Contacts of the helix formed by residues 293 - 308 (chain G) 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 GLY 293 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72G TRP* 2.8 36.9 + - - -
90G PHE* 4.3 4.9 - - - -
93G ILE* 4.9 1.1 - - - -
94G SER* 2.8 21.6 + - - -
97G ASP* 4.0 2.9 - - - -
291G THR 3.2 0.4 + - - -
292G CYS* 1.3 79.8 - - - +
294G GLY* 1.3 64.5 + - - +
297G GLU* 3.4 14.0 + - - +
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Residues in contact with GLY 294 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94G SER* 3.4 17.3 + - - -
97G ASP* 3.6 6.1 - - - -
98G ILE* 4.2 3.4 - - - -
289G LEU* 3.0 28.1 + - - +
292G CYS* 3.9 1.1 - - - -
293G GLY* 1.3 74.9 - - - +
295G PHE* 1.3 65.6 + - - -
296G THR 3.2 2.7 - - - -
298G PHE* 2.9 24.1 + - - +
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Residues in contact with PHE 295 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97G ASP* 2.8 4.2 + - - -
98G ILE* 3.9 22.8 - - + +
101G TRP* 3.5 43.5 - + + +
112G VAL* 3.9 9.4 - - + -
116G LEU* 3.7 28.4 - - + +
289G LEU* 3.7 19.8 - - + +
294G GLY* 1.3 71.5 - - - -
296G THR* 1.3 65.1 + - - +
298G PHE* 3.8 1.4 - - - +
299G LYS* 3.1 26.7 + - - +
325G ALA* 3.2 42.2 - - + -
328G HIS* 4.0 6.1 - - + -
329G ALA* 3.9 12.8 - - + -
373G ILE* 3.9 23.1 - - + -
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Residues in contact with THR 296 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68G THR* 3.9 8.1 + - - +
69G GLU* 3.6 28.5 - - + +
72G TRP* 4.0 20.2 - - + -
97G ASP* 2.6 32.6 + - - -
101G TRP* 3.0 22.1 + - + +
295G PHE* 1.3 80.3 - - - +
297G GLU* 1.3 62.9 + - - +
299G LYS* 3.9 4.6 - - - +
300G LYS* 3.4 36.2 + - + +
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Residues in contact with GLU 297 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72G TRP* 3.3 22.5 - - + -
269G SER* 3.5 12.3 - - - -
270G ARG* 2.8 63.8 + - - +
271G TRP* 3.7 2.8 - - - -
292G CYS 3.2 24.5 - - - +
293G GLY* 3.4 19.3 + - - +
294G GLY 3.4 2.0 + - - -
295G PHE 3.3 0.2 - - - -
296G THR* 1.3 76.9 - - - +
298G PHE* 1.3 55.0 + - - +
299G LYS 3.2 1.8 - - - -
300G LYS* 3.1 7.7 + - - +
301G ILE* 2.8 36.9 + - + +
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Residues in contact with PHE 298 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287G PRO* 3.6 33.8 - - + +
289G LEU* 3.5 21.8 - - + -
292G CYS* 3.8 13.7 - - - -
294G GLY 2.9 19.3 + - - +
295G PHE* 3.8 3.1 - - - +
297G GLU* 1.3 74.4 - - - +
299G LYS* 1.3 64.2 + - + +
301G ILE* 3.2 6.0 + - - +
302G ALA* 2.8 31.0 + - + +
312G VAL* 3.7 21.3 - - + -
314G ALA* 3.9 24.7 - - + -
329G ALA* 3.7 35.7 - - + -
330G GLU* 4.6 4.5 - - + -
333G ILE* 4.2 16.4 - - + -
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Residues in contact with LYS 299 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D GLU* 2.7 33.9 + - - +
299D LYS* 5.9 11.4 - - + -
300D LYS* 4.2 2.0 - - - +
101G TRP* 6.3 1.8 - - + -
116G LEU* 3.2 42.3 + - + +
295G PHE 3.1 14.6 + - - +
296G THR* 3.9 5.8 - - - +
298G PHE* 1.3 85.5 - - + +
300G LYS* 1.3 58.0 + - + +
302G ALA* 3.8 3.9 - - - -
303G ASP* 2.8 54.1 + - - +
332G ALA 5.2 1.6 + - - -
333G ILE* 5.1 9.5 - - + +
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Residues in contact with LYS 300 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299D LYS* 4.2 1.6 - - - +
303D ASP* 3.4 39.3 + - + +
334D PRO* 5.4 4.6 - - - +
69G GLU* 2.8 38.3 + - - -
72G TRP* 5.7 2.8 - - - +
270G ARG* 3.6 52.0 - - + +
296G THR* 3.4 23.7 + - - +
297G GLU* 3.1 15.7 + - - +
299G LYS* 1.3 76.2 - - + +
301G ILE* 1.3 63.4 + - - +
303G ASP* 3.9 6.5 - - - +
304G MET* 3.0 25.3 + - - +
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Residues in contact with ILE 301 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269G SER* 3.7 22.0 - - - +
