Contacts of the helix formed by residues 236 - 250 (chain A) in PDB entry 1O7F
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 236 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228A ILE* 3.7 16.5 - - - +
233A CYS 4.0 1.8 + - - -
234A VAL* 2.8 10.4 + - - +
235A HIS* 1.3 77.8 - - - +
237A ARG* 1.3 62.8 - - - +
238A THR* 2.9 23.3 + - - -
239A GLN* 3.2 16.1 + - - +
240A ALA* 3.4 14.9 + - - +
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Residues in contact with ARG 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 THR* 3.5 20.2 + - - +
224A VAL* 3.4 20.7 - - + +
225A ASP* 2.9 29.0 + - - -
228A ILE* 3.8 15.0 - - + +
236A SER* 1.3 72.5 - - - +
238A THR* 1.3 68.5 + - + +
240A ALA* 2.9 6.4 + - - +
241A VAL* 2.8 25.3 + - - +
264A ASP* 2.8 45.2 + - - +
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Residues in contact with THR 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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236A SER* 2.9 14.2 + - - -
237A ARG* 1.3 79.1 - - + +
239A GLN* 1.3 69.1 + - - -
241A VAL* 2.9 16.8 + - - +
242A GLY 3.1 9.7 + - - -
309A HIS* 3.2 20.7 + - - +
324A ASP* 2.9 33.0 + - + +
328A ILE* 4.4 10.7 - - + +
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Residues in contact with GLN 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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234A VAL* 2.4 45.8 + - + +
235A HIS* 3.9 12.5 + - - +
236A SER* 3.2 13.3 + - - +
238A THR* 1.3 81.5 + - - +
240A ALA* 1.3 62.0 + - - +
242A GLY* 3.2 3.5 + - - -
243A MET* 3.1 35.4 + - + +
302A SER* 3.4 26.8 + - - +
305A GLY* 5.6 0.3 - - - -
306A PRO* 6.3 3.4 - - + -
309A HIS* 5.1 3.1 - - - -
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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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224A VAL* 3.8 28.0 - - + +
227A MET* 4.1 22.2 - - + -
228A ILE* 4.4 8.1 - - + -
234A VAL* 4.1 4.2 - - + +
236A SER 3.4 10.8 + - - +
237A ARG 2.9 12.5 + - - +
239A GLN* 1.3 81.2 - - - +
241A VAL* 1.3 59.8 + - - +
243A MET* 3.2 3.0 + - - +
244A TRP* 3.0 29.3 + - + -
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Residues in contact with VAL 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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224A VAL* 4.1 7.4 - - + -
237A ARG 2.8 18.5 + - - +
238A THR* 2.9 11.0 + - - +
240A ALA* 1.3 76.5 - - - +
242A GLY* 1.3 63.4 + - - +
244A TRP 3.2 1.0 + - - -
245A GLN* 2.9 21.5 + - - +
262A PHE* 3.6 35.6 - - + +
264A ASP* 3.6 33.7 - - + +
309A HIS* 3.9 7.6 - - + +
312A MET* 3.8 17.5 - - + -
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Residues in contact with GLY 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 THR 3.1 10.9 + - - -
239A GLN 3.2 3.3 + - - -
241A VAL* 1.3 77.0 - - - +
243A MET* 1.3 63.1 + - - +
245A GLN* 3.2 8.1 + - - +
246A VAL* 3.1 24.6 + - - +
305A GLY* 4.0 12.4 - - - +
308A ALA* 4.1 0.7 - - - +
309A HIS* 3.7 31.6 - - - -
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Residues in contact with MET 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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227A MET* 3.7 24.9 - - + +
234A VAL* 4.1 14.8 - - + -
239A GLN* 3.1 33.4 + - + +
240A ALA 3.2 6.9 + - - +
242A GLY* 1.3 77.9 - - - +
244A TRP* 1.3 62.0 + - - +
246A VAL* 3.4 17.1 - - - +
247A LEU* 4.0 8.1 + - - +
298A MET* 3.4 39.9 - - + +
301A LEU* 3.5 40.1 - - + +
302A SER* 3.7 13.9 - - - +
305A GLY* 4.4 4.7 - - - -
306A PRO* 6.0 0.2 - - + -
