Contacts of the helix formed by residues 297 - 313 (chain A) in PDB entry 4OG6
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 297 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A ARG 3.6 2.0 + - - -
296A PRO* 1.3 76.2 - - - +
298A PRO* 1.3 76.9 - - + +
299A LEU* 3.5 12.0 + - - +
300A THR* 2.8 51.9 + - - -
301A LEU* 3.2 10.7 + - - +
327A TYR* 6.1 0.4 - - - +
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Residues in contact with PRO 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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284A ALA* 3.7 20.4 - - + +
287A GLU* 3.9 11.7 - - + +
288A GLU* 3.6 33.2 - - + +
291A PRO* 6.0 3.4 - - + -
297A ASP* 1.3 88.4 - - + +
299A LEU* 1.3 58.1 + - - +
301A LEU* 3.0 6.8 + - + +
302A TYR* 2.8 38.6 + - + -
327A TYR* 3.8 26.7 - - + +
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Residues in contact with LEU 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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297A ASP* 3.2 11.2 + - - +
298A PRO* 1.3 78.6 - - - +
300A THR* 1.3 63.7 + - - +
302A TYR* 3.3 3.8 + - + +
303A HIS* 3.0 39.5 + - + +
324A LEU* 3.5 29.6 - - + -
327A TYR* 3.7 27.1 + - + +
328A HIS* 3.6 23.6 - - + +
333A ASN* 5.9 0.9 - - - +
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Residues in contact with THR 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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296A PRO* 4.0 20.9 - - + +
297A ASP* 2.8 28.5 + - - -
299A LEU* 1.3 75.2 - - - +
301A LEU* 1.3 58.4 + - - +
303A HIS* 3.4 7.3 + - - +
304A LYS* 2.9 48.0 + - + +
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Residues in contact with LEU 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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265A TRP* 3.9 22.0 - - + -
268A TYR* 3.9 27.4 - - + -
280A LEU* 4.1 18.9 - - + +
283A LEU* 4.2 9.6 - - + -
284A ALA* 3.6 24.9 - - + +
287A GLU* 3.9 20.0 - - + -
296A PRO* 3.9 27.1 - - + +
297A ASP 3.2 7.6 + - - +
298A PRO* 3.0 7.9 + - + +
300A THR* 1.3 74.0 - - - +
302A TYR* 1.3 66.7 + - - +
304A LYS* 3.1 10.1 + - + +
305A GLY* 2.9 19.9 + - - -
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Residues in contact with TYR 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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280A LEU 5.3 0.4 - - - -
281A GLY* 3.9 8.5 - - - -
284A ALA* 3.3 21.9 + - + -
285A ASP* 2.6 36.7 + - - -
288A GLU* 3.7 4.9 + - - -
298A PRO* 2.8 36.3 + - + +
299A LEU* 3.8 9.0 - - - +
301A LEU* 1.3 72.7 - - - +
303A HIS* 1.3 58.7 + - - +
305A GLY* 3.1 4.4 + - - -
306A ILE* 3.0 31.2 + - - +
320A PRO* 4.7 2.4 - - - +
323A TYR* 3.6 34.1 - - + -
324A LEU* 3.9 25.1 - - + -
327A TYR* 3.4 36.9 - + + -
330A ARG* 3.7 10.7 + - - -
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Residues in contact with HIS 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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299A LEU* 3.0 37.3 + - + +
300A THR* 3.8 6.3 - - - +
301A LEU 3.2 0.2 - - - -
302A TYR* 1.3 77.5 - - - +
304A LYS* 1.3 54.7 + - - +
306A ILE* 3.4 15.0 + - + +
307A ALA* 2.9 28.8 + - - +
324A LEU* 3.7 38.0 - - + +
328A HIS* 5.3 1.4 + - - -
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Residues in contact with LYS 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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268A TYR* 3.2 36.8 - - + +
280A LEU* 3.8 12.8 - - + +
296A PRO* 5.1 4.0 - - - -
300A THR* 2.9 36.6 + - + +
301A LEU* 3.1 15.0 + - + +
303A HIS* 1.3 73.7 - - - +
305A GLY* 1.3 61.5 + - - +
307A ALA* 3.3 7.4 + - - +
308A SER* 2.8 30.7 + - - -
605A PEG 5.0 7.5 + - - +
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Residues in contact with GLY 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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277A PRO* 3.5 17.7 - - - +
