Contacts of the helix formed by residues 234 - 249 (chain A) in PDB entry 4OSV
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 GLY 234 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232A TRP* 3.2 36.5 - - - -
233A SER* 1.3 79.2 + - - +
235A ALA* 1.3 63.4 + - - +
236A ARG 3.4 0.4 - - - -
237A ALA* 3.4 11.1 + - - +
238A LEU* 3.0 20.4 + - - +
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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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231A GLN* 3.7 24.9 - - + +
232A TRP* 3.2 30.8 + - + +
233A SER 3.1 1.0 - - - -
234A GLY* 1.3 77.5 - - - +
236A ARG* 1.3 62.9 + - - +
238A LEU* 3.2 6.3 + - - +
239A GLU* 3.1 24.2 + - - +
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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
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231A GLN* 5.2 6.3 - - - +
233A SER 3.9 9.2 + - - +
234A GLY 3.4 0.2 - - - -
235A ALA* 1.3 79.0 - - - +
237A ALA* 1.3 58.5 + - - +
239A GLU* 3.3 8.1 + - - +
240A ALA* 3.0 27.8 + - - +
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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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233A SER 4.7 1.0 + - - +
234A GLY* 3.4 13.9 + - - +
235A ALA 3.3 0.4 - - - -
236A ARG* 1.3 79.4 - - - +
238A LEU* 1.3 57.2 + - - +
240A ALA* 3.3 8.9 - - - +
241A LEU* 2.8 29.3 + - - +
269A VAL* 4.1 18.1 - - + +
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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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232A TRP* 4.6 16.2 - - + -
234A GLY 3.0 17.4 + - - +
235A ALA* 3.6 6.3 - - - +
237A ALA* 1.3 73.8 - - - +
239A GLU* 1.3 61.2 + - - +
241A LEU* 3.3 13.8 + - + +
242A LEU* 2.8 61.7 + - + +
269A VAL* 5.9 0.2 - - - -
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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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235A ALA 3.1 12.3 + - - +
236A ARG* 3.6 9.4 - - - +
238A LEU* 1.3 73.3 - - - +
240A ALA* 1.3 55.1 + - - +
242A LEU* 3.1 8.3 + - + +
243A THR* 2.7 50.0 + - - +
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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 3.0 14.5 + - - +
237A ALA* 3.3 13.7 - - - +
239A GLU* 1.3 76.1 - - - +
241A LEU* 1.3 64.5 + - - +
243A THR* 3.3 4.9 + - - -
244A VAL* 3.1 30.8 + - + +
269A VAL* 4.6 4.5 - - + -
273A GLU* 4.4 14.6 - - - +
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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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237A ALA 2.8 17.7 + - - +
238A LEU* 3.3 18.2 - - + +
240A ALA* 1.3 73.4 - - - +
242A LEU* 1.3 73.9 + - + +
244A VAL* 4.1 2.2 - - - +
245A ALA* 2.9 34.7 + - + +
260A LEU 5.7 0.7 - - - +
264A ALA* 4.2 21.1 - - + -
269A VAL* 3.8 28.9 - - + +
272A VAL* 3.5 39.5 - - + -
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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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238A LEU* 2.8 50.3 + - + +
239A GLU* 3.8 7.4 - - + +
241A LEU* 1.3 83.7 - - + +
243A THR* 1.3 65.4 + - - +
245A ALA* 3.4 7.6 - - + +
246A GLY* 3.1 19.6 + - - -
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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* 2.7 38.4 + - - +
240A ALA* 3.7 6.0 - - - -
242A LEU* 1.3 74.2 - - - +
244A VAL* 1.3 70.1 + - + +
246A GLY* 3.4 5.5 + - - -
247A GLU* 3.3 26.4 + - + +
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Residues in contact with VAL 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* 3.1 18.5 + - + +
241A LEU* 4.2 2.5 - - - +
243A THR* 1.3 77.8 - - + +
245A ALA* 1.3 63.7 + - - +
247A GLU* 3.3 20.4 + - - +
248A LEU* 3.4 13.1 + - + +
272A VAL* 4.1 17.7 - - + +
273A GLU* 4.1 28.0 - - + +
276A HIS* 3.6 38.6 - - + +
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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
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241A LEU* 2.9 28.5 + - + +
242A LEU* 3.4 14.4 - - + +
243A THR 3.2 0.2 - - - -
244A VAL* 1.3 77.2 - - - +
246A GLY* 1.3 63.7 + - - +
248A LEU* 3.1 19.3 + - - +
249A ARG* 3.7 8.5 + - - +
260A LEU* 3.9 28.3 - - + +
272A VAL* 4.4 8.0 - - + +
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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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242A LEU 3.1 12.1 + - - -
243A THR 3.4 3.7 + - - -
245A ALA* 1.3 78.7 - - - +
247A GLU* 1.3 60.6 + - - +
249A ARG* 3.4 32.5 - - - +
250A GLY 4.3 0.9 + - - -
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Residues in contact with GLU 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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243A THR* 3.3 26.1 - - + +
244A VAL* 3.5 12.9 - - - +
245A ALA 3.1 0.8 + - - -
246A GLY* 1.3 72.0 - - - +
248A LEU* 1.3 53.8 + - - +
249A ARG 3.1 5.2 - - - -
250A GLY* 2.7 30.0 + - - -
251A PRO 4.9 1.9 - - - +
276A HIS* 3.1 39.6 + - + +
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Residues in contact with LEU 248 (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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244A VAL 3.4 10.5 + - - +
245A ALA 3.1 9.2 + - - +
247A GLU* 1.3 77.0 - - - +
249A ARG* 1.3 60.2 + - - +
250A GLY 3.1 10.5 - - - +
251A PRO 5.9 0.4 - - - -
253A LEU* 3.9 26.7 - - + +
254A GLN 3.2 12.1 + - - -
255A LEU* 3.3 19.2 + - + +
260A LEU* 4.1 18.8 - - + -
263A ILE* 5.9 1.3 - - + -
272A VAL* 3.6 40.2 - - + +
275A VAL* 4.1 5.8 - - + -
276A HIS* 3.6 36.8 - - + +
279A ARG* 4.8 6.1 - - - +
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Residues in contact with ARG 249 (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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245A ALA* 3.8 6.9 - - - +
246A GLY* 3.4 25.3 - - - +
247A GLU 3.1 0.2 - - - -
248A LEU* 1.3 72.7 - - - +
250A GLY* 1.3 61.1 + - - +
254A GLN* 3.1 25.9 + - - +
255A LEU 3.6 27.6 + - - +
256A ASP* 4.1 2.6 - - - +
257A THR* 2.7 36.6 + - - +
260A LEU* 3.7 21.0 - - + +
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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