Contacts of the helix formed by residues 293 - 308 (chain A) in PDB entry 2OLO
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 293 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A ALA* 4.3 6.4 - - + +
291A VAL 3.4 3.7 + - - -
292A ALA* 1.3 69.8 - - - +
294A ARG* 1.3 66.1 + - - +
295A ARG* 3.2 13.0 + - - +
296A GLN* 3.0 52.4 + - + +
297A MET* 3.0 22.9 + - - +
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Residues in contact with ARG 294 (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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292A ALA 3.2 8.1 + - - +
293A ASP* 1.3 72.9 + - - +
295A ARG* 1.3 63.8 + - - +
297A MET* 3.2 8.0 + - - +
298A ASP* 2.9 49.7 + - - +
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Residues in contact with ARG 295 (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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250A THR* 5.5 0.2 + - - -
252A GLN* 3.5 37.1 + - - +
253A ASP* 2.8 32.5 + - - +
277A PHE* 4.4 4.6 - - - -
293A ASP* 3.2 10.4 + - - +
294A ARG* 1.3 79.5 - - - +
296A GLN* 1.3 60.2 + - + +
298A ASP* 3.2 10.3 + - + +
299A ARG* 2.9 47.4 + - + +
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Residues in contact with GLN 296 (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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226A MET* 6.0 0.2 - - - +
227A ALA* 3.8 18.8 - - + +
275A PRO* 3.3 31.0 + - + +
277A PHE* 3.7 35.8 - - + +
278A GLU 4.7 1.7 - - - +
279A VAL* 3.7 24.6 - - - +
293A ASP* 3.0 33.6 + - - +
295A ARG* 1.3 77.7 - - + +
297A MET* 1.3 62.5 + - + +
299A ARG* 3.3 2.1 + - - +
300A LEU* 2.9 29.6 + - - +
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Residues in contact with MET 297 (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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227A ALA* 3.5 29.2 - - + -
228A ILE 4.4 2.9 - - - +
229A ALA* 3.9 25.1 - - + -
231A TYR* 5.2 0.7 - - - -
275A PRO* 3.8 21.3 - - + -
292A ALA* 3.7 18.2 - - + +
293A ASP 3.0 17.4 + - - +
294A ARG* 3.6 11.2 - - - +
296A GLN* 1.3 76.6 - - - +
298A ASP* 1.3 61.7 + - - +
300A LEU* 3.8 10.1 - - + +
301A SER* 3.0 36.0 + - - +
315A PRO* 5.9 2.5 - - + -
318A THR* 3.9 23.3 - - + +
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Residues in contact with ASP 298 (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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294A ARG* 2.9 52.6 + - - +
295A ARG* 3.6 10.9 - - + +
297A MET* 1.3 78.8 - - - +
299A ARG* 1.3 56.7 + - + +
301A SER* 4.1 3.3 - - - -
302A GLY* 2.9 27.4 + - - -
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Residues in contact with ARG 299 (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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250A THR* 4.1 7.7 - - - +
253A ASP* 2.8 35.4 + - - +
255A ASN* 2.6 38.2 - - - +
257A PHE* 3.8 21.5 - - - -
277A PHE* 4.0 14.4 - - + -
295A ARG* 2.9 48.3 + - + +
296A GLN 3.6 5.2 - - - +
298A ASP* 1.3 77.8 - - + +
300A LEU* 1.3 56.1 + - - +
302A GLY* 3.9 0.9 - - - -
303A TRP* 3.0 34.6 + - - +
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Residues in contact with LEU 300 (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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229A ALA* 4.2 6.7 - - + -
231A TYR* 3.2 20.9 - - + +
243A TRP* 5.5 0.4 - - + -
257A PHE* 3.7 27.3 - - + -
273A CYS* 3.6 33.0 - - + +
274A GLY* 3.7 21.1 - - - +
275A PRO* 4.1 7.2 - - + -
296A GLN 2.9 17.4 + - - +
297A MET* 3.8 8.7 - - + +
299A ARG* 1.3 77.2 - - - +
301A SER* 1.3 57.2 + - - +
303A TRP* 3.2 2.9 + - + +
304A LEU* 2.9 47.8 + - + +
