Contacts of the helix formed by residues 358 - 373 (chain G) in PDB entry 6CM9
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 358 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322G LYS* 4.9 0.9 - - - +
356G ASP* 3.4 7.5 - - - +
357G LEU* 1.3 78.7 - - - +
359G VAL* 1.3 77.9 + - - +
360G SER 3.5 6.1 + - - -
361G ILE* 3.4 24.9 + - + +
362G LYS* 3.3 29.6 + - - +
393G GLU* 5.8 0.2 - - - -
42S ARG* 3.2 21.0 + - - -
45S ARG 4.9 3.6 - - - +
46S THR* 2.9 25.4 - - - +
47S SER* 2.6 33.1 + - - -
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Residues in contact with VAL 359 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358G ASP* 1.3 79.8 + - - +
360G SER* 1.3 60.8 + - - +
362G LYS* 3.4 1.4 + - - +
363G ARG* 2.9 37.4 + - - +
393G GLU* 4.1 19.1 - - - +
395G GLU* 4.3 14.8 - - - +
396G PHE* 3.6 24.2 - - + -
42S ARG* 3.8 30.1 - - - +
50S VAL* 6.2 1.8 - - + -
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Residues in contact with SER 360 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326G TYR* 3.6 24.5 - - - -
358G ASP* 3.5 3.4 + - - -
359G VAL* 1.3 78.6 - - - +
361G ILE* 1.3 57.0 + - - +
363G ARG* 3.3 6.3 + - - +
364G ARG* 2.9 34.5 + - - +
42S ARG* 4.4 6.4 + - - -
47S SER* 3.8 9.4 - - - -
49S PHE 2.4 31.9 + - - -
50S VAL* 3.7 8.1 - - - -
51S ASP* 4.2 5.4 + - - +
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Residues in contact with ILE 361 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322G LYS* 3.9 14.1 - - + +
325G ARG* 4.0 11.9 - - + -
326G TYR* 3.6 43.1 - - + +
329G LEU* 3.6 8.7 - - + +
353G CYS* 3.7 35.7 - - + +
356G ASP* 4.2 16.2 - - + +
358G ASP* 3.4 29.8 + - + +
359G VAL 3.3 0.8 - - - -
360G SER* 1.3 77.0 - - - +
362G LYS* 1.3 57.2 + - - +
364G ARG 3.4 0.2 + - - -
365G ALA* 2.9 28.9 + - - +
47S SER* 4.4 3.8 - - - +
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Residues in contact with LYS 362 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353G CYS 3.6 9.0 - - - +
354G LEU* 3.3 33.7 - - + +
356G ASP 3.3 20.8 + - - +
357G LEU* 5.2 6.9 - - - +
358G ASP 3.3 23.7 + - - +
359G VAL 3.4 3.7 + - - +
360G SER 3.4 0.2 - - - -
361G ILE* 1.3 76.7 - - - +
363G ARG* 1.3 58.2 + - - +
365G ALA* 4.5 1.8 - - - -
366G MET* 2.9 30.2 + - - +
388G PHE* 4.7 14.7 - - + -
391G SER 5.5 3.0 + - - -
392G CYS 5.4 1.6 - - - -
393G GLU* 3.9 31.3 + - - +
396G PHE* 4.1 21.7 - - + -
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Residues in contact with ARG 363 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359G VAL* 2.9 24.5 + - - +
360G SER* 3.8 6.5 - - - +
361G ILE 3.2 0.4 - - - -
362G LYS* 1.3 77.7 - - - +
364G ARG* 1.3 60.8 + - + +
366G MET* 3.3 15.4 + - + +
367G GLU* 3.0 38.8 + - - +
395G GLU* 4.2 19.2 + - - +
396G PHE* 3.3 37.3 - - + -
399G ASP* 2.6 33.7 + - - +
51S ASP* 3.8 38.5 + - + +
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Residues in contact with ARG 364 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326G TYR* 3.0 43.3 + - + -
329G LEU* 3.7 28.6 - - + +
330G THR* 4.5 9.5 + - - +
333G LEU* 4.0 18.9 - - + +
360G SER 2.9 21.8 + - - +
363G ARG* 1.3 76.6 - - - +
365G ALA* 1.3 62.1 + - - +
367G GLU* 3.1 29.9 + - - +
368G LEU* 2.9 30.8 + - - +
51S ASP* 2.4 40.5 + - - +
56S LYS* 3.4 27.2 - - - +
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Residues in contact with ALA 365 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329G LEU* 3.4 9.0 - - + +
350G ILE* 3.6 30.5 - - + +
353G CYS* 3.8 13.5 - - + -
354G LEU* 3.7 17.9 - - + +
361G ILE 2.9 18.7 + - - +
364G ARG* 1.3 76.0 - - - +
366G MET* 1.3 57.7 + - - +
368G LEU* 3.9 1.5 - - - +
369G SER* 2.9 34.7 + - - -
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Residues in contact with MET 366 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354G LEU* 3.7 11.2 - - + +
