Contacts of the helix formed by residues 227 - 240 (chain A) in PDB entry 2H0A
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 227 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225A ARG* 2.9 15.2 + - - +
226A HIS* 1.3 75.2 - - - +
228A GLN* 1.3 63.3 + - - +
229A GLU* 3.4 21.3 + - - +
230A GLY* 3.0 19.9 + - - -
231A GLY 3.4 8.5 + - - -
254A GLN* 4.0 13.2 - - - -
255A VAL* 3.3 19.8 - - - +
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Residues in contact with GLN 228 (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 SER* 1.3 73.1 - - - +
229A GLU* 1.3 77.8 + - - +
231A GLY 3.2 1.7 + - - -
232A ARG* 3.0 23.9 + - - +
254A GLN* 2.9 40.2 - - - +
257A LEU* 3.8 29.9 + - - +
258A GLY* 3.2 16.3 - - - -
261A GLU* 3.5 22.4 + - - +
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Residues in contact with GLU 229 (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 SER* 3.2 18.9 + - - +
228A GLN* 1.3 90.1 - - - +
230A GLY* 1.3 57.1 + - - +
232A ARG* 3.2 22.8 + - - +
233A LEU* 2.8 41.3 + - + +
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Residues in contact with GLY 230 (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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222A TYR* 4.2 0.2 - - - -
224A THR* 3.3 36.3 - - - +
225A ARG* 4.3 1.1 - - - -
227A SER* 3.0 18.9 + - - -
228A GLN 3.2 0.2 - - - -
229A GLU* 1.3 77.3 - - - +
231A GLY* 1.3 56.0 + - - +
233A LEU* 3.3 9.3 + - - +
234A ALA* 2.9 29.8 + - - +
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Residues in contact with GLY 231 (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 SER 3.4 7.5 + - - -
228A GLN 3.2 4.7 + - - -
230A GLY* 1.3 76.8 - - - +
232A ARG* 1.3 56.2 + - - +
234A ALA* 3.3 4.6 + - - +
235A LEU* 3.0 25.6 + - - +
255A VAL* 3.4 35.9 - - - +
259A VAL* 3.6 18.8 - - - +
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Residues in contact with ARG 232 (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 GLN* 3.0 18.6 + - - +
229A GLU* 3.2 23.1 + - - +
231A GLY* 1.3 74.9 - - - +
233A LEU* 1.3 68.1 + - + +
235A LEU* 3.4 1.7 + - - +
236A ARG* 3.2 24.2 + - - +
258A GLY 3.2 20.4 - - - +
261A GLU* 3.0 30.8 + - - -
262A GLU* 3.1 32.9 + - + +
265A ARG* 3.3 30.7 - - - +
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Residues in contact with LEU 233 (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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222A TYR* 3.8 21.0 + - + +
224A THR* 5.3 2.5 - - - +
229A GLU* 2.8 30.0 + - + +
230A GLY* 3.5 9.6 - - - +
232A ARG* 1.3 76.4 - - - +
234A ALA* 1.3 56.7 + - - +
236A ARG* 3.3 8.9 - - + +
237A HIS* 3.0 26.0 + - - +
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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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183A ILE* 3.7 24.5 - - + -
222A TYR* 3.4 33.4 - - + -
230A GLY 2.9 14.3 + - - +
231A GLY 3.5 5.2 - - - +
233A LEU* 1.3 73.3 - - - +
235A LEU* 1.3 66.1 + - - +
236A ARG 3.1 1.3 - - - -
237A HIS* 2.8 15.0 + - - +
238A PHE* 2.8 23.4 + - + -
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Residues in contact with LEU 235 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231A GLY 3.0 15.9 + - - +
232A ARG 3.4 4.0 + - - +
234A ALA* 1.3 75.8 - - - +
236A ARG* 1.3 57.7 + - - +
238A PHE* 3.3 8.0 + - + +
239A LEU* 2.9 55.1 + - + +
246A LEU* 4.7 3.6 - - + -
248A VAL* 4.5 5.2 - - + -
259A VAL* 3.3 39.4 - - + +
262A GLU* 3.9 9.4 - - + -
263A ALA* 3.5 28.5 - - + +
273A ASP* 4.0 2.9 - - - +
274A VAL* 3.2 31.9 - - + -
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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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232A ARG 3.2 9.3 + - - +
233A LEU* 3.3 16.2 - - + +
234A ALA 3.1 0.8 - - - -
235A LEU* 1.3 79.7 - - - +
237A HIS* 1.3 63.0 + - - +
239A LEU* 3.5 17.7 + - + +
240A GLU* 3.5 26.2 + - - +
262A GLU* 4.0 22.9 + - + +
265A ARG* 5.4 8.9 - - - +
266A LEU* 6.1 4.4 - - + +
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Residues in contact with HIS 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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221A LEU 4.5 7.6 + - - -
222A TYR* 3.4 37.8 - + + -
233A LEU 3.0 13.8 + - - +
234A ALA 2.8 9.1 + - - +
236A ARG* 1.3 74.3 - - - +
238A PHE* 1.3 75.7 + + - +
240A GLU* 2.9 38.7 + - + +
241A LYS* 3.2 36.9 + - - +
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Residues in contact with PHE 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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181A PHE* 3.1 51.7 - + + -
182A ALA 3.6 19.5 - - - -
183A ILE* 3.8 10.8 - - + -
220A ARG 3.8 8.1 - - - -
221A LEU 4.4 0.7 - - - -
222A TYR* 3.6 27.6 - - + -
234A ALA* 2.8 29.1 + - + -
235A LEU* 3.7 10.5 - - - +
237A HIS* 1.3 82.7 - + - +
239A LEU* 1.3 56.5 + - - +
241A LYS* 2.9 21.7 + - - +
242A ALA* 3.0 13.2 + - - +
246A LEU* 4.0 14.5 - - + +
248A VAL* 3.9 29.4 - - + -
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Residues in contact with LEU 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 LEU* 2.9 44.6 + - + +
236A ARG* 3.8 14.1 - - + +
237A HIS 3.2 0.6 - - - -
238A PHE* 1.3 75.9 - - - +
240A GLU* 1.3 59.3 + - - +
241A LYS 3.2 0.9 - - - -
242A ALA 3.1 25.2 + - - +
243A SER* 5.1 0.3 - - - -
244A PRO* 4.6 10.5 - - + -
246A LEU* 4.1 15.5 - - + -
262A GLU* 6.0 1.1 - - + -
266A LEU* 4.1 25.1 - - + -
273A ASP* 3.6 23.3 - - - +
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Residues in contact with GLU 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* 3.5 23.5 + - - +
237A HIS* 2.9 35.3 + - + +
239A LEU* 1.3 77.8 - - - +
241A LYS* 1.3 62.2 + - + +
242A ALA 3.6 0.2 - - - -
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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