Contacts of the helix formed by residues 245 - 255 (chain A) in PDB entry 3OYG
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 LEU 245 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231A LEU* 3.9 16.4 - - + -
234A LEU* 3.9 34.3 - - + +
235A LEU* 3.6 33.9 - - + -
241A LYS 4.1 9.2 - - - +
242A TRP* 2.8 11.8 + - - +
244A ASP* 1.3 83.4 - - + +
246A LEU* 1.3 64.8 + - - +
247A PRO* 3.3 2.9 - - - -
248A VAL* 2.9 20.0 + - + +
249A VAL* 2.9 24.6 + - + +
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Residues in contact with LEU 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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142A VAL* 4.0 24.5 - - + -
155A LEU* 3.7 29.8 - - + +
156A TYR 4.2 2.9 - - - -
157A PRO* 3.7 44.2 - - + -
227A ILE* 5.2 1.6 - - + -
231A LEU* 4.5 18.2 - - + -
242A TRP* 3.2 24.1 + - + +
243A TYR 3.3 8.9 + - - +
245A LEU* 1.3 76.3 - - - +
247A PRO* 1.4 71.5 - - + +
249A VAL* 3.2 3.6 + - + +
250A GLN* 2.8 24.7 + - - +
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Residues in contact with PRO 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 TYR 3.8 6.3 - - - +
244A ASP* 3.7 12.3 - - - +
245A LEU 3.5 3.6 - - - -
246A LEU* 1.4 94.1 - - + +
248A VAL* 1.3 63.9 + - + +
250A GLN* 3.3 7.1 + - + +
251A LEU* 3.0 24.5 + - - +
171B ASN* 5.0 6.1 - - + +
172B VAL* 6.3 0.9 - - - -
175B SER* 3.9 26.3 - - - +
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Residues in contact with VAL 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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234A LEU* 5.0 12.1 - - + -
244A ASP 4.1 13.9 - - - +
245A LEU* 2.9 22.8 + - + +
247A PRO* 1.3 75.5 - - + +
249A VAL* 1.3 59.3 + - + +
251A LEU* 3.4 8.2 + - + +
252A ALA* 2.8 34.5 + - + +
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Residues in contact with VAL 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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155A LEU* 4.3 12.3 - - + -
227A ILE* 4.2 19.7 - - + +
230A LEU* 4.0 26.2 - - + -
231A LEU* 3.7 26.5 - - + +
234A LEU* 4.4 11.4 - - + -
245A LEU 2.9 17.2 + - - +
246A LEU* 3.7 7.0 - - + +
248A VAL* 1.3 72.8 - - - +
250A GLN* 1.3 66.8 + - - +
252A ALA 3.0 1.0 + - - -
253A LEU* 2.8 45.9 + - + +
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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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153A THR* 3.3 26.7 - - - +
154A TRP* 3.5 6.9 - - - +
155A LEU* 2.9 46.5 + - + +
156A TYR* 5.8 0.5 - - - -
246A LEU 2.8 16.7 + - - +
247A PRO* 3.4 10.5 - - + +
249A VAL* 1.3 75.4 - - - +
251A LEU* 1.3 64.1 + - - +
253A LEU* 3.4 3.2 + - - +
254A ASN* 3.0 31.8 + - - +
175B SER* 2.8 40.0 + - - -
176B ILE* 3.7 15.7 - - - +
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Residues in contact with LEU 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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247A PRO 3.0 13.5 + - - +
248A VAL* 3.8 9.0 - - + +
250A GLN* 1.3 79.3 - - - +
252A ALA* 1.3 64.1 + - - +
254A ASN* 3.5 3.1 + - + -
255A ASN* 2.9 52.5 + - - +
274A SER* 5.6 0.2 - - - +
276A THR* 4.2 14.8 - - + -
277A PRO* 6.5 0.2 - - + -
174B THR 3.9 23.6 - - - +
175B SER* 3.9 20.2 + - - +
176B ILE 4.5 9.9 - - - +
177B ALA* 5.3 0.9 - - - -
178B ILE* 4.1 17.0 - - + -
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Residues in contact with ALA 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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230A LEU* 3.7 22.0 - - + -
248A VAL* 2.8 22.6 + - + +
249A VAL 3.0 3.6 + - - +
251A LEU* 1.3 78.4 - - - +
253A LEU* 1.3 61.1 - - - +
255A ASN* 3.4 4.2 + - - +
256A THR* 2.8 26.7 + - - +
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Residues in contact with LEU 253 (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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153A THR* 5.8 3.8 - - + -
155A LEU* 6.0 0.4 - - + -
223A LYS* 4.5 20.1 + - + +
226A ASP* 3.9 22.4 - - + +
227A ILE* 3.7 44.6 - - + +
230A LEU* 4.0 17.9 - - + -
249A VAL* 2.8 30.1 + - + +
250A GLN* 4.0 3.8 - - - +
252A ALA* 1.3 69.7 - - - +
254A ASN* 1.3 63.4 + - - +
255A ASN 3.0 6.3 + - - -
256A THR* 3.1 25.0 + - + +
265A PRO* 3.8 10.6 - - - +
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Residues in contact with ASN 254 (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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151A GLY 4.2 0.9 - - - +
152A PHE* 3.4 38.6 - - + -
153A THR* 2.6 54.4 + - - -
223A LYS* 5.5 0.5 + - - -
250A GLN* 3.0 31.1 + - - +
251A LEU* 4.1 5.3 - - + +
253A LEU* 1.3 75.7 - - - +
255A ASN* 1.3 62.2 + - - +
256A THR 3.5 0.4 - - - -
265A PRO* 3.1 12.4 - - - +
266A HIS* 2.9 31.2 + - + +
175B SER 4.9 1.8 + - - -
176B ILE 6.0 0.4 - - - +
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Residues in contact with ASN 255 (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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251A LEU* 2.9 48.7 + - + +
252A ALA* 3.7 5.2 - - - +
253A LEU 3.0 1.2 - - - -
254A ASN* 1.3 83.4 - - - +
256A THR* 1.3 55.7 + - - +
257A TYR* 4.0 3.3 + - - -
264A THR* 3.4 20.3 + - - +
266A HIS* 3.5 31.1 + - - +
273A ASP* 4.5 5.4 - - - +
274A SER* 5.4 0.4 + - - -
276A THR* 3.9 26.1 + - - +
176B ILE 5.3 1.0 + - - -
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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