP* 6.3 3.1 - - + -
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Residues in contact with VAL 243 (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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117A ILE* 4.0 29.4 - - + -
120A TRP* 4.2 9.2 - - + -
146A VAL* 3.9 23.3 - - + -
147A PRO 3.9 6.7 - - - +
148A ILE* 4.2 19.3 - - + +
239A ARG 3.4 13.5 - - - +
240A LEU* 3.2 8.9 + - - +
242A TRP* 1.3 75.5 - - - +
244A ARG* 1.3 62.6 + - - +
247A TYR* 3.0 27.7 + - + -
248A THR* 2.8 19.8 + - - +
19B TRP* 4.1 11.2 - - + -
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Residues in contact with ARG 244 (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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115A GLN* 3.5 22.9 + - - +
117A ILE* 3.9 12.9 - - - +
148A ILE 2.8 28.6 + - - -
149A ARG* 4.2 0.8 - - - +
240A LEU* 3.0 29.0 + - + +
241A SER* 3.4 11.9 - - - +
243A VAL* 1.3 80.0 - - - +
245A GLN* 1.3 72.2 + - - +
248A THR* 2.9 46.2 + - - +
251A ASN* 4.2 13.1 - - - +
270A ARG 3.7 18.6 - - - +
271A ASP* 3.3 36.6 + - - +
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Residues in contact with GLN 245 (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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241A SER* 2.8 32.0 + - - +
242A TRP* 3.2 8.0 + - + +
244A ARG* 1.3 85.8 + - - +
246A LYS* 1.3 74.3 + - + +
248A THR 5.2 1.4 - - - +
272A ILE* 5.3 5.0 - - - +
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Residues in contact with LYS 246 (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 TRP* 2.8 62.4 + - + +
245A GLN* 1.3 87.9 - - + +
247A TYR* 1.3 78.4 + - + +
248A THR 3.7 1.8 - - - -
174B TRP* 4.6 23.4 - - - +
4F XYS 5.2 10.1 - - - -
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Residues in contact with TYR 247 (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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117A ILE* 3.1 4.3 - - + -
118A TYR* 2.9 61.3 + - + +
119A LEU 3.8 12.3 - - - -
120A TRP* 3.5 14.6 - + + +
242A TRP* 4.0 19.0 + + - -
243A VAL* 3.0 23.1 + - + +
246A LYS* 1.3 91.4 - - + +
248A THR* 1.3 61.1 + - - +
249A ILE* 3.7 4.0 + - - +
19B TRP* 3.7 24.9 + + - -
40B TYR 2.9 29.0 + - - -
41B THR* 3.1 23.4 + - - -
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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