Contacts of the helix formed by residues 286 - 300 (chain A) in PDB entry 2ABJ
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 GLY 286 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A ARG* 3.7 1.3 - - - -
260A ASN* 3.3 15.5 - - - +
284A LEU 2.9 10.9 + - - -
285A PRO* 1.3 75.6 - - - +
287A VAL* 1.3 61.7 + - - -
288A THR 3.4 1.1 - - - -
289A ARG* 3.6 6.4 + - - +
290A ARG* 3.1 26.0 + - - +
420A PLP 3.4 25.4 - - - -
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Residues in contact with VAL 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A PHE* 4.3 10.1 - - + +
110A GLN* 3.9 27.6 - - + +
113A LEU* 3.9 31.6 - - + -
114A ASN* 4.2 21.1 - - - +
117A ARG* 3.7 9.8 - - - +
285A PRO 5.2 0.2 - - - +
286A GLY* 1.3 69.0 - - - -
288A THR* 1.3 62.5 + - - +
290A ARG* 3.2 7.0 + - - +
291A CYS* 2.9 41.8 + - - -
331A THR* 5.3 3.8 - - - +
420A PLP 2.8 19.4 + - - +
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Residues in contact with THR 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A PHE* 5.8 2.8 - - - -
287A VAL* 1.3 77.9 - - - +
289A ARG* 1.3 56.0 + - - +
291A CYS* 3.2 6.7 + - - +
292A ILE* 2.9 42.4 + - + +
329A SER* 3.9 8.3 - - - -
330A GLY 3.4 20.9 + - - +
331A THR* 3.7 6.4 + - - -
334A VAL* 3.4 31.8 - - + +
367A LEU* 4.0 16.6 - - + -
420A PLP 2.8 16.8 + - - -
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Residues in contact with ARG 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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260A ASN* 3.4 41.0 + - + +
262A PHE* 3.7 22.7 - - + -
276A THR* 3.9 9.0 + - - +
277A PRO 3.1 26.5 + - - -
279A LEU* 3.7 32.2 - - - +
283A ILE* 4.3 3.4 - - - +
284A LEU 4.4 2.2 - - - -
285A PRO* 5.3 1.0 - - - +
286A GLY 3.6 14.6 + - - +
288A THR* 1.3 79.1 - - - +
290A ARG* 1.3 72.8 + - - +
292A ILE 3.4 0.2 + - - -
293A LEU* 3.1 42.1 + - + +
306A GLU* 2.7 33.1 + - - +
329A SER* 3.7 10.1 + - - +
420A PLP 4.3 0.6 + - - -
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Residues in contact with ARG 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A GLN* 5.4 1.6 - - - +
113A LEU* 4.7 16.8 - - + -
279A LEU* 5.2 4.9 - - - +
286A GLY 3.1 14.0 + - - +
287A VAL* 3.2 10.3 + - - +
289A ARG* 1.3 89.9 - - - +
291A CYS* 1.3 59.3 + - - +
293A LEU* 3.4 35.3 + - - +
294A ASP* 2.9 64.2 + - - +
297A HIS* 5.1 6.5 + - - -
306A GLU* 4.0 13.3 + - - -
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Residues in contact with CYS 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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109A PHE* 3.6 32.1 - - - -
110A GLN* 3.7 21.1 - - - -
287A VAL* 2.9 21.2 + - - -
288A THR* 3.2 9.6 + - - +
290A ARG* 1.3 77.7 - - - +
292A ILE* 1.3 58.3 + - - +
294A ASP* 3.4 1.0 + - - -
295A LEU* 2.9 30.5 + - - +
367A LEU* 4.0 11.4 - - + -
379A TRP* 3.5 30.9 - - + -
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Residues in contact with ILE 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A PHE* 3.7 28.0 - - + -
274A LEU* 4.0 11.0 - - + -
288A THR* 2.9 26.2 + - + +
289A ARG 3.8 4.0 - - - +
290A ARG 3.3 0.2 - - - -
291A CYS* 1.3 71.9 - - - +
293A LEU* 1.3 62.1 + - - +
295A LEU* 3.3 7.9 + - - +
296A ALA* 2.9 29.0 + - + +
299A TRP* 5.7 0.6 - - + -
327A PHE* 4.3 3.4 - - + -
329A SER* 3.7 28.3 - - - -
335A VAL* 4.2 7.4 - - + -
