Contacts of the helix formed by residues 286 - 300 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117G ARG* 3.6 1.3 - - - -
260G ASN* 3.2 22.8 - - - +
284G LEU* 2.8 11.5 + - - -
285G PRO* 1.3 75.1 - - - +
287G VAL* 1.3 61.1 + - - -
288G THR 3.4 1.3 - - - -
289G ARG* 3.4 6.3 + - - +
290G ARG* 3.0 24.6 + - - +
420G PLP 3.4 19.7 - - - -
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Residues in contact with VAL 287 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109G PHE* 4.4 16.2 - - + +
110G GLN* 4.2 21.3 - - + -
113G LEU* 3.9 33.4 - - + +
114G ASN* 4.0 21.3 - - - +
117G ARG* 3.8 10.3 - - - +
285G PRO 5.0 0.9 - - - +
286G GLY* 1.3 70.1 - - - -
288G THR* 1.3 65.3 + - - +
290G ARG* 3.2 7.1 + - - +
291G CYS* 2.8 34.5 + - - -
331G THR* 5.2 5.2 - - - +
420G PLP 2.9 17.2 + - - +
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Residues in contact with THR 288 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109G PHE* 5.7 2.5 - - + -
287G VAL* 1.3 81.0 - - - +
289G ARG* 1.3 56.0 + - - +
291G CYS* 3.3 6.7 + - - +
292G ILE* 2.9 39.0 + - + +
329G SER* 3.9 12.6 - - - -
330G GLY 3.3 16.4 - - - +
331G THR* 3.6 5.7 + - - -
334G VAL* 3.4 30.5 - - + +
367G LEU* 3.9 23.1 - - + -
420G PLP 2.8 16.4 + - - -
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Residues in contact with ARG 289 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260G ASN* 3.4 40.6 - - + +
262G PHE* 3.7 27.8 - - + -
276G THR* 3.8 11.0 + - - +
277G PRO 3.0 26.9 + - - -
279G LEU* 3.5 34.7 - - - +
283G ILE* 4.3 3.6 - - - +
284G LEU 4.3 2.0 - - - -
285G PRO* 5.2 1.0 - - - +
286G GLY 3.4 14.9 + - - +
288G THR* 1.3 78.2 - - - +
290G ARG* 1.3 74.8 + - - +
292G ILE* 3.3 2.8 + - - +
293G LEU* 3.0 42.5 + - + +
306G GLU* 2.7 30.1 + - - -
329G SER* 3.7 3.0 + - - -
420G PLP 4.3 0.6 + - - -
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Residues in contact with ARG 290 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A GLU* 3.7 35.9 + - - +
152A TYR* 4.1 3.2 + - - -
110G GLN* 5.1 3.4 - - - +
113G LEU* 4.3 19.5 - - + -
279G LEU* 5.2 5.9 - - - +
286G GLY 3.0 12.0 + - - +
287G VAL* 3.2 11.6 + - - +
289G ARG* 1.3 95.4 - - - +
291G CYS* 1.3 58.7 + - - +
293G LEU* 3.4 31.0 + - - +
294G ASP* 2.9 62.7 + - - +
297G HIS* 5.3 1.0 + - - -
306G GLU* 4.5 3.2 + - - -
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Residues in contact with CYS 291 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109G PHE* 3.6 31.9 - - - -
110G GLN* 3.6 26.0 - - - -
287G VAL 2.8 23.5 + - - +
288G THR* 3.6 7.0 - - - +
290G ARG* 1.3 72.4 - - - +
292G ILE* 1.3 58.0 + - - +
294G ASP* 3.3 3.4 + - - +
295G LEU* 2.9 32.4 + - - +
367G LEU* 3.9 11.9 - - + -
379G TRP* 3.6 26.8 - - + -
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Residues in contact with ILE 292 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262G PHE* 3.8 30.7 - - + -
274G LEU* 3.9 11.9 - - + -
288G THR* 2.9 28.9 + - + +
289G ARG 3.3 4.0 + - - +
291G CYS* 1.3 67.2 - - - +
293G LEU* 1.3 61.1 + - - +
295G LEU* 3.3 8.9 + - - +
296G ALA* 2.8 30.4 + - + +
299G TRP* 5.7 0.2 - - - -
327G PHE* 4.3 1.6 - - + -
329G SER* 3.5 28.7 - - - -
335G VAL* 4.1 7.6 - - + -
363G ILE* 3.6 47.6 - - + -
367G LEU* 4.4 5.2 - - + -
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Residues in contact with LEU 293 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262G PHE* 3.7 20.9 - - + -
