Contacts of the helix formed by residues 278 - 292 (chain A) in PDB entry 2O7R
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 MET 278 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202A PRO 4.4 4.3 - - - +
203A GLY* 3.5 26.5 - - - -
204A PHE 3.7 20.9 - - - +
213A GLU* 4.8 7.6 - - - +
222A LEU* 4.6 6.1 - - + -
227A LEU* 4.3 20.9 - - + -
231A TRP* 5.3 1.1 - - - -
276A ASP* 2.8 16.4 + - - +
277A PRO* 1.4 72.0 - - - +
279A ILE* 1.3 63.7 + - - +
280A ASP 3.3 1.3 - - - -
281A ARG* 3.1 15.8 + - - +
282A GLN* 3.2 22.8 + - + +
306A HIS* 3.3 38.8 - - + +
369A 4PA 3.8 25.8 - - - +
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Residues in contact with ILE 279 (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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212A SER* 3.4 19.1 - - - -
215A ARG* 3.6 14.4 - - - +
273A CYS* 3.4 29.6 - - - +
274A HIS* 4.0 11.2 - - - +
276A ASP* 2.9 25.9 + - - +
277A PRO 3.2 0.4 - - - -
278A MET* 1.3 76.6 - - - +
280A ASP* 1.3 69.7 + - - +
282A GLN* 3.1 17.1 + - - +
283A MET* 2.9 40.3 + - + +
300A PHE* 3.4 34.3 - - + -
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Residues in contact with ASP 280 (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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210A THR* 3.6 17.4 - - + +
211A GLY* 3.3 13.5 + - - -
212A SER* 2.9 45.1 + - - +
215A ARG* 5.2 0.7 + - - -
278A MET 3.2 0.4 + - - -
279A ILE* 1.3 80.8 - - - +
281A ARG* 1.4 58.2 + - - +
283A MET* 3.5 8.6 + - - +
284A GLU* 3.0 28.8 + - - +
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Residues in contact with ARG 281 (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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204A PHE* 3.5 28.2 - - + +
205A GLY* 3.3 42.7 + - - +
206A GLY* 3.5 13.9 - - - +
208A LYS 2.7 29.9 + - - -
210A THR* 3.6 22.2 - - + +
213A GLU* 2.8 31.1 + - - +
247A ASN* 4.0 14.9 + - - +
248A PRO* 5.4 5.4 - - + +
249A THR* 5.3 2.5 + - - +
278A MET* 3.1 9.5 + - - +
280A ASP* 1.4 74.6 - - - +
282A GLN* 1.3 62.1 + - - +
284A GLU* 3.5 7.6 + - - +
285A LEU* 3.0 27.0 + - - +
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Residues in contact with GLN 282 (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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201A GLU* 3.2 23.8 + - - +
202A PRO* 2.9 41.0 + - + +
204A PHE* 4.9 5.6 - - + -
270A VAL* 4.0 6.5 - - + +
272A GLY* 4.0 11.4 - - - -
276A ASP* 3.2 21.2 + - - +
278A MET* 3.2 22.6 + - - +
279A ILE* 3.1 25.0 + - - +
281A ARG* 1.3 79.3 - - + +
283A MET* 1.3 60.6 + - - +
285A LEU* 3.4 6.7 + - - +
286A ALA* 3.1 21.8 + - - +
300A PHE* 3.8 15.4 - - + -
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Residues in contact with MET 283 (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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274A HIS* 6.3 0.2 - - - -
279A ILE* 2.9 47.3 + - + +
280A ASP* 3.9 9.6 - - - +
282A GLN* 1.3 74.5 - - - +
284A GLU* 1.3 64.0 + - - +
286A ALA* 3.2 3.1 + - - +
287A GLU* 3.0 40.7 + - - +
300A PHE* 3.8 39.7 - - + -
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Residues in contact with GLU 284 (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 ASN* 5.3 0.7 - - - +
249A THR* 2.5 35.0 + - - +
280A ASP 3.0 18.5 + - - +
281A ARG* 3.8 8.5 - - - +
283A MET* 1.3 72.5 - - - +
285A LEU* 1.4 65.7 + - - +
287A GLU* 3.2 16.1 + - - +
288A ARG* 2.9 34.9 + - + +
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Residues in contact with LEU 285 (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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176A TYR* 3.8 32.1 - - + +