362G LYS 2.9 19.1 + - - +
363G ARG* 3.4 17.3 - - + +
365G ALA* 1.3 77.8 - - - +
367G GLU* 1.3 80.6 + - + +
369G SER* 3.3 4.8 + - - -
370G PHE* 2.9 53.4 + - + -
385G LEU* 5.9 1.3 - - + -
388G PHE* 4.2 16.2 - - + -
396G PHE* 4.6 12.1 - - - +
399G ASP* 3.7 24.5 - - + +
400G CYS* 3.9 26.5 - - - -
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Residues in contact with GLU 367 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333G LEU* 3.7 21.9 - - + +
363G ARG* 3.0 30.1 + - - +
364G ARG* 3.1 32.8 + - - +
366G MET* 1.3 92.2 - - + +
368G LEU* 1.3 58.0 + - - +
370G PHE* 3.4 8.2 + - + +
371G ALA* 2.9 29.1 + - - +
51S ASP* 4.9 5.5 - - - +
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Residues in contact with LEU 368 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329G LEU* 4.1 20.0 - - + +
332G LEU* 3.5 52.3 - - + +
333G LEU* 3.7 13.4 - - + +
336G VAL* 3.9 10.5 - - + -
343G VAL* 4.8 7.9 - - + -
350G ILE* 3.7 36.6 - - + -
364G ARG 2.9 17.9 + - - +
365G ALA 3.9 3.1 - - - +
367G GLU* 1.3 75.4 - - - +
369G SER* 1.3 58.9 + - - +
371G ALA* 3.4 1.1 + - - +
372G LEU* 2.9 33.1 + - + +
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Residues in contact with SER 369 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350G ILE* 3.8 13.2 - - - +
351G VAL* 4.8 8.0 - - - +
354G LEU* 4.6 10.5 - - - +
365G ALA 2.9 24.7 + - - -
366G MET* 3.7 5.8 - - - -
368G LEU* 1.3 77.2 - - - +
370G PHE* 1.3 62.4 + - - +
372G LEU* 3.1 18.2 + - - +
373G VAL* 3.3 20.3 + - - +
381G MET* 4.1 12.8 - - - +
385G LEU* 4.4 20.0 - - - -
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Residues in contact with PHE 370 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366G MET* 2.9 44.7 + - + +
367G GLU* 3.8 7.4 - - + +
369G SER* 1.3 75.3 - - - +
371G ALA* 1.3 60.3 + - - +
372G LEU 3.6 0.2 + - - -
373G VAL* 4.2 11.4 + - + +
385G LEU* 3.6 38.8 - - + -
399G ASP 3.8 3.6 - - - -
400G CYS* 3.6 41.1 - - - -
403G GLY* 3.6 33.7 - - - +
404G ILE* 4.0 8.5 - - + -
407G ALA* 4.7 13.4 - - + +
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Residues in contact with ALA 371 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333G LEU* 4.5 7.9 - - + -
336G VAL* 3.3 40.8 - - + +
340G HIS* 5.0 1.9 - - - -
367G GLU 2.9 17.8 + - - +
368G LEU 3.7 2.2 - - - +
369G SER 3.2 0.2 - - - -
370G PHE* 1.3 76.7 - - - +
372G LEU* 1.3 60.9 + - - +
373G VAL 3.4 3.6 + - - +
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Residues in contact with LEU 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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336G VAL* 4.7 6.7 - - + -
340G HIS* 3.9 13.5 - - + +
343G VAL* 3.8 26.5 - - + -
344G GLN* 3.6 47.0 + - + -
347G ARG* 4.9 9.4 - - + +
350G ILE* 4.2 25.4 - - + -
368G LEU* 2.9 19.9 + - + +
369G SER* 3.1 11.1 + - - +
371G ALA* 1.3 77.6 - - - +
373G VAL* 1.3 64.1 + - - +
374G ASN 3.2 3.6 + - - -
377G ASN* 3.9 5.1 + - - +
381G MET* 4.4 17.5 - - + -
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Residues in contact with VAL 373 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340G HIS* 5.8 0.4 - - - -
369G SER 3.3 17.9 - - - +
370G PHE* 4.6 8.5 - - - +
371G ALA 3.4 5.2 - - - +
372G LEU* 1.3 73.9 - - - +
374G ASN* 1.3 70.7 + - - +
377G ASN* 3.5 10.8 - - - +
378G ILE* 3.7 31.0 - - + -
381G MET* 3.6 24.7 - - + -
382G MET* 5.4 1.8 - - + -
385G LEU* 4.8 11.0 - - + -
407G ALA* 5.1 13.2 - - + +
411G TYR* 3.2 24.9 - - + -
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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
------------------------------------------------------------
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