Contacts of the helix formed by residues 357 - 372 (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 PRO 357 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197G PHE* 4.0 20.2 - - + -
325G GLU* 3.3 18.6 - - - +
337G PRO* 4.2 2.5 - - + -
352G THR* 3.3 26.9 - - + +
353G MET* 3.9 29.4 - - + -
355G ASN 3.3 4.7 - - - +
356G GLY* 1.3 79.3 - - - +
358G LYS* 1.3 63.9 + - - +
359G LEU 3.5 0.7 - - - -
360G ALA* 3.8 14.1 - - + -
361G SER* 2.8 33.2 + - - +
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Residues in contact with LYS 358 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264G TYR* 5.8 0.9 - - + -
324G ARG* 4.3 21.5 - - - +
325G GLU* 3.1 4.9 + - - +
355G ASN 2.9 20.2 + - - +
356G GLY* 3.4 5.4 - - - -
357G PRO* 1.3 71.0 - - - +
359G LEU* 1.3 57.6 + - - +
361G SER* 3.7 4.8 - - - -
362G ARG* 3.1 27.9 + - - +
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Residues in contact with LEU 359 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264G TYR* 3.7 38.4 - - + -
274G LEU* 3.8 26.5 - - + -
299G TRP* 3.7 30.5 - - + -
302G PHE* 3.8 21.8 - - + -
325G GLU* 2.7 21.0 + - - +
327G PHE* 4.2 8.3 - - + -
358G LYS* 1.3 72.5 - - - +
360G ALA* 1.3 64.6 + - - +
362G ARG* 3.2 11.2 + - - +
363G ILE* 3.0 36.6 + - + +
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Residues in contact with ALA 360 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197G PHE* 4.1 5.4 - - + -
325G GLU* 2.8 17.1 + - - +
327G PHE* 4.2 19.0 - - + -
335G VAL* 3.7 28.3 - - + +
337G PRO* 4.7 3.4 - - + -
352G THR* 5.4 0.7 - - + -
357G PRO* 3.8 19.7 - - + -
358G LYS 3.4 0.2 - - - -
359G LEU* 1.3 76.8 - - - +
361G SER* 1.3 56.5 + - - +
363G ILE* 3.5 3.9 + - - +
364G LEU* 3.0 28.9 + - - +
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Residues in contact with SER 361 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197G PHE* 3.7 20.3 - - - -
356G GLY 4.9 1.2 - - - -
357G PRO* 2.8 26.8 + - - +
358G LYS* 3.7 4.9 - - - -
360G ALA* 1.3 74.0 - - - +
362G ARG* 1.3 61.2 + - - +
364G LEU* 3.4 4.5 + - - +
365G SER* 2.9 35.5 + - - -
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Residues in contact with ARG 362 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299G TRP* 3.4 56.9 - - + +
301G GLU* 2.8 43.6 + - - -
302G PHE* 5.0 4.8 - - - -
358G LYS 3.1 18.8 + - - +
359G LEU* 3.5 11.1 - - - +
361G SER* 1.3 76.8 - - - +
363G ILE* 1.3 51.6 + - - +
365G SER* 3.7 5.2 - - - -
366G LYS* 2.8 39.3 + - + +
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Residues in contact with ILE 363 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274G LEU* 5.3 0.4 - - + -
292G ILE* 3.6 39.3 - - + -
295G LEU* 5.2 4.0 - - + -
299G TRP* 4.1 20.0 - - + -
327G PHE* 3.6 33.9 - - + -
334G VAL* 5.0 0.2 - - + -
335G VAL* 3.8 13.9 - - + -
359G LEU* 3.0 32.9 + - + +
360G ALA* 3.7 4.0 - - - +
362G ARG* 1.3 72.4 - - - +
364G LEU* 1.3 66.9 + - - +
366G LYS* 3.2 5.7 + - - +
367G LEU* 2.9 40.5 + - + +
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Residues in contact with LEU 364 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197G PHE* 3.7 32.3 - - + -
333G CYS 4.5 4.7 - - - +
334G VAL* 3.9 33.9 - - + -
335G VAL* 4.8 4.2 - - + +
360G ALA 3.0 19.1 + - - +
361G SER* 3.7 4.5 - - - +
363G ILE* 1.3 75.4 - - - +
365G SER* 1.3 57.3 + - - +
367G LEU* 4.1 0.3 - - - +
368G THR* 2.6 58.9 + - - +