363A ILE* 3.7 46.4 - - + -
367A LEU* 4.2 7.4 - - + -
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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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262A PHE* 3.8 20.9 - - + -
274A LEU* 5.0 4.0 - - + +
276A THR* 3.9 13.0 - - + -
289A ARG* 3.1 53.2 + - + +
290A ARG* 3.5 26.7 - - - +
292A ILE* 1.3 78.0 - - - +
294A ASP* 1.3 61.6 + - - +
296A ALA* 3.9 2.3 - - - +
297A HIS* 3.0 38.0 + - + +
304A VAL* 3.7 25.5 - - + +
305A SER 5.5 1.1 - - - +
306A GLU* 4.0 16.6 - - + +
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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
----------------------------------------------------------
290A ARG* 2.9 52.0 + - - +
291A CYS* 3.5 5.6 - - - +
293A LEU* 1.3 73.6 - - - +
295A LEU* 1.3 61.2 + - - +
297A HIS* 4.6 3.6 + - - -
298A GLN* 2.9 45.7 + - + +
379A TRP* 3.8 26.5 + - + -
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Residues in contact with LEU 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 CYS 2.9 20.0 + - - +
292A ILE* 3.6 8.5 - - - +
294A ASP* 1.3 76.8 - - - +
296A ALA* 1.3 58.3 + - - +
298A GLN* 3.1 10.0 + - + +
299A TRP* 3.0 55.9 + - + +
363A ILE* 5.2 4.7 - - + -
366A LYS* 3.7 37.2 - - + -
367A LEU* 3.9 27.6 - - + -
370A ILE* 4.9 3.1 - - + -
379A TRP* 3.7 21.3 - - + -
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Residues in contact with ALA 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A LEU* 3.8 21.3 - - + -
292A ILE* 2.9 17.6 + - + +
293A LEU 4.0 2.2 - - - +
295A LEU* 1.3 74.3 - - - +
297A HIS* 1.3 65.6 + - - +
299A TRP* 3.7 16.5 + - + +
300A GLY* 3.3 17.7 + - - -
301A GLU 4.6 1.9 + - - -
302A PHE* 3.9 14.1 - - + +
304A VAL* 3.6 27.4 - - + +
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Residues in contact with HIS 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A ARG* 5.1 5.8 + - - -
293A LEU* 3.0 34.7 + - + +
294A ASP* 3.6 7.9 + - - +
296A ALA* 1.3 77.8 - - - +
298A GLN* 1.3 72.1 + - - +
300A GLY* 3.4 12.6 + - - -
304A VAL* 3.6 40.5 + - + +
306A GLU* 5.4 6.1 - - + -
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Residues in contact with GLN 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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294A ASP* 2.9 38.2 + - + +
295A LEU* 3.1 10.1 + - + +
297A HIS* 1.3 87.2 - - - +
299A TRP* 1.3 70.4 + - + +
300A GLY* 3.3 1.2 + - - -
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Residues in contact with TRP 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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274A LEU* 6.4 0.2 - - + -
295A LEU* 3.0 38.5 + - + +
296A ALA* 3.8 23.6 - - + +
298A GLN* 1.3 78.6 - - + +
300A GLY* 1.3 64.2 + - - +
301A GLU* 3.4 25.8 + - + +
302A PHE* 4.2 10.5 - + + -
359A LEU* 3.7 22.9 - - + -
362A ARG* 3.6 51.7 - - + +
363A ILE* 4.0 23.8 - - + -
366A LYS* 4.2 25.5 - - + +
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Residues in contact with GLY 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 ALA 3.3 9.4 + - - -
297A HIS 3.8 10.1 - - - -
298A GLN 3.2 3.9 - - - -
299A TRP* 1.3 78.8 - - - +
301A GLU* 1.3 59.5 + - - +
302A PHE 3.7 5.6 - - - -
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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