Contacts of the helix formed by residues 231 - 243 (chain A) in PDB entry 1O69
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 231 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A VAL* 3.6 4.0 - - - +
54A ASN* 5.9 0.2 - - - +
229A ARG 3.6 2.4 + - - -
230A LEU* 1.3 82.7 - - - +
232A ASN* 1.3 59.5 + - - +
234A LEU* 3.3 26.2 + - - +
235A GLY 2.9 23.4 + - - -
187B THR* 3.4 11.7 - - - +
188B THR 3.4 14.2 + - - -
189B SER 3.6 18.6 - - - -
190B GLY* 4.3 2.0 - - - -
234B LEU* 4.0 11.3 - - - +
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Residues in contact with ASN 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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21A VAL* 3.8 24.5 + - + +
25A ASN* 5.5 5.9 - - - +
29A PRO 5.3 1.4 + - - -
31A GLY* 3.5 14.7 - - - +
32A GLU* 4.1 11.5 + - - +
33A PHE* 2.9 36.1 + - - +
34A VAL* 3.3 12.5 + - - +
231A SER* 1.3 71.8 - - - +
233A VAL* 1.3 58.0 + - - +
235A GLY* 3.1 1.0 + - - -
236A ALA* 2.9 29.5 + - - +
186B ILE* 4.3 4.9 - - + +
187B THR 2.9 18.4 + - - +
188B THR* 3.9 11.6 + - - -
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Residues in contact with VAL 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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18A ILE* 4.2 18.0 - - + +
21A VAL* 4.0 11.0 - - + -
22A PHE* 3.9 20.0 - - + -
231A SER* 4.3 2.5 - - - +
232A ASN* 1.3 76.7 - - - +
234A LEU* 1.3 64.6 + - + +
236A ALA* 3.4 8.8 + - - +
237A ILE* 3.3 19.8 + - - +
188B THR* 2.9 41.4 + - + +
233B VAL* 4.0 27.1 - - + -
234B LEU* 4.4 1.6 - - + -
237B ILE* 4.0 14.1 - - + -
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Residues in contact with LEU 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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54A ASN* 6.4 0.7 - - + -
188A THR* 3.2 30.7 - - - +
190A GLY 3.3 24.0 - - - +
230A LEU* 3.8 22.7 - - + -
231A SER* 3.3 16.7 + - - +
233A VAL* 1.3 74.8 - - - +
235A GLY* 1.3 60.5 + - - +
237A ILE* 3.3 16.1 + - + +
238A GLY 2.9 22.5 + - - -
231B SER* 4.0 16.8 - - - +
233B VAL* 4.1 9.4 - - + -
234B LEU* 3.8 35.2 - - + -
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Residues in contact with GLY 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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33A PHE 3.8 19.1 - - - -
34A VAL* 4.3 2.7 - - - -
37A PHE* 3.7 8.0 - - - +
230A LEU* 3.7 17.6 - - - +
231A SER 2.9 13.4 + - - -
232A ASN 3.1 4.4 + - - -
234A LEU* 1.3 75.7 - - - +
236A ALA* 1.3 55.3 + - - +
238A GLY* 3.1 2.6 + - - -
239A VAL* 2.9 31.9 + - - +
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Residues in contact with ALA 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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14A GLU 5.3 0.7 - - - -
17A TYR* 3.6 35.8 - - + +
18A ILE* 4.1 4.3 - - + +
21A VAL* 3.8 19.1 - - + -
33A PHE* 3.6 14.7 - - + +
232A ASN 2.9 12.0 + - - +
233A VAL 3.4 10.1 - - - +
235A GLY* 1.3 72.7 - - - +
237A ILE* 1.3 65.2 + - - +
239A VAL* 3.3 4.9 + - - +
240A ALA* 3.2 17.5 + - - +
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Residues in contact with ILE 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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14A GLU* 4.1 18.4 - - + -