274G LEU* 4.9 6.5 - - + +
276G THR* 3.9 15.9 - - + -
289G ARG* 3.0 54.0 + - + +
290G ARG* 3.5 24.5 - - - +
292G ILE* 1.3 77.2 - - - +
294G ASP* 1.3 56.2 + - - +
296G ALA* 3.9 2.7 - - - +
297G HIS* 2.9 42.3 + - + +
304G VAL* 3.8 24.2 - - + -
305G SER 5.9 0.2 - - - -
306G GLU* 4.1 15.9 - - + +
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Residues in contact with ASP 294 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ASN* 3.9 22.6 + - - -
152A TYR* 4.2 8.9 + - - -
110G GLN* 5.1 1.7 + - - -
290G ARG* 2.9 49.3 + - - +
291G CYS 3.4 8.3 - - - +
292G ILE 3.3 0.2 - - - -
293G LEU* 1.3 74.2 - - - +
295G LEU* 1.3 57.6 + - - +
297G HIS* 3.5 3.3 + - - +
298G GLN* 2.4 48.4 + - - +
379G TRP* 3.8 26.8 + - + -
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Residues in contact with LEU 295 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291G CYS 2.9 19.9 + - - +
292G ILE* 3.5 8.1 - - - +
294G ASP* 1.3 77.2 - - - +
296G ALA* 1.3 56.6 + - - +
298G GLN* 3.1 9.8 + - + +
299G TRP* 2.8 65.4 + - + +
363G ILE* 5.2 5.4 - - + -
366G LYS* 4.2 22.7 - - + -
367G LEU* 3.9 28.5 - - + -
370G ILE* 5.0 6.7 - - + -
379G TRP* 3.5 25.1 - - + -
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Residues in contact with ALA 296 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274G LEU* 3.8 15.0 - - + -
292G ILE* 2.8 21.2 + - + +
293G LEU 3.9 2.9 - - - +
295G LEU* 1.3 72.0 - - - +
297G HIS* 1.3 61.2 + - - +
299G TRP* 3.6 16.0 + - + +
300G GLY* 3.4 17.3 + - - -
301G GLU 4.7 0.9 + - - -
302G PHE* 3.8 23.0 - - + +
304G VAL* 3.6 26.1 - - + +
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Residues in contact with HIS 297 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A GLU* 4.8 3.4 - - - -
152A TYR* 3.5 72.6 - + + +
290G ARG* 5.3 0.4 - - - -
293G LEU* 2.9 33.2 + - + +
294G ASP 3.6 3.8 - - - +
296G ALA* 1.3 76.3 - - - +
298G GLN* 1.3 64.0 + - - +
300G GLY* 3.4 13.6 + - - -
304G VAL* 3.6 40.8 + - + +
306G GLU* 5.5 3.8 - - + -
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Residues in contact with GLN 298 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ASN* 4.5 21.2 - - - +
152A TYR* 4.3 10.6 - - - -
294G ASP* 2.4 46.0 + - - +
295G LEU* 3.5 10.7 - - + +
297G HIS* 1.3 82.8 - - - +
299G TRP* 1.3 65.0 + - + +
300G GLY* 3.5 0.7 + - - -
379G TRP* 5.4 4.9 - - - -
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Residues in contact with TRP 299 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274G LEU* 6.5 0.2 - - + -
292G ILE* 5.7 0.7 - - + -
295G LEU* 2.8 49.8 + - + +
296G ALA* 3.9 20.9 - - + +
297G HIS 3.3 0.2 - - - -
298G GLN* 1.3 78.6 - - + +
300G GLY* 1.3 64.0 + - - +
301G GLU* 3.3 26.1 + - + +
302G PHE* 4.1 12.1 - + + -
359G LEU* 3.7 24.2 - - + -
362G ARG* 3.4 51.7 - - + +
363G ILE* 4.1 21.1 - - + -
366G LYS* 3.9 25.4 - - + +
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Residues in contact with GLY 300 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296G ALA 3.4 9.5 + - - -
297G HIS 3.4 10.5 + - - -
298G GLN 3.3 2.9 - - - -
299G TRP* 1.3 78.6 - - - +
301G GLU* 1.3 59.7 + - - +
302G PHE 3.6 5.4 - - - -
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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
------------------------------------------------------------
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