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Residues in contact with TRP 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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192A LEU* 3.8 27.8 - - + -
196A ILE* 4.0 13.5 - - + -
223A LEU* 3.2 56.5 + - + -
224A VAL* 3.8 4.2 - - + +
226A TRP* 4.3 7.2 - + - -
227A MET* 3.8 26.1 - - + +
240A ALA 3.0 28.0 + - - +
243A MET* 1.3 74.2 - - - +
245A GLN* 1.3 66.2 + - - +
247A LEU* 2.9 30.9 + - + +
248A LEU* 3.1 11.3 + - - +
253A LEU* 3.6 20.9 - - + +
262A PHE* 3.5 43.3 - + + -
271A PHE* 3.9 15.5 - + - -
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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 VAL 2.9 14.3 + - - +
242A GLY* 3.3 14.4 - - - +
244A TRP* 1.3 76.7 - - - +
246A VAL* 1.3 64.2 + - - +
248A LEU* 2.9 6.8 + - - +
249A GLU* 2.8 45.4 + - + +
260A ARG 3.2 20.8 + - - -
261A HIS* 3.5 1.3 - - - +
262A PHE* 2.7 35.7 + - + +
308A ALA* 4.1 22.4 + - + +
312A MET* 3.4 29.7 - - + +
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Residues in contact with VAL 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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185A ILE* 3.8 26.6 - - + +
242A GLY 3.1 14.7 + - - +
243A MET* 3.4 13.5 - - - +
244A TRP 3.1 0.4 - - - -
245A GLN* 1.3 76.7 - - - +
247A LEU* 1.3 67.2 + - + +
249A GLU* 3.7 16.9 - - - +
250A ASP* 3.7 12.3 - - - +
301A LEU* 4.6 10.1 - - + +
304A MET* 3.4 48.2 - - + +
305A GLY* 3.9 2.7 - - - +
308A ALA* 3.7 12.8 - - + -
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Residues in contact with LEU 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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185A ILE* 3.9 20.9 - - + +
188A ALA* 4.2 15.5 - - + +
189A GLY* 4.4 11.4 - - - +
192A LEU* 4.1 15.3 - - + -
243A MET 4.1 7.4 - - - +
244A TRP* 2.9 40.5 + - + +
246A VAL* 1.3 85.1 - - + +
248A LEU* 1.3 62.0 + - - +
250A ASP 3.4 1.4 + - - -
251A GLY 3.2 4.5 + - - -
252A VAL* 3.0 52.8 + - + +
253A LEU* 3.9 9.0 - - + -
271A PHE* 4.7 5.6 - - + -
301A LEU* 4.6 7.9 - - + -
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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 TRP 3.1 9.8 + - - +
245A GLN* 2.9 17.5 + - - +
247A LEU* 1.3 80.2 - - - +
249A GLU* 1.3 61.3 + - - +
251A GLY* 3.4 8.8 + - - -
253A LEU* 2.9 25.8 + - + +
254A ASN* 4.3 5.3 - - - +
255A HIS 4.1 6.1 - - - +
259A GLU 3.9 8.7 - - - +
260A ARG* 3.0 36.6 - - - +
261A HIS 4.2 1.6 - - - -
262A PHE* 4.0 16.8 - - + +
269A TYR* 3.5 38.1 - - + -
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Residues in contact with GLU 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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185A ILE* 5.7 3.0 - - + +
245A GLN* 2.8 37.0 + - - +
246A VAL* 3.7 11.0 - - - +
248A LEU* 1.3 74.4 - - - +
250A ASP* 1.3 64.1 + - + +
251A GLY 3.1 5.9 + - - -
260A ARG 5.1 1.6 - - - +
304A MET* 6.1 1.0 - - - +
308A ALA* 4.0 13.8 - - - +
311A ARG* 2.9 42.5 + - - -
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Residues in contact with ASP 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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180A VAL 3.8 5.8 - - - +
181A PRO* 3.1 26.4 - - - +
182A SER* 2.8 46.2 + - - -
185A ILE* 3.0 39.0 - - + +
246A VAL 3.7 7.4 + - - +
247A LEU 3.4 1.7 + - - +
248A LEU 3.3 0.6 - - - -
249A GLU* 1.3 79.9 - - + +
251A GLY* 1.3 57.6 + - - +
252A VAL 3.4 0.9 - - - -
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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