199A LEU* 3.8 26.0 - - + -
202A PRO* 5.2 2.0 - - + -
204A PHE* 3.7 30.3 - - + -
248A PRO* 4.4 5.4 - - + -
249A THR* 4.0 21.4 - - + +
258A PHE* 3.9 13.5 - - + -
270A VAL* 5.3 3.1 - - + -
281A ARG 3.0 17.4 + - - +
282A GLN* 3.7 5.6 - - - +
283A MET 3.4 0.2 - - - -
284A GLU* 1.4 76.0 - - - +
286A ALA* 1.3 65.4 + - - +
288A ARG* 3.2 1.0 + - - -
289A LEU* 2.9 31.8 + - + +
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Residues in contact with ALA 286 (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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270A VAL* 4.4 7.8 - - + +
282A GLN 3.1 14.4 + - - +
283A MET 3.2 8.7 + - - +
285A LEU* 1.3 76.0 - - - +
287A GLU* 1.3 59.4 + - + +
289A LEU* 3.4 11.6 + - - +
290A GLU* 3.0 35.1 + - - +
296A VAL* 4.0 16.7 - - + +
298A ALA* 4.6 3.6 - - + -
300A PHE* 3.8 23.3 - - + -
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Residues in contact with GLU 287 (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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283A MET* 3.0 31.8 + - + +
284A GLU* 3.6 18.9 - - + +
285A LEU 3.2 0.2 - - - -
286A ALA* 1.3 76.1 - - + +
288A ARG* 1.3 60.9 + - + +
290A GLU* 3.3 13.2 + - - +
291A LYS* 2.8 31.1 + - - +
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Residues in contact with ARG 288 (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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249A THR* 3.9 33.3 - - + +
254A PRO* 4.5 12.5 + - - +
255A LEU* 3.2 42.2 - - + +
258A PHE* 3.8 6.4 - - + -
284A GLU* 2.9 29.9 + - + +
285A LEU 3.8 3.1 - - - +
287A GLU* 1.3 76.4 - - + +
289A LEU* 1.3 64.9 + - - +
291A LYS* 3.5 34.5 + - - +
292A LYS* 3.2 23.7 + - - +
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Residues in contact with LEU 289 (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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176A TYR* 5.4 3.4 - - + -
199A LEU* 5.2 1.1 - - + -
258A PHE* 3.8 40.1 - - + -
261A ILE* 4.7 7.0 - - + -
268A VAL* 3.9 31.2 - - + -
270A VAL* 4.5 5.2 - - + -
285A LEU* 2.9 38.8 + - + +
286A ALA* 3.6 5.8 - - - +
288A ARG* 1.3 75.2 - - - +
290A GLU* 1.3 63.8 - - - +
292A LYS* 3.1 8.7 + - - +
294A VAL* 3.0 45.3 + - + +
296A VAL* 3.6 14.4 - - + -
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Residues in contact with GLU 290 (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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286A ALA* 3.0 23.4 + - - +
287A GLU* 3.5 12.1 - - - +
289A LEU* 1.3 74.9 - - - +
291A LYS* 1.3 59.2 + - - +
293A GLY* 2.9 21.3 + - - -
294A VAL 4.1 7.8 - - - +
296A VAL* 3.8 33.3 - - + +
298A ALA* 5.1 6.6 + - - +
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Residues in contact with LYS 291 (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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287A GLU 2.8 20.5 + - - +
288A ARG* 3.8 37.4 - - - +
289A LEU 3.3 0.4 - - - -
290A GLU* 1.3 73.8 - - - +
292A LYS* 1.3 78.0 + - - +
293A GLY 3.2 2.8 + - - -
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Residues in contact with LYS 292 (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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254A PRO 4.1 12.8 + - - -
255A LEU* 3.5 20.8 + - + +
256A TYR* 4.9 6.5 - - - +
258A PHE* 3.7 28.7 - - + -
259A ASP* 2.7 38.9 + - - +
262A ARG* 2.8 33.0 + - - +
288A ARG* 3.2 16.5 + - - +
289A LEU 3.1 7.4 + - - +
291A LYS* 1.3 92.0 - - - +
293A GLY* 1.3 60.1 + - - +
294A VAL* 3.3 2.5 + - + -
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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