Contacts of the helix formed by residues 323 - 336 (chain B) in PDB entry 1JFZ
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 323 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A ASN* 3.1 21.5 + - - +
317B TYR* 3.6 1.1 + - - -
320B SER* 2.8 29.2 + - - +
321B GLY 5.0 0.7 - - - -
322B ARG* 1.3 72.0 - - - +
324B ALA* 1.3 60.2 + - - +
325B ASN* 3.1 3.1 + - - +
326B PHE* 2.7 44.4 + - + +
327B THR* 2.8 27.2 + - - -
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Residues in contact with ALA 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A PHE* 4.3 15.5 - - + -
124A ALA* 3.7 23.1 - - + -
125A ASN* 2.5 18.9 + - - +
128A ARG* 4.3 4.0 - - - +
246B LEU* 5.7 0.2 - - + -
249B PHE* 5.1 3.6 - - + -
250B PHE* 4.2 6.7 - - + -
317B TYR* 3.7 21.3 - - + -
322B ARG 3.3 2.8 + - - -
323B ASP* 1.3 73.4 - - - +
325B ASN* 1.3 52.0 + - - +
327B THR* 3.7 2.1 - - - -
328B ARG* 2.7 35.6 + - - +
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Residues in contact with ASN 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ARG 4.3 1.3 - - - -
123A ASP* 2.8 31.3 + - - +
124A ALA* 2.8 27.3 + - - +
125A ASN* 3.6 14.5 - - - +
323B ASP* 3.1 4.9 + - - +
324B ALA* 1.3 73.6 - - - +
326B PHE* 1.3 68.1 + - - +
328B ARG* 3.1 29.1 + - - +
329B GLU* 2.9 28.1 + - + +
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Residues in contact with PHE 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B GLY 5.6 1.1 - - - -
213B TYR* 3.8 27.1 - + - -
316B VAL* 5.7 0.2 - - + -
320B SER* 4.5 15.9 - - - -
323B ASP* 2.7 33.7 + - + +
325B ASN* 1.3 72.5 - - - +
327B THR* 1.3 60.0 + - - +
329B GLU* 3.0 9.9 + - + +
330B LEU* 2.8 68.6 + - + +
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Residues in contact with THR 327 (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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250B PHE* 3.8 15.9 - - + -
313B TRP* 3.8 29.3 - - + +
316B VAL* 3.9 17.7 - - + +
317B TYR* 3.4 24.4 + - + +
320B SER* 3.7 6.9 + - - -
323B ASP 2.8 22.4 + - - -
324B ALA* 3.7 4.9 - - - -
326B PHE* 1.3 78.0 - - - +
328B ARG* 1.3 62.4 + - - +
330B LEU* 3.2 9.9 + - - +
331B PHE* 2.9 23.2 + - - +
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Residues in contact with ARG 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A TYR* 3.0 25.4 + - - -
122A ARG* 2.5 36.5 + - - +
124A ALA* 4.4 1.2 - - - +
249B PHE* 4.5 5.6 - - + -
250B PHE* 3.5 34.0 - - + -
253B ASP* 4.1 2.2 + - - -
324B ALA 2.7 20.0 + - - +
325B ASN* 3.2 36.1 + - - +
327B THR* 1.3 73.3 - - - +
329B GLU* 1.3 87.9 + - - +
331B PHE* 3.2 4.5 + - - +
332B TYR* 2.9 69.8 + - + +
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Residues in contact with GLU 329 (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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325B ASN* 2.9 21.2 + - + +
326B PHE* 3.7 9.6 - - + +
328B ARG* 1.3 98.3 + - - +
330B LEU* 1.3 61.2 + - + +
332B TYR* 3.2 23.8 + - - +
333B LYS* 2.8 31.6 + - - +
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Residues in contact with LEU 330 (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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211B LEU 3.8 19.9 - - - +
212B GLY* 4.0 14.1 - - - +
213B TYR* 4.1 17.9 - - + -
313B TRP* 3.6 12.6 - - + -
316B VAL* 4.2 14.6 - - + -
326B PHE* 2.8 59.3 + - + +
327B THR* 3.5 5.6 - - - +
329B GLU* 1.3 78.0 - - + +
331B PHE* 1.3 63.5 - - - +
333B LYS* 3.4 19.1 + - + +
334B LEU* 3.5 19.9 + - - +
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Residues in contact with PHE 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B VAL* 3.7 21.8 - - + -
250B PHE* 3.3 24.7 - + + -
251B ILE* 3.4 33.9 - - + -
283B LEU* 4.8 4.7 - - + -
309B PHE* 4.1 17.0 - + - -
313B TRP* 3.5 31.3 - + + -
327B THR 2.9 13.5 + - - +
328B ARG 3.3 9.0 - - - +
330B LEU* 1.3 77.0 - - - +
332B TYR* 1.3 74.7 + + - +
334B LEU 3.1 2.9 + - - -
335B PHE* 3.0 48.6 + + - -
339B ILE* 3.9 20.0 - - + -
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Residues in contact with TYR 332 (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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250B PHE* 3.0 37.9 + - + -
253B ASP* 3.6 14.7 + - - +
254B LEU* 3.3 50.1 - - + +
257B GLN* 5.2 0.9 - - - -
328B ARG* 2.9 45.0 + - - +
329B GLU* 3.2 26.4 + - - +
331B PHE* 1.3 79.4 - + - +
333B LYS* 1.3 65.0 + - - +
334B LEU 3.0 2.0 - - - -
336B LYS* 2.8 52.8 + - + +
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Residues in contact with LYS 333 (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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211B LEU 5.9 2.9 - - - +
212B GLY* 6.2 4.3 - - - -
329B GLU 2.8 20.2 + - - +
330B LEU* 3.7 15.7 - - + +
331B PHE 3.3 0.4 - - - -
332B TYR* 1.3 74.0 - - - +
334B LEU* 1.3 68.4 + - + +
336B LYS 5.1 0.2 + - - -
337B GLU* 6.0 1.2 - - - +
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Residues in contact with LEU 334 (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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210B LYS 3.4 22.9 - - - +
211B LEU* 4.0 24.2 - - + +
286B LYS* 4.1 16.5 + - + +
287B LEU* 4.7 9.0 - - + -
313B TRP* 3.4 39.0 - - + -
330B LEU 3.5 6.7 + - - +
331B PHE 3.1 5.2 + - - +
332B TYR 3.0 0.2 - - - -
333B LYS* 1.3 90.1 - - + +
335B PHE* 1.3 80.9 + - + +
336B LYS 3.8 0.2 - - - -
337B GLU* 4.8 7.4 - - - +
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Residues in contact with PHE 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B LEU* 3.2 54.5 - - + -
286B LYS* 3.7 18.2 - - + -
287B LEU* 4.1 14.4 - - + -
309B PHE* 3.7 29.6 - + - -
313B TRP* 3.7 20.9 - + - -
331B PHE* 3.0 30.9 + + - +
334B LEU* 1.3 98.6 - - + +
336B LYS* 1.3 67.9 + - - +
337B GLU 3.0 3.6 - - - -
338B ASP* 3.3 6.3 + - + +
339B ILE* 3.0 33.2 + - + +
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Residues in contact with LYS 336 (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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254B LEU* 4.1 27.6 - - + +
258B TYR* 3.2 43.0 + - - -
332B TYR* 2.8 47.6 + - + +
334B LEU 3.8 0.2 - - - -
335B PHE* 1.3 72.0 - - - +
337B GLU* 1.3 65.6 + - - +
339B ILE* 3.3 1.6 + - - +
340B LEU* 3.1 39.5 + - + +
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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