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Residues in contact with SER 365 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361G SER* 2.9 20.8 + - - -
362G ARG* 3.7 5.6 - - - -
364G LEU* 1.3 75.0 - - - +
366G LYS* 1.3 60.7 + - - +
368G THR* 3.8 4.4 - - - -
369G ASP* 2.9 44.7 + - - +
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Residues in contact with LYS 366 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295G LEU* 4.2 20.6 - - + -
299G TRP* 3.9 29.3 - - + +
362G ARG* 2.8 25.4 + - + +
363G ILE* 3.6 4.7 - - - +
365G SER* 1.3 74.2 - - - +
367G LEU* 1.3 62.5 + - - +
369G ASP* 3.2 6.6 + - - +
370G ILE* 3.0 33.3 + - + +
375G GLU* 3.1 38.0 + - - +
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Residues in contact with LEU 367 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109G PHE* 3.9 13.4 - - + -
288G THR* 3.9 19.1 - - + -
291G CYS* 3.9 11.4 - - + -
292G ILE* 4.4 5.4 - - + -
295G LEU* 3.9 14.8 - - + -
334G VAL* 3.6 30.5 - - + -
363G ILE* 2.9 34.4 + - + +
366G LYS* 1.3 70.5 - - - +
368G THR* 1.3 60.7 + - - +
370G ILE* 3.3 5.5 + - + +
371G GLN* 2.9 44.5 + - - +
379G TRP* 3.8 29.4 - - + -
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Residues in contact with THR 368 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154G THR 4.7 3.6 - - - +
334G VAL* 5.2 1.4 - - - +
364G LEU* 2.6 41.5 + - - +
365G SER* 3.8 5.4 - - - -
367G LEU* 1.3 76.1 - - - +
369G ASP* 1.3 57.6 + - - +
371G GLN* 3.2 12.1 + - - -
372G TYR* 2.9 52.4 + - + +
374G ARG* 3.3 24.2 - - - +
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Residues in contact with ASP 369 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365G SER* 2.9 32.0 + - - +
366G LYS* 3.5 7.9 - - - +
368G THR* 1.3 76.6 - - - +
370G ILE* 1.3 60.2 + - - +
373G GLY 3.3 1.6 + - - -
374G ARG* 2.9 67.6 + - + +
375G GLU* 3.2 23.5 + - + +
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Residues in contact with ILE 370 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107G ARG* 4.8 0.2 - - - -
109G PHE* 3.9 13.7 - - + -
295G LEU* 5.0 4.9 - - + -
366G LYS* 3.0 26.1 + - + +
367G LEU* 3.7 9.0 - - + +
369G ASP* 1.3 75.0 - - - +
371G GLN* 1.3 65.4 + - - +
373G GLY* 3.1 13.7 + - - -
375G GLU* 3.9 33.4 - - + +
377G SER* 3.8 31.2 - - - +
379G TRP* 3.8 30.1 - - + -
380G THR* 3.5 26.4 + - + +
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Residues in contact with GLN 371 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99G PHE* 3.5 61.8 - - + +
107G ARG* 4.0 16.5 + - - +
109G PHE* 3.6 35.2 - - + -
334G VAL* 4.5 20.0 - - - +
367G LEU* 2.9 36.4 + - - +
368G THR* 3.7 13.6 + - - +
370G ILE* 1.3 76.1 - - - +
372G TYR* 1.3 63.1 + - + +
373G GLY 3.3 2.5 + - - -
380G THR* 4.3 7.0 - - - -
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Residues in contact with TYR 372 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99G PHE* 3.6 33.0 - + + -
100G ARG 3.3 26.9 - - - -
101G GLY* 3.3 8.4 - - - -
102G VAL* 2.8 31.5 + - - +
107G ARG* 4.0 0.4 - - - -
153G SER 3.8 1.1 - - - -
154G THR* 3.2 38.6 + - + -
155G SER 3.8 1.9 - - - -
156G ALA 2.6 40.0 + - - -
157G SER* 4.3 0.2 - - - -
368G THR* 2.9 43.3 + - + +
369G ASP 4.7 0.2 - - - +
371G GLN* 1.3 80.6 - - + +
373G GLY* 1.3 61.6 + - - +
374G ARG* 3.2 22.2 + - - +
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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