Contacts of the helix formed by residues 233 - 246 (chain A) in PDB entry 3UGM
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 SER 233 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207A ALA* 5.6 1.0 - - - +
231A GLN* 3.1 0.6 + - - -
232A TRP* 1.3 106.7 + - - +
234A GLY* 1.3 63.7 + - - +
235A ALA 3.7 1.3 - - - -
236A ARG* 3.7 15.7 + - - +
237A ALA* 3.0 20.5 + - - +
268A GLY* 3.6 9.2 - - - -
269A VAL* 3.2 31.6 + - - -
-2B T 5.0 5.7 + - - -
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Residues in contact with GLY 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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207A ALA* 4.8 5.6 - - - +
209A THR* 5.5 0.6 - - - +
228A VAL* 3.4 24.4 - - - +
229A GLY* 3.6 14.8 - - - -
231A GLN* 3.0 11.5 + - - -
233A SER* 1.3 74.3 - - - +
235A ALA* 1.3 64.5 + - - +
237A ALA* 3.0 8.2 + - - +
238A LEU* 2.9 22.6 + - - +
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Residues in contact with ALA 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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209A THR* 3.9 35.3 + - + +
210A TYR 6.5 0.7 - - - -
229A GLY* 4.6 2.0 - - - -
234A GLY* 1.3 72.3 - - - +
236A ARG* 1.3 58.2 + - + +
238A LEU* 2.7 33.1 + - - +
239A GLU* 3.0 25.2 + - + +
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Residues in contact with ARG 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A TRP* 4.7 0.2 - - - -
233A SER* 3.7 25.1 + - - +
234A GLY 3.4 0.8 - - - -
235A ALA* 1.3 78.8 - - + +
237A ALA* 1.3 57.3 - - - +
239A GLU* 4.1 12.5 - - - +
240A ALA* 3.1 20.8 + - - +
269A VAL* 3.1 37.6 - - + +
273A GLU* 5.5 2.2 + - - -
-2B T 4.3 26.0 + - - -
-1B A 2.7 34.7 + - - -
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Residues in contact with ALA 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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228A VAL* 4.5 6.1 - - + +
233A SER* 3.0 22.0 + - - +
234A GLY* 3.0 9.6 + - - +
235A ALA 2.9 0.6 - - - -
236A ARG* 1.3 77.4 - - - +
238A LEU* 1.3 61.8 + - - +
241A LEU* 3.1 8.5 + - - +
264A ALA* 4.3 17.2 - - + +
269A VAL* 3.7 19.9 - - - +
272A MET* 2.7 33.8 - - + +
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Residues in contact with LEU 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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210A TYR 6.0 1.3 - - - +
211A GLN 5.4 7.6 - - - +
225A ILE* 4.1 39.7 - - + +
228A VAL* 3.8 20.9 - - + -
229A GLY* 4.7 9.4 - - - -
234A GLY 2.9 14.5 + - - +
235A ALA* 2.7 21.4 + - - +
237A ALA* 1.3 71.7 - - - +
239A GLU* 1.3 56.9 + - + +
241A LEU* 3.2 31.7 - - + +
242A LEU* 3.2 9.9 + - - +
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Residues in contact with GLU 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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213A ILE* 5.6 5.9 - - - +
235A ALA* 3.0 27.6 + - - +
236A ARG* 4.1 10.8 - - + +
238A LEU* 1.3 74.2 - - + +
240A ALA* 1.3 66.0 + - - +
241A LEU 3.2 1.3 - - - -
242A LEU* 2.8 41.2 + - + +
243A THR* 3.2 1.0 + - - -
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Residues in contact with ALA 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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236A ARG 3.1 20.3 + - - +
238A LEU 3.6 0.2 - - - -
239A GLU* 1.3 73.9 - - - +
241A LEU* 1.3 56.4 - - - +
243A THR* 2.7 29.3 + - - +
244A ASP 3.0 9.7 + - - -
269A VAL* 3.9 14.6 - - + +
272A MET* 3.7 23.6 - - + -
273A GLU* 5.1 5.8 - - + +
276A HIS* 3.4 12.9 + - + +
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Residues in contact with LEU 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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225A ILE* 5.8 4.9 - - + -
237A ALA 3.1 15.9 + - - +
238A LEU* 3.2 26.9 - - + +
240A ALA* 1.3 74.6 - - - +
242A LEU* 1.3 53.3 + - - +
244A ASP* 3.2 2.5 + - - +
245A ALA* 2.6 45.8 + - + +
260A LEU* 3.4 47.6 - - + +
261A VAL* 5.1 12.8 - - + -
264A ALA* 4.2 7.6 - - + -
272A MET* 3.5 20.1 - - - +
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Residues in contact with LEU 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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215A THR* 5.4 10.1 - - - +
217A LEU* 6.0 2.2 - - - -
238A LEU 3.2 8.0 + - - +
239A GLU* 2.8 31.1 + - + +
241A LEU* 1.3 80.6 - - - +
243A THR* 1.3 74.3 + - - +
245A ALA* 4.4 4.9 - - - -
246A GLY* 3.3 19.8 + - - -
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Residues in contact with THR 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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239A GLU 3.2 3.9 + - - -
240A ALA* 2.7 18.8 + - - -
242A LEU* 1.3 89.1 - - - +
244A ASP* 1.3 48.5 + - - -
247A GLU* 2.7 32.7 + - + +
276A HIS* 3.6 18.8 - - + +
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Residues in contact with ASP 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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240A ALA 3.0 5.3 + - - +
241A LEU* 3.9 8.1 - - - +
243A THR* 1.3 77.7 - - - +
245A ALA* 1.3 55.4 + - - +
247A GLU* 2.7 32.0 - - - +
248A LEU* 3.0 4.5 + - - +
253A LEU* 3.2 20.0 - - - +
255A LEU* 5.1 1.4 - - - +
260A LEU* 3.1 33.1 - - + +
272A MET* 4.8 5.2 - - + -
275A VAL* 4.6 8.7 - - - +
276A HIS* 3.2 48.4 + - + +
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Residues in contact with ALA 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A LEU* 4.0 25.4 - - + +
241A LEU* 2.6 35.2 + - + +
242A LEU* 4.3 3.4 - - - +
244A ASP* 1.3 72.9 + - - +
246A GLY* 1.3 59.5 + - - +
247A GLU 3.1 1.1 - - - -
248A LEU* 3.1 17.1 - - + +
249A ARG* 3.0 27.2 + - - +
260A LEU* 5.7 4.0 - - + -
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Residues in contact with GLY 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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217A LEU* 5.0 5.0 - - - +
242A LEU* 3.3 15.3 + - - -
243A THR 4.8 0.2 - - - -
245A ALA* 1.3 72.4 - - - +
247A GLU* 1.3 56.8 + - - +
248A LEU 2.8 10.6 + - - -
249A ARG* 3.6 10.7 + - - -
250A GLY* 4.1 7.4 + - - -
251A PRO* 4.3 3.8 - - - +
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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