Contacts of the helix formed by residues 285 - 295 (chain A) in PDB entry 4B18
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 PRO 285 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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284A GLY* 1.3 90.0 - - - +
286A ASN* 1.3 61.8 + - - +
287A ASP* 3.2 15.3 - - - +
288A LYS* 3.0 44.7 + - + +
289A ILE* 3.2 8.4 + - - +
223B ARG* 4.3 4.7 - - - +
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Residues in contact with ASN 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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285A PRO* 1.3 73.5 - - - +
287A ASP* 1.3 51.2 + - - +
289A ILE* 3.2 5.3 + - - +
290A GLN* 2.7 29.9 + - - +
325A THR 4.2 0.4 + - - +
326A GLY* 3.2 19.2 - - - -
327A ASP* 3.5 28.5 + - - +
330A GLN* 2.8 28.4 + - - +
223B ARG* 3.3 14.9 + - - -
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Residues in contact with ASP 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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249A PHE* 5.1 0.6 - - - -
285A PRO* 3.3 22.3 - - - +
286A ASN* 1.3 71.4 + - - +
288A LYS* 1.3 68.5 + - - +
290A GLN* 3.5 9.7 - - - +
291A ALA* 3.0 25.5 + - - +
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Residues in contact with LYS 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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246A PRO* 3.8 29.2 - - - +
247A PRO* 4.1 11.1 + - - +
249A PHE* 3.6 54.0 - - + +
281A LEU 4.0 13.5 - - - +
283A ASP 5.3 2.0 + - - +
284A GLY* 4.7 5.8 - - - +
285A PRO* 3.0 36.7 + - + +
287A ASP* 1.3 83.6 + - - +
289A ILE* 1.3 64.5 + - - +
291A ALA* 3.2 5.4 + - - +
292A VAL* 3.1 24.9 + - - +
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Residues in contact with ILE 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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282A SER* 3.4 23.1 - - - +
284A GLY 3.7 16.8 - - - +
285A PRO 3.2 4.4 + - - +
286A ASN* 3.2 25.4 + - - +
288A LYS* 1.3 72.4 - - - +
290A GLN* 1.3 67.4 + - - +
292A VAL* 2.8 11.4 + - - +
293A ILE* 2.8 35.0 + - + +
322A ASN 3.7 6.7 - - - +
323A ILE* 3.8 26.9 - - + +
325A THR* 3.6 24.0 - - - +
326A GLY 4.0 5.4 - - - +
330A GLN* 3.8 13.5 - - - +
223B ARG* 3.9 0.7 - - - +
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Residues in contact with GLN 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 ASN 2.7 19.4 + - - +
287A ASP* 3.5 12.6 - - + +
288A LYS 3.2 0.2 - - - -
289A ILE* 1.3 73.2 - - - +
291A ALA* 1.3 63.5 + - - +
293A ILE* 3.0 24.0 + - - +
294A ASP* 2.8 59.7 + - - +
330A GLN* 3.1 28.3 + - - +
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Residues in contact with ALA 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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249A PHE* 3.6 28.7 - - + -
253A SER* 5.6 0.4 - - - -
256A LEU* 3.9 17.1 - - + +
287A ASP 3.0 11.6 + - - +
288A LYS 3.4 9.6 - - - +
289A ILE 3.1 0.6 - - - -
290A GLN* 1.3 77.5 - - - +
292A VAL* 1.3 60.6 + - - +
294A ASP* 3.3 9.5 + - - +
295A ALA* 3.3 16.1 + - - +
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Residues in contact with VAL 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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249A PHE* 5.3 0.7 - - + -
256A LEU* 4.0 22.7 - - + -
278A LEU* 4.1 14.4 - - + +
281A LEU* 4.1 29.2 - - + -
282A SER* 4.1 10.1 - - - +
288A LYS 3.1 12.4 + - - +
289A ILE* 2.8 10.3 + - - +
291A ALA* 1.3 73.4 - - - +
293A ILE* 1.3 66.7 + - - +
295A ALA* 3.3 10.2 + - - +
296A GLY 3.7 0.3 + - - -
297A VAL* 3.4 34.8 - - + +
301A LEU* 5.2 0.7 - - + -
319A ALA* 6.4 0.2 - - + -
323A ILE* 4.3 19.5 - - + -
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Residues in contact with ILE 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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289A ILE* 2.8 17.8 + - + +
290A GLN* 3.0 29.1 + - - +
292A VAL* 1.3 76.7 - - - +
294A ASP* 1.3 52.7 + - - +
296A GLY* 2.7 30.1 + - - -
298A CYS* 4.0 23.1 - - - -
323A ILE* 3.8 22.2 - - + -
330A GLN* 3.6 43.5 - - + +
333A VAL* 4.5 22.2 - - + +
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Residues in contact with ASP 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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290A GLN* 2.8 55.6 + - - +
291A ALA* 3.7 9.1 - - - +
292A VAL 3.3 0.2 - - - -
293A ILE* 1.3 69.0 - - - +
295A ALA* 1.3 59.0 + - - +
296A GLY* 3.0 6.1 + - - -
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Residues in contact with ALA 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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256A LEU* 3.9 43.1 - - + +
257A ASN* 5.0 4.3 - - - +
260A SER* 3.2 26.2 + - - -
291A ALA 3.3 8.5 + - - +
292A VAL 3.3 8.9 + - - +
293A ILE 3.2 1.0 + - - -
294A ASP* 1.3 76.5 - - - +
296A GLY* 1.4 58.7 + - - +
297A VAL* 3.5 3.8 - - + -
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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