18A ILE* 3.7 21.5 - - + -
187A THR* 3.2 25.1 - - + +
188A THR* 3.4 23.8 - - - +
189A SER* 4.7 0.7 - - - +
233A VAL 3.3 7.8 + - - +
234A LEU* 3.3 23.2 + - + +
236A ALA* 1.3 75.0 - - - +
238A GLY* 1.3 57.0 + - - +
240A ALA* 3.2 3.1 + - - +
241A GLN* 2.8 38.9 + - + +
22B PHE* 3.9 24.0 - - + -
233B VAL* 4.0 12.6 - - + -
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Residues in contact with GLY 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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37A PHE* 3.5 20.1 - - - -
180A TYR* 5.5 0.2 - - - -
188A THR* 3.4 21.9 - - - +
234A LEU 2.9 11.1 + - - -
235A GLY 3.1 5.1 + - - -
237A ILE* 1.3 75.6 - - - +
239A VAL* 1.3 56.0 + - - +
241A GLN* 3.8 4.0 - - - +
242A MET* 2.9 35.0 + - - +
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Residues in contact with VAL 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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17A TYR* 3.6 22.9 - - + -
33A PHE* 3.7 12.8 - - + +
36A ARG* 3.8 32.3 - - + +
37A PHE* 3.5 27.6 - - - +
40A SER* 4.7 6.8 + - - -
235A GLY 2.9 20.8 + - - +
236A ALA 3.3 7.1 + - - +
238A GLY* 1.3 74.1 - - - +
240A ALA* 1.3 63.5 + - - +
242A MET* 3.3 7.9 + - - +
243A GLU* 3.2 30.8 + - + +
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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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12A GLY* 5.6 0.9 - - - -
13A ASN 3.7 11.7 + - - +
14A GLU* 3.5 46.6 - - + +
17A TYR* 3.8 9.6 - - + -
236A ALA 3.2 2.5 + - - +
237A ILE 3.2 8.8 + - - +
239A VAL* 1.3 79.0 - - - +
241A GLN* 1.3 61.9 + - - +
243A GLU* 3.3 26.8 + - - +
244A VAL* 3.8 8.8 + - - +
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Residues in contact with GLN 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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14A GLU* 2.4 34.8 + - - +
186A ILE* 3.2 34.4 - - + +
187A THR* 2.8 47.8 + - - +
237A ILE* 2.8 20.6 + - + +
238A GLY* 3.8 7.2 - - - +
240A ALA* 1.3 74.8 - - - +
242A MET* 1.3 64.7 + - - +
244A VAL* 3.0 15.5 + - - +
245A LEU 3.3 3.8 + - - -
248A ARG* 2.9 38.7 + - - +
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Residues in contact with MET 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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37A PHE* 3.8 9.2 - - + -
40A SER* 3.2 38.6 - - - +
41A VAL* 4.0 17.0 - - + -
44A TYR* 3.6 36.5 - - + -
160A LEU* 3.8 27.1 - - + -
180A TYR* 4.1 7.0 - - + -
186A ILE* 4.8 0.9 - - - -
238A GLY 2.9 20.7 + - - +
239A VAL 3.3 4.9 + - - +
241A GLN* 1.3 74.8 - - - +
243A GLU* 1.3 61.8 + - + +
244A VAL 3.3 0.5 + - - -
245A LEU* 3.4 32.4 + - + +
246A GLU 4.9 0.7 + - - -
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Residues in contact with GLU 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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13A ASN* 2.7 32.6 + - - +
17A TYR* 2.6 30.1 + - - -
36A ARG* 4.8 1.4 + - - -
239A VAL* 3.2 22.1 + - + +
240A ALA* 3.4 10.8 - - - +
241A GLN 3.1 1.2 - - - -
242A MET* 1.3 75.8 - - - +
244A VAL* 1.3 64.2 + - + +
245A LEU 3.6 0.2 - - - -
246A GLU 5.4 0.3 + - - -
247A GLN* 3.4 14.6 + - - -
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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