Contacts of the helix formed by residues 265 - 275 (chain C) in PDB entry 4OE5
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 ASP 265 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77C ASP* 5.8 0.4 - - - +
96C TYR* 3.5 33.5 + - + +
97C ALA 4.9 1.4 + - - -
264C ALA* 1.3 74.5 - - - +
266C GLY* 1.3 60.5 + - - +
267C PRO* 3.2 19.3 - - - +
268C LEU* 3.1 38.5 + - + +
269C PHE* 2.9 29.0 + - - +
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Residues in contact with GLY 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207C ILE* 6.2 1.5 - - - +
210C PHE* 5.9 5.9 - - - +
233C LYS* 4.3 18.5 - - - +
264C ALA 3.4 4.7 + - - -
265C ASP* 1.3 71.1 + - - +
267C PRO* 1.3 67.7 - - - +
269C PHE* 3.2 2.9 + - - +
270C GLY* 2.8 27.9 + - - -
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Residues in contact with PRO 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265C ASP* 3.2 16.6 - - - +
266C GLY* 1.3 87.8 - - - +
268C LEU* 1.3 56.7 + - - +
270C GLY* 3.3 1.8 + - - +
271C ASP* 2.9 40.3 + - - +
293C HIS* 6.2 5.4 - - + +
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Residues in contact with LEU 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C ALA 4.2 12.1 - - - +
98C ASP* 4.8 3.4 - - - -
99C LYS* 3.9 25.1 - - + +
102C LEU* 3.6 24.0 - - + -
264C ALA* 5.2 1.3 - - + -
265C ASP* 3.1 28.3 + - + +
267C PRO* 1.3 76.0 - - - +
269C PHE* 1.3 61.6 + - - +
271C ASP* 3.3 9.4 + - - +
272C THR* 2.9 36.1 + - - +
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Residues in contact with PHE 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C LEU* 3.7 40.2 - - + -
205C ALA* 4.0 3.1 - - + -
207C ILE* 3.6 36.8 - - + -
231C LEU* 3.8 23.6 - - + -
233C LYS* 3.8 37.7 - - + -
262C VAL* 3.8 11.9 - - + -
264C ALA* 3.9 9.2 - - + -
265C ASP 2.9 18.3 + - - +
266C GLY 3.6 3.1 - - - +
268C LEU* 1.3 77.7 - - - +
270C GLY* 1.3 63.4 + - - +
272C THR* 3.3 1.9 + - - -
273C VAL* 3.1 46.0 + - + +
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Residues in contact with GLY 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207C ILE* 5.2 1.3 - - - -
266C GLY 2.8 14.3 + - - -
267C PRO* 3.7 3.6 - - - -
269C PHE* 1.3 79.9 - - - +
271C ASP* 1.3 59.1 + - - +
273C VAL* 3.6 4.6 + - - +
274C THR* 2.9 33.1 + - - +
293C HIS* 6.5 0.2 - - - -
294C LEU* 3.9 22.2 - - - -
297C GLN* 3.6 8.3 - - - -
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Residues in contact with ASP 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267C PRO* 2.9 27.8 + - - +
268C LEU* 3.6 8.7 - - - +
269C PHE 3.3 0.2 - - - -
270C GLY* 1.3 76.9 - - - +
272C THR* 1.3 59.0 + - - +
274C THR* 3.5 2.1 + - - -
275C SER* 2.7 34.4 + - - +
293C HIS* 4.5 4.7 + - - -
297C GLN* 2.6 34.9 + - - +
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Residues in contact with THR 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C LYS* 4.2 11.0 - - + +
102C LEU* 3.6 41.0 - - + +
103C ASN* 3.9 27.2 - - - +
106C ILE* 4.5 5.8 - - + -
268C LEU* 2.9 24.3 + - - +
269C PHE 3.8 0.9 - - - -
270C GLY 3.3 0.2 - - - -
271C ASP* 1.3 76.1 - - - +
273C VAL* 1.3 64.9 + - + +
275C SER* 3.3 15.0 + - - -
276C SER* 3.4 12.1 + - - -
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Residues in contact with VAL 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C LEU* 5.6 0.4 - - + -
106C ILE* 4.7 2.9 - - + -
203C PHE* 3.7 32.0 - - + -
205C ALA* 3.9 16.6 - - + -
207C ILE* 4.8 5.4 - - + -
231C LEU* 4.4 7.9 - - + -
269C PHE* 3.1 49.0 + - + +
270C GLY* 3.7 9.4 - - - +
272C THR* 1.3 79.5 - - + +
274C THR* 1.3 68.6 + - + +
276C SER* 3.2 20.7 + - - -
279C LEU* 3.5 20.4 - - + +
282C ILE* 5.0 2.0 - - + -
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Residues in contact with THR 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270C GLY 2.9 22.1 + - - +
271C ASP 3.5 5.7 + - - -
273C VAL* 1.3 79.4 - - + +
275C SER* 1.3 53.3 + - - +
276C SER 3.3 0.4 - - - -
279C LEU* 4.2 6.7 - - + -
282C ILE* 4.1 16.6 - - + -
294C LEU* 4.3 6.1 - - + +
297C GLN* 3.4 41.7 + - + +
298C VAL* 4.0 22.7 - - + -
301C ASN* 2.8 24.2 + - - +
305C PHE* 3.4 18.9 - - - -
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Residues in contact with SER 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A ARG* 5.9 0.2 + - - -
271C ASP* 2.7 22.9 + - - +
272C THR* 3.7 7.2 - - - -
273C VAL 3.2 0.4 - - - -
274C THR* 1.3 77.1 + - - +
276C SER* 1.3 60.8 + - - +
277C GLU 3.6 1.2 + - - -
301C ASN* 3.5 13.6 + - - +
304C ARG* 2.7 32.8 + - - +
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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