270G ARG* 3.7 22.2 - - - +
273G PHE* 3.7 30.5 - - + -
277G LEU* 5.0 1.7 - - + +
285G ILE* 3.5 24.7 - - + -
287G PRO* 4.4 6.5 - - + -
292G CYS* 3.7 32.5 - - + -
297G GLU* 2.8 25.6 + - + +
298G PHE* 3.5 6.3 - - - +
300G LYS* 1.3 73.6 - - - +
302G ALA* 1.3 57.7 + - - +
304G MET* 3.3 7.1 + - - +
305G ALA* 2.9 27.4 + - + +
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Residues in contact with ALA 302 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285G ILE* 4.5 1.1 - - - -
287G PRO* 6.0 0.2 - - - +
298G PHE* 2.8 25.1 + - + +
299G LYS 3.9 1.6 - - - +
301G ILE* 1.3 73.0 - - - +
303G ASP* 1.3 58.2 + - - +
305G ALA* 3.3 1.9 + - - -
306G HIS* 3.0 24.6 + - - +
312G VAL* 3.9 28.0 - - + -
333G ILE* 3.9 31.0 - - + -
335G ASN* 3.0 14.2 + - - +
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Residues in contact with ASP 303 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D GLU* 4.5 1.9 - - - +
270D ARG* 2.9 30.4 + - - +
300D LYS* 3.3 56.1 + - + +
299G LYS* 2.8 48.1 + - - +
300G LYS* 3.9 6.1 + - - +
302G ALA* 1.3 77.3 - - - +
304G MET* 1.3 63.9 + - - +
306G HIS* 3.5 7.8 + - - +
307G ILE* 3.8 1.2 - - - +
333G ILE* 4.8 5.7 - - - +
334G PRO* 5.1 4.7 - - - +
335G ASN* 5.4 0.5 - - - +
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Residues in contact with MET 304 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270D ARG* 5.3 0.7 - - - +
304D MET* 3.9 35.0 - - + -
307D ILE* 3.6 26.9 - - + -
270G ARG* 3.6 38.6 - - + +
273G PHE* 4.8 3.8 - - + -
274G LEU* 4.4 13.2 - - - +
277G LEU* 3.7 24.7 - - + -
300G LYS 3.0 16.6 + - - +
301G ILE* 3.6 4.9 - - - +
303G ASP* 1.3 73.0 - - - +
305G ALA* 1.3 66.3 + - - +
307G ILE* 3.1 19.3 + - - +
308G PHE* 3.3 22.3 - - + -
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Residues in contact with ALA 305 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277G LEU* 4.0 19.2 - - + +
285G ILE* 3.7 23.1 - - + -
301G ILE 2.9 17.9 + - - +
302G ALA 3.6 5.4 - - - +
304G MET* 1.3 76.7 - - - +
306G HIS* 1.3 61.9 + - - +
308G PHE* 2.9 12.6 + - - -
310G VAL* 3.2 36.3 + - + +
335G ASN* 4.2 5.4 - - - +
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Residues in contact with HIS 306 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D GLU* 3.0 40.0 + - - -
77D LYS* 3.9 14.4 + - - -
270D ARG* 3.7 19.3 - - - +
271D TRP* 4.1 21.1 - + - -
182E GLU* 4.7 5.8 - - - -
302G ALA 3.0 8.0 + - - +
303G ASP* 3.5 13.0 - - - +
304G MET 3.2 0.4 - - - -
305G ALA* 1.3 76.3 - - - +
307G ILE* 1.3 61.1 + - - +
309G GLU* 3.1 18.4 + - - +
310G VAL 4.1 2.6 + - - -
334G PRO* 4.2 12.1 - - + +
335G ASN* 3.4 37.0 - - + +
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Residues in contact with ILE 307 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270D ARG* 3.3 46.4 - - + +
271D TRP* 3.5 46.7 + - + +
274D LEU* 3.6 36.3 - - + -
304D MET* 4.8 5.6 - - - -
246E ASN* 3.1 16.6 + - - +
249E LEU* 3.6 8.7 - - - +
303G ASP 3.8 4.3 - - - +
304G MET* 3.1 18.4 + - - +
306G HIS* 1.3 74.5 - - - +
308G PHE* 1.3 63.0 + - + +
309G GLU* 3.4 1.4 - - - +
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Residues in contact with PHE 308 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274D LEU* 3.8 28.7 - - + -
278D GLU* 4.5 6.1 - - + -
304D MET* 5.6 0.4 - - - -
246E ASN* 3.8 15.3 - - - -
248E ARG* 3.3 31.6 - - - -
249E LEU* 3.6 13.0 - - + +
274G LEU* 6.0 3.8 - - + -
277G LEU* 3.4 41.1 - - + -
278G GLU* 4.6 5.2 - - + -
280G ARG* 2.8 35.8 + - - -
304G MET* 3.3 33.9 - - + -
305G ALA 2.9 8.0 + - - +
307G ILE* 1.3 87.3 - - + +
309G GLU* 1.3 60.4 + - - +
310G VAL* 3.3 11.9 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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