Contacts of the helix formed by residues 296 - 303 (chain B) in PDB entry 1HJW
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 296 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B THR 3.1 20.3 + - - +
295B ALA* 1.3 71.3 - - - +
297B TYR* 1.3 56.3 + - - +
299B ILE* 3.1 18.0 + - + +
300B CYS* 2.9 50.5 + - - -
303B LEU* 5.4 4.5 - - + +
328B TYR* 4.2 13.4 - + - -
329B ASP 3.4 20.2 - - - -
330B ASP* 3.9 11.7 - - - +
331B GLN* 3.4 19.3 + - - -
356B LEU 2.8 16.9 + - - +
357B ASP* 4.0 6.1 - - - -
358B ASP 4.3 1.6 - - - -
364B CYS* 3.6 12.6 - - + -
371B PRO* 3.8 21.5 - - + -
372B LEU* 3.4 33.4 - - + -
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Residues in contact with TYR 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ARG* 4.0 12.5 + - - -
39B GLY* 4.0 9.8 + - - -
287B PHE* 3.4 33.0 - + + +
288B THR* 3.8 11.6 - - - +
295B ALA* 3.6 15.5 - - + -
296B TYR* 1.3 80.4 - - - +
298B GLU* 1.3 90.4 + - + +
300B CYS* 3.5 5.0 + - - +
301B ASP* 3.3 21.0 + - - +
355B ASP 3.5 21.8 - - - -
357B ASP 3.4 18.8 - - - -
358B ASP* 3.7 11.1 - - - +
359B PHE* 3.9 13.9 - + - -
363B PHE* 3.5 52.1 - + + +
364B CYS* 4.4 5.8 - - - -
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Residues in contact with GLU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B GLY* 3.3 7.6 - - - -
286B ARG* 3.2 7.6 + - + +
287B PHE* 2.8 36.4 + - + -
288B THR* 2.8 30.4 + - - -
294B LEU* 3.3 18.4 - - + +
295B ALA* 2.8 29.1 + - + +
297B TYR* 1.3 93.4 - - + +
299B ILE* 1.3 65.5 + - - +
301B ASP* 3.0 28.3 - - - +
302B PHE* 3.0 7.8 + - - +
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Residues in contact with ILE 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B THR 4.9 0.2 - - - +
261B PHE 4.5 0.9 - - - -
262B GLY* 3.8 9.2 - - - +
294B LEU* 3.8 33.7 - - + +
295B ALA 2.8 20.9 + - - +
296B TYR* 3.1 17.9 + - + +
298B GLU* 1.3 77.4 - - - +
300B CYS* 1.3 52.5 + - - +
302B PHE* 2.9 11.4 + - + +
303B LEU* 2.7 49.7 + - + +
326B VAL* 4.5 8.5 - - + -
328B TYR* 3.5 52.9 - - + -
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Residues in contact with CYS 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B TYR* 2.9 33.4 + - - -
297B TYR 3.6 9.0 - - - +
298B GLU 3.3 0.2 - - - -
299B ILE* 1.3 75.3 - - - +
301B ASP* 1.3 61.4 + - - +
303B LEU* 3.7 22.0 - - - +
304B ARG* 4.0 8.8 + - - +
363B PHE 3.7 6.1 - - - +
364B CYS* 2.0 60.7 - - - -
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Residues in contact with ASP 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287B PHE* 5.0 4.9 - - - -
297B TYR 3.3 15.0 + - - +
298B GLU* 3.0 15.8 + - + +
299B ILE 2.9 0.4 - - - -
300B CYS* 1.3 75.9 - - - +
302B PHE* 1.3 65.7 + - - +
304B ARG* 2.5 71.6 + - - +
321B LYS* 4.4 1.6 + - - -
363B PHE* 3.5 24.1 - - - +
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Residues in contact with PHE 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B LEU* 4.8 14.1 - - + -
298B GLU 3.0 6.4 + - - +
299B ILE* 2.9 15.0 + - + +
301B ASP* 1.3 79.6 - - - +
303B LEU* 1.3 62.7 + - + +
306B ALA* 3.4 19.1 - - + +
319B ALA* 3.9 23.6 - - + -
320B THR 4.1 0.2 - - - -
321B LYS* 2.9 55.8 + - + +
324B GLN* 3.5 41.3 - - + -
325B TRP 5.1 0.2 - - - -
326B VAL* 3.8 29.6 - - + -
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Residues in contact with LEU 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B TYR* 5.4 4.5 - - - +
299B ILE* 2.7 34.0 + - + +
300B CYS* 3.7 20.0 - - - +
301B ASP 3.1 0.6 - - - -
302B PHE* 1.3 72.9 - - + +
304B ARG* 1.3 56.5 + - - +
305B GLY 3.1 1.9 + - - -
306B ALA* 3.1 24.5 + - + +
308B VAL* 3.8 16.2 - - + +
319B ALA* 3.7 29.6 - - + -
328B TYR* 3.8 24.5 - - + +
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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