Contacts of the helix formed by residues 287 - 294 (chain A) in PDB entry 3I5H
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 TYR 287 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233A ALA 3.9 5.6 - - - +
234A TYR 2.7 23.3 - - - +
235A GLY* 3.5 19.1 - - - -
236A ASN 2.8 23.8 - - - +
237A ALA* 3.7 1.7 - - + +
247A ARG* 3.6 11.9 - - + +
272A LEU* 3.3 9.2 - - + +
273A GLU* 2.9 49.0 + - - +
276A ARG* 3.9 13.6 - - + +
277A VAL* 4.1 7.9 - - + -
286A ASN* 1.3 95.6 + - - +
288A HIS* 1.3 66.3 + - - +
289A ILE* 3.3 1.8 + - + +
290A PHE* 3.3 13.2 + - + +
291A TYR* 3.2 12.0 - - - -
434A TYR* 3.6 35.4 - + - +
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Residues in contact with HIS 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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232A GLU* 3.9 6.5 - - + -
233A ALA* 3.7 7.1 + - - +
236A ASN* 3.5 12.0 + - + -
237A ALA* 3.2 32.7 + - - -
238A LYS* 3.9 2.2 - - - -
243A ASN 3.6 15.9 - - - -
244A ASN* 2.9 32.2 + - + -
285A ARG* 3.7 25.9 + - - +
286A ASN 3.5 1.0 + - - -
287A TYR* 1.3 70.8 - - - +
289A ILE* 1.3 63.9 + - - +
290A PHE 3.1 0.9 + - - -
291A TYR* 3.1 11.7 + - - +
292A GLN* 3.0 42.3 + - + +
327A ILE* 4.3 13.9 - - + +
329A ASP* 5.5 0.2 - - - +
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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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233A ALA* 2.8 35.1 + - + +
234A TYR* 2.9 54.7 - - + +
287A TYR* 4.6 0.7 - - + -
288A HIS* 1.3 70.3 - - - +
290A PHE* 1.3 80.8 + - + +
292A GLN* 3.9 9.6 - - - +
293A LEU* 3.2 27.0 + - + +
333A MET* 4.4 14.4 - - + -
336A THR* 5.6 2.7 - - + -
354A TYR* 5.1 7.0 - - + -
357A THR* 3.6 18.8 - - + +
434A TYR* 4.2 5.8 - - - +
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Residues in contact with PHE 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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277A VAL* 4.5 5.4 - - + -
286A ASN* 3.0 33.4 - - - -
287A TYR* 3.3 14.3 + + + +
288A HIS 3.1 0.8 + - - -
289A ILE* 1.3 83.6 - - + +
291A TYR* 1.3 68.0 + - + +
293A LEU* 3.5 13.4 + - - +
294A LEU* 3.6 12.1 - - - +
316A PHE* 6.6 0.2 - - + -
317A ILE* 3.4 21.7 - - + +
357A THR* 3.5 36.3 - - + -
360A ILE* 3.8 34.8 - - + -
361A LEU* 3.8 24.3 - - + +
434A TYR* 3.7 26.7 - + - -
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Residues in contact with TYR 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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285A ARG* 3.0 44.9 - - + +
286A ASN* 2.9 46.8 + - + +
287A TYR 3.2 15.0 - - - -
288A HIS 3.1 4.7 + - - +
290A PHE* 1.3 76.0 - - + +
292A GLN* 1.3 66.6 + - - +
294A LEU* 3.0 25.2 + - - +
295A SER* 4.6 2.1 - - - -
311A PRO* 4.4 14.7 - - + +
317A ILE* 2.8 44.8 + - + -
321A THR 3.8 9.7 + - - -
322A LEU* 3.3 24.5 - - + +
329A ASP* 4.4 8.2 - - - +
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Residues in contact with GLN 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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233A ALA* 4.6 7.3 - - - +
288A HIS* 3.0 41.0 + - + +
289A ILE* 3.9 6.1 - - - +
290A PHE 3.3 0.2 - - - -
291A TYR* 1.3 78.9 - - - +
293A LEU* 1.3 65.2 + - - +
294A LEU 2.8 1.9 + - - -
295A SER* 3.1 14.7 + - - -
329A ASP* 4.3 18.2 - - + +
332A GLU* 3.5 24.7 + - + +
333A MET* 2.9 49.3 + - + +
336A THR* 3.1 26.0 + - - +
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Residues in contact with LEU 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* 3.2 14.8 + - + +
290A PHE* 3.6 9.6 - - - +
292A GLN* 1.3 78.7 - - - +
294A LEU* 1.3 64.1 + - + +
295A SER 3.3 6.8 + - - +
298A PHE* 5.5 2.8 + - - +
301A ASN* 5.4 5.1 - - + +
302A ILE* 3.6 18.4 + - - +
305A ILE* 4.0 25.1 - - + +
333A MET* 3.4 23.1 - - + +
354A TYR* 3.3 38.1 - - + +
357A THR* 3.5 37.0 - - + -
358A GLY* 4.8 2.7 - - - +
361A LEU* 5.7 3.6 - - + -
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Residues in contact with LEU 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 PHE 3.6 14.6 - - - +
291A TYR 3.0 10.1 + - - +
292A GLN 2.8 5.6 + - - -
293A LEU* 1.3 81.3 - - + +
295A SER* 1.3 57.4 + - - +
296A PRO* 4.9 0.5 - - - +
302A ILE* 4.4 8.3 - - + -
305A ILE* 5.6 4.0 - - + -
307A ALA* 4.3 23.8 - - + -
308A VAL 4.8 0.2 - - - +
309A PRO* 3.7 39.0 - - + +
310A ASP 4.4 0.9 - - - +
311A PRO* 3.5 39.5 - - + +
314A TYR* 4.4 15.0 - - + -
317A ILE* 4.7 6.5 - - + -
361A LEU* 4.4 16.4 - - + -
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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