280A LEU* 3.8 21.9 - - - +
281A GLY 5.4 0.7 - - - -
301A LEU 2.9 13.4 + - - -
302A TYR* 3.1 5.1 + - - -
304A LYS* 1.3 77.9 - - - +
306A ILE* 1.3 61.1 + - - +
308A SER* 3.3 4.0 + - - -
309A ALA* 3.0 19.1 + - - +
320A PRO* 4.1 8.3 - - - -
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Residues in contact with ILE 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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302A TYR 3.0 13.9 + - - +
303A HIS* 3.7 20.0 - - + +
305A GLY* 1.3 75.2 - - - +
307A ALA* 1.3 59.0 + - - +
309A ALA* 3.2 5.0 + - - +
310A LYS* 2.9 41.2 + - - +
315A ASP* 5.0 0.2 - - - +
320A PRO* 3.7 31.6 - - + +
321A TYR* 3.5 42.2 - - + +
324A LEU* 3.7 31.4 - - + -
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Residues in contact with ALA 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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303A HIS 2.9 17.4 + - - +
304A LYS* 3.3 8.3 + - - +
306A ILE* 1.3 78.2 - - - +
308A SER* 1.3 58.7 + - - +
310A LYS* 3.3 11.3 + - - +
311A THR* 2.8 38.1 + - - +
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Residues in contact with SER 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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274A GLU 2.7 28.1 + - - -
275A ARG* 3.6 5.0 - - - -
276A TYR 3.6 0.5 + - - -
277A PRO* 3.5 21.7 - - - +
280A LEU* 4.3 9.4 - - - -
304A LYS 2.8 18.0 + - - -
305A GLY 3.5 6.1 - - - -
306A ILE 3.2 0.2 - - - -
307A ALA* 1.3 76.9 - - - +
309A ALA* 1.3 58.0 + - - +
311A THR* 3.2 1.2 + - - -
312A TYR* 2.9 38.4 + - - +
313A TYR* 4.0 0.5 - - - -
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Residues in contact with ALA 309 (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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277A PRO* 3.7 11.6 - - + +
305A GLY 3.0 13.1 + - - +
306A ILE* 3.2 8.0 + - + +
308A SER* 1.3 76.8 - - - +
310A LYS* 1.3 56.6 + - - +
313A TYR* 3.0 25.2 + - - -
315A ASP* 3.0 26.8 + - - +
317A HIS* 4.2 15.9 - - + +
320A PRO* 3.9 22.0 - - + -
321A TYR* 6.0 0.7 - - + -
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Residues in contact with LYS 310 (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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306A ILE* 2.9 29.5 + - + +
307A ALA* 3.3 11.9 + - - +
309A ALA* 1.3 77.2 - - - +
311A THR* 1.3 63.3 + - - +
314A ARG* 3.9 11.4 + - - -
315A ASP* 2.9 45.6 + - + +
321A TYR* 3.2 16.6 + - - -
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Residues in contact with THR 311 (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 GLU* 5.2 1.1 - - - +
307A ALA* 2.8 22.5 + - - +
308A SER* 3.2 2.9 + - - -
310A LYS* 1.3 79.8 - - - +
312A TYR* 1.3 93.5 + - + +
314A ARG 5.1 0.3 + - - -
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Residues in contact with TYR 312 (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 GLU* 2.6 60.0 + - + +
275A ARG* 3.5 48.8 + - + +
308A SER* 2.9 22.4 + - - +
311A THR* 1.3 100.6 - - + +
313A TYR* 1.3 85.1 + - + +
314A ARG* 3.7 3.2 + - - +
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Residues in contact with TYR 313 (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 SER* 3.5 16.8 - - - +
227A TYR 3.5 25.1 - - - -
228A MET* 3.5 22.0 - - + +
229A ARG* 4.9 2.3 + - - -
234A MET* 4.1 4.2 - - - +
275A ARG* 2.7 39.1 + - - +
277A PRO* 3.7 20.4 - - + -
308A SER 4.0 4.7 - - - -
309A ALA* 3.0 8.8 + - - +
312A TYR* 1.3 100.9 - - + +
314A ARG* 1.3 72.2 + - - +
315A ASP 3.0 3.9 + - - -
316A GLU* 3.0 17.5 + - - +
317A HIS* 3.3 38.8 - + + +
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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