Contacts of the helix formed by residues 288 - 299 (chain A) in PDB entry 3DRW
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 GLU 288 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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287A ASP* 1.3 78.2 - - - +
289A ALA* 1.3 63.0 + - - +
291A ILE* 3.1 28.0 + - + +
292A ALA 3.9 2.3 + - - -
307A ILE* 4.7 10.9 - - + +
311A ASN* 3.3 45.1 + - - +
316A SER* 3.9 21.3 + - - +
334A VAL* 4.3 0.4 - - - +
335A HIS 3.5 5.1 + - - -
336A THR* 3.7 33.4 - - + +
339A TYR* 4.8 5.3 + - - -
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Residues in contact with ALA 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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287A ASP* 3.3 11.2 + - - +
288A GLU* 1.3 79.5 - - - +
290A GLU* 1.3 62.3 + - + +
291A ILE 3.3 0.2 - - - -
292A ALA* 3.5 8.3 + - - +
293A GLN* 3.2 31.6 + - + +
307A ILE* 6.2 0.4 - - - -
308A PHE* 5.9 10.8 - - + -
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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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261A PHE* 3.9 23.7 - - + +
262A ALA* 3.2 15.4 - - - +
263A SER* 3.1 23.5 + - - +
286A ILE* 3.3 21.9 - - + +
287A ASP* 2.9 46.3 + - - +
288A GLU 3.1 0.8 - - - -
289A ALA* 1.3 77.6 - - + +
291A ILE* 1.3 65.6 + - - +
293A GLN* 3.6 20.4 - - - +
294A ILE* 2.9 28.1 + - - +
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Residues in contact with ILE 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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286A ILE* 3.6 20.2 - - + -
287A ASP 3.4 4.5 + - - +
288A GLU* 3.1 15.6 + - + +
290A GLU* 1.3 76.1 - - - +
292A ALA* 1.3 59.7 + - - +
294A ILE* 3.8 0.3 - - - -
295A LEU* 2.9 34.0 + - + +
307A ILE* 3.7 22.7 - - + -
316A SER* 3.9 34.1 - - - +
319A GLY* 3.9 22.4 - - - -
320A GLY* 5.0 1.6 - - - +
323A ILE* 3.9 17.1 - - + +
334A VAL* 3.7 27.1 - - + -
341A MET* 4.7 0.2 - - + -
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Residues in contact with ALA 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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288A GLU 3.9 1.2 + - - -
289A ALA* 3.5 10.6 + - - +
290A GLU 3.3 0.4 - - - -
291A ILE* 1.3 82.0 - - - +
293A GLN* 1.3 56.8 + - + +
295A LEU* 3.4 4.2 + - - -
296A SER* 2.9 31.4 + - - -
304A ALA* 3.5 33.7 - - + +
307A ILE* 4.0 17.9 - - + +
308A PHE* 4.7 14.1 - - + +
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Residues in contact with GLN 293 (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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261A PHE* 5.1 1.9 - - + -
262A ALA 4.8 0.5 - - - +
263A SER* 4.1 22.1 + - - -
264A VAL 4.2 5.8 + - - -
270A ARG* 3.5 50.1 + - - +
289A ALA* 3.2 18.6 + - + +
290A GLU* 3.6 28.8 + - - +
291A ILE 3.3 0.4 - - - -
292A ALA* 1.3 77.5 - - + +
294A ILE* 1.3 63.7 + - + +
296A SER* 3.5 6.2 + - - -
297A VAL* 3.3 23.2 + - - +
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Residues in contact with ILE 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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261A PHE* 3.7 35.4 - - + -
274A ILE* 3.8 20.6 - - + -
278A LEU* 4.4 13.5 - - + -
284A VAL* 5.7 0.4 - - + -
286A ILE* 4.0 24.7 - - + -
290A GLU 2.9 21.2 + - - +
291A ILE 3.9 2.9 - - - +
293A GLN* 1.3 73.9 - - - +
295A LEU* 1.3 67.2 + - - +
297A VAL* 3.1 4.9 + - - +
298A LEU* 3.0 34.0 + - + +
323A ILE* 3.7 30.3 - - + -
327A LEU* 4.5 6.3 - - + -
332A LEU* 6.1 0.4 - - + -
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Residues in contact with LEU 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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291A ILE* 2.9 22.9 + - + +
292A ALA 3.7 4.0 - - - +
294A ILE* 1.3 75.6 - - - +
296A SER* 1.3 64.6 + - - +
298A LEU* 3.0 11.7 + - + +
299A GLY 3.1 0.3 + - - -
300A TYR* 3.0 44.2 + - + +
303A LEU* 3.6 24.5 - - + -
304A ALA* 4.2 5.4 - - + +
307A ILE* 3.6 31.4 - - + -
319A GLY* 3.7 17.5 - - - +
322A ILE* 3.7 31.2 - - + -
323A ILE* 4.1 7.2 - - + -
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Residues in contact with SER 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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267A ARG* 3.2 31.8 + - - -
292A ALA 2.9 18.6 + - - -
293A GLN* 3.6 7.4 - - - -
294A ILE 3.1 0.4 - - - -
295A LEU* 1.3 77.2 - - - +
297A VAL* 1.3 62.2 + - - +
299A GLY* 3.1 14.7 + - - -
300A TYR 4.4 3.1 - - - -
301A ARG* 3.7 24.3 + - - +
304A ALA* 4.0 14.1 - - - +
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Residues in contact with VAL 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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267A ARG* 3.7 33.9 - - - +
270A ARG* 4.3 9.9 - - - +
271A LYS* 3.9 42.4 - - + +
274A ILE* 3.3 32.8 - - + -
293A GLN 3.3 16.4 - - - +
294A ILE 3.1 2.9 + - - +
296A SER* 1.3 78.5 - - - +
298A LEU* 1.3 62.5 + - - +
299A GLY 3.3 1.3 + - - -
271B LYS* 5.9 0.3 + - - -
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Residues in contact with LEU 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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274A ILE* 4.2 11.7 - - + -
294A ILE* 3.0 37.9 + - + +
295A LEU* 3.0 8.9 + - + +
297A VAL* 1.3 78.7 - - - +
299A GLY* 1.3 58.0 + - - +
300A TYR* 3.5 22.9 + - + -
323A ILE* 4.4 14.4 - - + -
326A GLU* 4.0 34.6 - - + +
327A LEU* 4.1 25.4 - - + -
271B LYS* 4.9 18.2 + - - +
275B THR* 6.2 0.2 - - - +
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Residues in contact with GLY 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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295A LEU 3.9 0.2 - - - -
296A SER 3.1 12.1 + - - -
297A VAL 3.3 2.6 + - - -
298A LEU* 1.3 78.8 - - - +
300A TYR* 1.3 61.8 + - - +
301A ARG* 3.0 15.8 + - - +
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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