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Residues in contact with SER 301 (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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231A TYR* 3.0 19.9 + - - -
297A MET* 3.0 18.4 + - - +
298A ASP* 4.1 3.8 - - - -
300A LEU* 1.3 73.3 - - - +
302A GLY* 1.3 60.5 + - - +
304A LEU* 3.8 3.5 - - - -
305A ARG* 2.8 30.7 + - - +
313A PRO* 3.2 28.1 + - - +
315A PRO* 3.5 14.8 - - - +
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Residues in contact with GLY 302 (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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298A ASP 2.9 17.9 + - - -
299A ARG* 3.9 1.1 - - - -
301A SER* 1.3 77.2 - - - +
303A TRP* 1.3 58.0 + - - +
305A ARG* 3.2 30.3 + - - +
306A ASP* 3.1 33.5 + - - +
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Residues in contact with TRP 303 (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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92A PHE* 4.3 7.2 - + - -
132A PHE* 3.9 23.8 - + - -
135A LEU* 4.7 8.7 - - + -
139A TYR* 5.8 0.9 - + - -
243A TRP* 3.6 31.9 - + - -
245A ALA* 4.1 15.0 - - + -
247A GLN* 3.4 24.8 + - - +
255A ASN* 4.8 2.5 - - - -
257A PHE* 3.6 33.9 - + + -
299A ARG* 3.0 24.8 + - - +
300A LEU* 3.6 4.3 - - + +
302A GLY* 1.3 73.4 - - - +
304A LEU* 1.3 75.9 + - + +
306A ASP* 3.3 3.4 + - - -
307A HIS* 2.7 69.2 + + + +
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Residues in contact with LEU 304 (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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231A TYR* 3.4 40.8 - - + -
243A TRP* 3.8 33.7 - - + -
273A CYS* 4.1 7.4 - - - -
300A LEU* 2.9 38.5 + - + +
301A SER* 3.8 3.8 - - - +
303A TRP* 1.3 77.8 - - + +
305A ARG* 1.3 64.2 + - - +
308A LEU* 2.8 54.3 + - + +
311A VAL* 4.4 13.8 - - + +
313A PRO* 4.4 5.8 - - + -
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Residues in contact with ARG 305 (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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301A SER 2.8 18.9 + - - +
302A GLY* 3.2 26.9 + - - +
304A LEU* 1.3 78.1 - - - +
306A ASP* 1.3 98.3 + - - +
308A LEU 4.8 0.3 + - - -
309A PRO* 4.9 11.3 - - - +
313A PRO* 3.6 27.7 - - + +
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Residues in contact with ASP 306 (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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133A ARG* 3.6 16.5 - - - +
134A GLY* 4.8 1.6 + - - -
302A GLY 3.1 13.9 + - - +
303A TRP* 3.9 4.1 - - - +
305A ARG* 1.3 114.6 + - - +
307A HIS* 1.3 76.4 + - + +
309A PRO* 5.1 1.0 - - - +
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Residues in contact with HIS 307 (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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132A PHE* 3.0 12.6 - - - -
133A ARG 2.8 42.8 + - - +
134A GLY* 3.1 24.5 + - - -
135A LEU* 4.1 11.3 - - + +
136A PRO* 5.1 5.2 - - + -
247A GLN* 5.7 0.4 + - - -
303A TRP* 2.7 71.8 + + + +
306A ASP* 1.3 89.8 + - + +
308A LEU* 1.3 58.1 + - - +
309A PRO* 3.6 5.8 - - - -
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Residues in contact with LEU 308 (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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130A PHE 3.8 19.3 - - - +
131A GLY 3.9 7.4 - - - +
132A PHE* 3.9 24.7 - - + -
243A TRP* 3.9 27.4 - - + +
271A VAL* 6.3 0.4 - - + -
273A CYS* 5.4 2.2 - - - -
303A TRP* 4.8 0.9 - - + -
304A LEU* 2.8 45.4 + - + +
307A HIS* 1.3 75.4 - - - +
309A PRO* 1.3 59.5 - - - +
310A THR* 3.0 34.0 + - - +
311A VAL* 3.3 29.1 + - + +
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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