Contacts of the helix formed by residues 237 - 252 (chain A) in PDB entry 1OJ7
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 ASN 237 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A GLU* 3.0 46.2 + - + +
235A PRO 3.4 0.4 - - - -
236A GLU* 1.3 73.7 - - - +
238A TYR* 1.3 64.7 + - - +
239A ASP* 3.1 20.3 + - - +
240A VAL* 3.2 24.4 + - + +
241A ARG* 3.0 24.6 + - - +
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Residues in contact with TYR 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PHE* 4.2 4.2 - - - -
15A GLY* 3.3 11.6 - - - -
16A LYS* 3.1 43.1 + - + +
177A PRO* 3.7 29.7 - - + +
178A VAL* 4.0 10.1 - - + -
181A TYR* 3.3 25.1 - - - +
236A GLU 3.2 6.2 + - - +
237A ASN* 1.3 71.8 + - - +
239A ASP* 1.3 72.7 + - - +
241A ARG* 3.3 1.2 + - - +
242A ALA* 2.8 37.1 + - + +
0D GLY* 5.6 1.1 - - - -
1D LEU* 4.4 23.0 + - + +
3D ASN* 4.1 3.8 + - - -
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Residues in contact with ASP 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ASN* 3.1 8.4 + - - +
238A TYR* 1.3 89.6 - - - +
240A VAL* 1.3 63.8 + - + +
242A ALA* 3.8 4.1 - - - +
243A ASN* 3.0 31.0 + - - -
-2D LYS 4.2 8.5 - - - +
-1D ALA 4.0 9.7 - - - +
0D GLY* 3.4 25.6 - - - -
1D LEU 4.5 1.6 + - - -
209D ASP* 3.5 32.7 - - + +
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Residues in contact with VAL 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A ASP* 3.3 41.7 - - + +
230A LYS* 3.7 27.1 - - + +
231A ALA* 3.5 24.7 - - + +
234A GLU* 4.9 1.1 - - - +
237A ASN* 3.2 35.2 + - + +
239A ASP* 1.3 78.0 - - - +
241A ARG* 1.3 61.8 + - - +
243A ASN* 3.3 3.8 + - - +
244A VAL* 3.1 22.7 + - - +
209D ASP* 5.2 4.7 - - - +
211D LYS* 5.5 0.2 - - - +
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Residues in contact with ARG 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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140A PRO* 5.4 3.6 - - - +
177A PRO* 4.1 6.4 - - + +
180A THR* 2.8 56.4 + - - +
181A TYR* 3.7 20.8 + - + +
183A LEU* 3.7 5.5 + - - +
188A VAL* 3.6 28.1 - - - +
231A ALA* 3.8 31.3 + - - +
234A GLU 4.4 1.1 - - - -
235A PRO* 2.8 54.3 + - - +
237A ASN 3.0 20.4 + - - +
238A TYR 3.9 3.1 - - - +
240A VAL* 1.3 74.7 - - - +
242A ALA* 1.3 57.7 + - - +
244A VAL* 3.4 8.2 + - - +
245A MET* 3.0 29.5 + - - +
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Residues in contact with ALA 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PHE* 3.9 15.2 - - + -
177A PRO* 3.7 25.3 - - + +
238A TYR* 2.8 28.9 + - + +
239A ASP* 3.8 6.1 - - - +
241A ARG* 1.3 75.8 - - - +
243A ASN* 1.3 59.9 + - - +
245A MET* 3.8 1.3 - - - +
246A TRP* 3.0 32.6 + - - +
1D LEU* 4.6 12.5 - - + +
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Residues in contact with ASN 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A THR* 4.2 12.5 - - + +
227A ASP* 2.8 30.1 + - + +
239A ASP 3.0 18.4 + - - +
240A VAL 3.6 2.2 - - - +
242A ALA* 1.3 75.1 - - - +
244A VAL* 1.3 60.4 + - - +
246A TRP* 4.1 2.9 - - - +
247A ALA* 3.0 31.0 + - - +
1D LEU* 5.7 2.3 - - - +
209D ASP* 3.4 31.6 + - - +
210D ALA* 3.8 2.9 - - - -
211D LYS* 3.0 33.0 + - - +
212D ILE* 4.2 7.6 + - - +
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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
----------------------------------------------------------
140A PRO* 4.5 18.6 - - + +
188A VAL* 5.6 2.9 - - + +
191A GLY 5.7 0.4 - - - -
192A VAL* 4.1 22.2 - - + +
223A THR* 5.7 0.7 - - + +
224A LEU* 4.6 11.0 - - + +
227A ASP* 4.0 29.8 - - + +
228A GLY* 4.1 7.9 - - - +
231A ALA* 4.3 12.3 - - + -
240A VAL 3.1 15.2 + - - +
241A ARG* 3.9 9.6 - - - +
242A ALA 3.3 0.2 - - - -
243A ASN* 1.3 73.0 - - - +
245A MET* 1.3 66.8 + - - +
247A ALA* 3.3 6.8 + - - +
248A ALA* 3.0 23.8 + - + +
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Residues in contact with MET 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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14A PHE* 4.3 7.2 - - + -
137A LEU* 3.7 34.8 - - + +
140A PRO* 3.6 20.4 - - + +
145A GLU* 4.6 0.5 - - - +
