Contacts of the helix formed by residues 290 - 301 (chain A) in PDB entry 5IWS
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 290 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285A LEU* 3.1 35.0 + - + +
286A LEU* 5.8 0.9 - - - -
288A ASN* 3.6 28.7 + - - +
289A GLY* 1.3 71.6 - - - +
291A THR* 1.3 60.9 + - - +
292A LYS* 3.2 3.6 - - - +
293A ALA* 4.3 9.0 - - + +
294A TYR* 3.1 25.7 + - - +
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Residues in contact with THR 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 LEU* 5.8 3.6 - - - -
289A GLY 2.6 15.2 + - - +
290A ASP* 1.3 70.5 - - - +
292A LYS* 1.3 67.3 + - + +
294A TYR* 3.8 9.4 - - - -
295A ASN* 3.2 39.1 + - - -
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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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290A ASP* 3.2 1.7 - - - +
291A THR* 1.3 81.3 - - + +
293A ALA* 1.3 64.0 + - + +
295A ASN* 3.5 4.7 + - - +
296A ASP* 3.0 55.1 + - - +
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Residues in contact with ALA 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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259A LEU* 5.2 6.5 - - + +
285A LEU* 3.5 28.0 - - + +
290A ASP* 3.7 10.6 + - + +
292A LYS* 1.3 82.5 - - + +
294A TYR* 1.3 61.2 + - - +
296A ASP* 3.9 7.9 - - - +
297A LEU* 3.0 29.8 + - - +
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Residues in contact with TYR 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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282A LEU* 3.6 32.0 - - + +
285A LEU* 3.7 11.8 - - + +
286A LEU* 3.6 41.0 - - + +
290A ASP 3.1 20.2 + - - +
291A THR* 3.7 10.8 - - - +
292A LYS 3.2 0.2 - - - -
293A ALA* 1.3 77.6 - - - +
295A ASN* 1.3 83.0 + - - +
297A LEU* 3.4 2.6 + - - +
298A LEU* 3.2 49.4 + - + +
408A ALA 2.7 31.2 + - - -
409A GLY* 3.6 11.8 + - - -
410A LEU* 5.1 0.2 - - - +
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Residues in contact with ASN 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 THR* 3.2 29.1 + - - +
292A LYS* 4.1 3.7 - - - +
294A TYR* 1.3 93.7 - - - +
296A ASP* 1.3 66.9 + - - +
298A LEU* 3.4 8.5 + - - +
299A ASN* 3.0 36.2 + - - +
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Residues in contact with ASP 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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292A LYS* 3.0 51.2 + - - +
293A ALA* 3.9 8.2 - - - +
295A ASN* 1.3 80.0 - - - +
297A LEU* 1.3 56.6 + - - +
299A ASN* 3.2 6.0 + - - +
300A ASN* 2.9 48.8 + - - +
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Residues in contact with LEU 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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256A TYR* 3.3 37.2 - - + +
259A LEU* 4.1 20.0 - - + -
278A TRP* 3.5 22.5 + - + +
281A ASP* 3.6 21.1 - - + -
282A LEU* 3.7 19.7 - - + -
285A LEU* 4.3 4.0 - - + -
293A ALA 3.0 19.6 + - - +
294A TYR 3.9 3.8 - - - +
296A ASP* 1.3 76.7 - - - +
298A LEU* 1.3 62.0 + - - +
300A ASN* 4.5 4.0 - - + +
301A VAL* 3.2 32.9 + - + +
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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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278A TRP* 3.6 27.1 - - + +
282A LEU* 3.7 19.7 - - + -
294A TYR* 3.2 46.1 + - + +
295A ASN* 3.7 13.2 - - - +
296A ASP 3.2 0.6 - - - -
297A LEU* 1.3 77.6 - - - +
299A ASN* 1.3 65.5 + - - +
301A VAL 3.7 11.0 - - - +
302A VAL* 4.4 7.8 - - - +
389A ARG* 3.6 25.5 + - - +
409A GLY 6.0 0.4 - - - +
410A LEU* 4.3 8.5 - - + -
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Residues in contact with ASN 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 ASN* 3.0 22.8 + - - +
296A ASP* 3.9 7.2 + - - +
298A LEU* 1.3 83.5 - - - +
300A ASN* 1.3 66.7 + - - +
301A VAL 5.3 0.4 - - - -
302A VAL* 5.2 5.2 - - - +
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Residues in contact with ASN 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 ASP* 2.9 38.4 + - - +
297A LEU* 4.3 3.7 - - + +
298A LEU 3.4 0.2 - - - -
299A ASN* 1.3 84.8 - - - +
301A VAL* 1.3 70.1 + - + +
302A VAL* 4.1 3.0 + - - +
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Residues in contact with VAL 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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256A TYR* 3.9 24.2 - - + -
274A LEU* 3.7 32.8 - - + -
278A TRP* 3.4 37.3 + - + -
297A LEU* 3.2 16.9 + - + +
298A LEU 3.7 8.0 - - - +
300A ASN* 1.3 85.4 - - + +
302A VAL* 1.3 62.7 + - - +
303A PRO* 3.7 4.1 - - + +
389A ARG* 5.1 0.5 - - - -
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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