Contacts of the helix formed by residues 268 - 279 (chain E) in PDB entry 2OX4
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 TYR 268 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81D TRP* 3.5 10.5 - + - -
84D GLY* 3.6 22.3 - - - -
86E GLY* 4.0 6.1 - - - -
87E THR* 2.7 54.7 + - + +
90E PHE* 3.6 22.1 - + + -
265E GLU 3.5 18.8 - - - -
266E ARG* 3.5 24.7 - - - -
267E ILE* 1.3 81.6 - - - +
269E SER* 1.3 78.6 + - - +
272E GLY* 3.1 13.5 + - - -
291E THR* 3.6 38.4 - - + +
292E CYS* 4.2 2.7 - - - +
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Residues in contact with SER 269 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90E PHE* 3.7 31.0 - - - -
268E TYR* 1.3 82.5 + - - +
270E ARG* 1.3 63.8 + - - +
271E TRP* 3.1 27.4 + - - +
272E GLY 3.0 4.2 + - - -
273E PHE* 3.2 14.4 + - - -
292E CYS* 3.0 26.1 + - - +
297E GLU* 3.4 14.6 - - - -
301E ILE* 3.6 10.6 - - - +
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Residues in contact with ARG 270 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E TRP* 4.0 10.9 - - - -
73E GLU* 5.4 0.4 + - - -
269E SER* 1.3 70.5 - - - +
271E TRP* 1.3 82.2 + - + +
273E PHE 3.4 1.1 + - - +
274E LEU* 2.9 30.2 + - - +
297E GLU* 2.8 40.4 + - - +
300E LYS* 3.6 49.5 - - + +
301E ILE* 3.6 8.9 - - - +
304E MET* 3.6 20.9 - - + +
303F ASP* 2.8 43.7 + - - +
304F MET* 5.0 1.1 - - - +
306F HIS* 3.7 20.0 - - - +
307F ILE* 3.3 27.7 - - + +
334F PRO* 6.1 0.6 - - - +
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Residues in contact with TRP 271 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243D THR* 4.9 5.8 - - + +
245D LEU* 3.5 56.8 - - + +
246D ASN* 3.8 12.9 - - + +
249D LEU* 6.0 0.2 - - - +
72E TRP* 4.0 11.7 - + - -
76E PHE* 3.5 36.1 - + - -
269E SER* 3.1 22.9 + - - +
270E ARG* 1.3 112.9 - - - +
272E GLY* 1.3 60.8 + - - +
274E LEU* 3.7 7.6 + - - +
275E PRO* 3.4 17.3 - - - +
297E GLU* 3.7 7.2 - - - -
306F HIS* 4.0 16.6 + + - -
307F ILE* 3.5 42.2 + - + -
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Residues in contact with GLY 272 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247E PRO* 5.5 0.2 - - - +
267E ILE* 3.3 21.1 - - - +
268E TYR 3.1 20.8 + - - -
269E SER 3.0 4.0 + - - -
271E TRP* 1.3 79.7 - - - +
273E PHE* 1.3 60.0 + - - +
275E PRO* 3.4 13.4 - - - +
276E PHE* 3.5 10.2 - - - -
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Residues in contact with PHE 273 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263E SER 3.9 1.6 - - - -
264E GLY* 3.7 30.1 - - - -
267E ILE* 3.3 43.3 - - + -
268E TYR* 4.6 0.4 - - - -
269E SER 3.2 24.9 + - - +
270E ARG 4.2 2.5 - - - +
272E GLY* 1.3 74.8 - - - +
274E LEU* 1.3 65.9 + - - +
275E PRO* 3.4 0.4 - - - -
276E PHE* 3.1 8.9 + - + +
277E LEU* 3.0 34.5 + - + +
282E ILE* 4.7 3.8 - - + -
285E ILE* 3.8 34.1 - - + -
287E PRO* 3.8 17.3 - - + -
292E CYS* 4.8 0.2 - - + -
301E ILE* 3.6 36.3 - - + -
304E MET* 4.8 2.0 - - + -
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Residues in contact with LEU 274 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246D ASN* 3.5 36.8 - - + +
270E ARG 2.9 17.5 + - - +
271E TRP* 3.8 6.3 - - - +
273E PHE* 1.3 75.2 - - - +
275E PRO* 1.4 66.2 - - + +
277E LEU* 3.1 6.9 + - + +
278E GLU* 2.8 57.3 + - + +
304E MET* 4.4 19.9 - - + +
308E PHE* 5.9 4.0 - - + -
307F ILE* 3.6 15.5 - - + -
308F PHE* 3.8 21.8 - - + -
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Residues in contact with PRO 275 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247E PRO* 3.8 33.2 - - + -
271E TRP 3.4 8.7 - - - +
272E GLY 3.4 16.4 - - - +
274E LEU* 1.4 95.2 - - + +
276E PHE* 1.3 56.2 + - + +
278E GLU* 3.4 17.7 + - - +
279E ASP* 3.0 37.4 + - - +
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Residues in contact with PHE 276 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242E ASN* 6.2 0.2 - - - -
244E PRO* 3.5 30.3 - - + -
247E PRO* 3.6 36.6 - - + -
250E LEU* 3.8 17.3 - - + -
263E SER* 5.6 0.4 - - - -
267E ILE* 3.6 29.6 - - + -
272E GLY 3.5 22.9 - - - -
273E PHE* 3.1 10.0 + - + +
275E PRO* 1.3 78.8 - - + +
277E LEU* 1.3 61.3 + - + +
279E ASP* 4.6 0.7 - - - -
280E ARG* 2.9 20.8 + - - -
281E SER* 3.0 31.4 + - - +
282E ILE* 3.6 30.7 + - + -
285E ILE* 6.1 0.2 - - + -
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Residues in contact with LEU 277 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273E PHE* 3.0 19.9 + - + +
274E LEU* 3.5 7.9 - - + +
276E PHE* 1.3 77.1 - - + +
278E GLU* 1.3 64.8 + - - +
280E ARG* 3.0 12.4 + - - +
282E ILE* 5.2 2.7 - - + +
285E ILE* 4.8 9.9 - - + -
301E ILE* 4.8 1.8 - - + +
304E MET* 3.6 43.7 - - + -
305E ALA* 4.0 25.4 - - + +
308E PHE* 3.4 28.0 - - + -
310E VAL* 3.9 30.5 - - + -
248H ARG* 3.1 12.5 + - - -
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Residues in contact with GLU 278 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246D ASN* 5.1 1.0 - - - +
248D ARG* 4.3 19.4 + - - +
274E LEU* 2.8 52.5 + - + +
275E PRO* 3.6 19.3 - - - +
277E LEU* 1.3 73.0 - - - +
279E ASP* 1.3 59.7 + - - +
308E PHE* 4.6 6.2 - - + -
278F GLU* 5.9 8.0 - - + -
308F PHE* 4.4 6.6 - - + -
248H ARG* 3.1 26.7 + - - +
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Residues in contact with ASP 279 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247E PRO* 4.2 5.7 - - - +
248E ARG* 3.8 27.1 + - - +
251E LYS* 3.9 47.5 + - + +
254E LYS* 5.8 0.3 - - - +
275E PRO* 3.0 21.4 + - - +
276E PHE* 4.0 4.2 - - - +
278E GLU* 1.3 78.4 - - - +
280E ARG* 1.3 68.0 + - - +
281E SER* 3.3 9.3 + - - +
248H ARG* 4.2 4.0 + - - +
252H GLU* 4.4 7.4 - - - +
255H LYS* 5.6 0.5 + - - -
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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