175A LEU* 3.8 26.5 - - + +
176A ASP 3.8 14.4 - - - +
177A PRO* 3.6 28.5 - - + -
180A THR* 3.6 25.8 - - + -
241A ARG 3.0 18.6 + - - +
242A ALA* 3.8 4.9 - - - +
244A VAL* 1.3 76.3 - - - +
246A TRP* 1.3 63.5 + - - +
248A ALA* 3.3 4.5 + - - +
249A THR* 3.2 24.5 + - - -
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Residues in contact with TRP 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ILE* 3.8 26.5 - - + -
14A PHE* 3.9 21.0 - + + -
175A LEU* 4.1 2.5 - - + -
242A ALA 3.0 18.3 + - - +
243A ASN* 4.2 3.4 - - - +
245A MET* 1.3 73.9 - - - +
247A ALA* 1.3 64.1 + - - +
249A THR* 3.3 26.3 + - + -
250A GLN* 3.0 52.6 + - + +
1D LEU* 5.6 3.1 - - + -
4D PHE* 3.8 30.1 - + - -
6D LEU* 4.0 15.5 - - + -
212D ILE* 3.8 27.0 - - + +
213D HIS* 3.4 31.5 + + - -
255D LEU* 3.8 21.5 - - + +
258D ALA* 5.2 0.2 - - + -
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Residues in contact with ALA 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A ALA* 4.8 1.3 - - - -
220A ILE* 4.0 8.4 - - + +
223A THR* 4.6 3.6 - - + -
224A LEU* 3.8 27.4 - - + -
243A ASN 3.0 20.8 + - - +
244A VAL 3.3 4.5 + - - +
246A TRP* 1.3 76.3 - - - +
248A ALA* 1.3 56.5 + - - +
250A GLN* 3.3 3.9 + - - +
251A ALA* 3.0 28.8 + - - +
212D ILE* 3.7 26.3 - - + +
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Residues in contact with ALA 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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140A PRO* 3.9 9.9 - - + +
141A ALA* 3.8 29.5 - - - +
142A THR 4.6 1.3 - - - +
143A GLY* 3.7 16.1 + - - +
145A GLU* 4.4 3.1 - - - +
191A GLY 5.2 0.4 - - - +
195A ALA* 3.8 23.7 - - + +
244A VAL* 3.0 17.4 + - + +
245A MET 3.7 4.3 - - - +
246A TRP 3.3 0.2 - - - -
247A ALA* 1.3 75.8 - - - +
249A THR* 1.3 62.6 + - - +
251A ALA* 3.4 13.3 + - - +
252A LEU* 4.0 1.2 + - - +
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Residues in contact with THR 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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12A ILE* 4.6 5.4 - - + -
143A GLY* 4.5 2.5 - - - -
145A GLU* 2.6 28.1 + - + +
146A SER* 3.4 22.0 + - - +
175A LEU* 3.3 16.4 - - + +
245A MET* 3.2 13.8 + - - +
246A TRP* 3.5 32.4 - - + -
248A ALA* 1.3 79.2 - - - +
250A GLN* 1.3 66.0 + - - +
251A ALA 3.4 0.5 + - - -
252A LEU 3.6 8.1 + - - -
253A ASN* 3.6 17.7 + - - +
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Residues in contact with GLN 250 (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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220A ILE* 3.7 20.9 - - + +
246A TRP* 3.0 54.2 + - - +
247A ALA* 3.3 4.9 + - - +
249A THR* 1.3 78.4 - - - +
251A ALA* 1.3 63.0 + - - +
252A LEU 3.3 1.0 + - - -
253A ASN* 3.5 32.1 + - - +
255A LEU* 4.3 6.9 - - - +
256A ILE* 4.1 13.5 - - - +
212D ILE* 4.2 11.9 - - + -
216D PHE* 4.0 11.5 - - + -
255D LEU* 3.8 32.4 - - - +
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Residues in contact with ALA 251 (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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195A ALA* 3.6 20.0 - - + +
198A HIS* 4.0 9.8 - - + +
199A THR* 3.6 19.5 - - - +
202A GLN* 2.7 31.9 + - - -
220A ILE* 4.0 9.9 - - + -
247A ALA 3.0 16.7 + - - +
248A ALA 3.7 8.1 - - - +
249A THR 3.2 0.8 - - - -
250A GLN* 1.3 78.5 - - - +
252A LEU* 1.3 54.8 + - + +
256A ILE* 3.6 7.3 - - - +
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Residues in contact with LEU 252 (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 THR 3.6 16.6 - - - +
143A GLY* 4.0 5.4 - - - +
147A ASN* 3.1 25.4 + - + +
198A HIS* 3.6 38.6 - - + +
202A GLN* 3.7 25.6 - - - +
248A ALA 4.0 1.6 + - - -
249A THR 3.6 5.5 + - - -
251A ALA* 1.3 79.0 - - + +
253A ASN* 1.3 60.6 + - - +
254A GLY* 3.4 5.8 + - - +
262A GLN* 5.8 0.2 - - - +
264A TRP* 3.8 23.1 - - + -
1388A NZQ 3.7 19.1 - - + +
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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
------------------------------------------------------------
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