Contacts of the helix formed by residues 347 - 358 (chain G) in PDB entry 4P0S
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 347 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343G SER 3.0 5.0 + - - -
344G ILE* 3.2 6.9 + - - -
345G ILE 3.1 5.1 + - - -
346G ASP* 1.3 77.4 - - - +
348G ARG* 1.3 63.9 + - - +
349G PHE 3.2 2.7 - - - -
350G ARG* 3.3 16.7 + - - +
351G GLU 3.3 7.3 + - - -
461H LEU* 2.9 44.3 - - - +
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Residues in contact with ARG 348 (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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335G LYS* 3.4 19.2 - - - +
339G ASP* 3.5 16.4 + - - -
342G SER* 4.4 13.1 - - - -
343G SER* 2.8 32.9 + - - +
346G ASP* 3.3 35.2 + - - +
347G GLY* 1.3 71.0 - - - +
349G PHE* 1.3 60.5 + - - +
351G GLU* 2.7 35.7 + - - +
352G GLN* 2.8 29.1 + - + +
461H LEU 4.5 0.7 - - - -
463H SER* 4.5 15.0 - - - +
54P G 4.2 23.8 + - - +
55P T 3.8 25.1 + - - +
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Residues in contact with PHE 349 (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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340G LEU* 3.5 22.9 - - + -
343G SER* 3.1 18.3 + - - +
344G ILE* 3.8 28.0 - - + +
347G GLY 5.0 0.4 - - - -
348G ARG* 1.3 82.6 - - - +
350G ARG* 1.3 69.1 + - + +
352G GLN* 3.8 4.4 + - - +
353G LYS* 3.3 56.6 + - + +
366G TYR* 3.5 39.5 - + - -
387G ALA* 5.1 10.3 - - + -
391G THR* 3.3 26.9 - - + -
1M G 5.1 4.7 - - - -
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Residues in contact with ARG 350 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344G ILE 6.0 1.1 - - - +
347G GLY* 3.3 10.4 + - - +
348G ARG 3.1 1.0 - - - -
349G PHE* 1.3 85.4 - - + +
351G GLU* 1.3 63.4 + - - +
353G LYS* 3.6 14.2 + - - +
354G PHE* 3.4 20.3 + - - +
448H PHE* 5.4 1.2 - - - -
449H LYS* 4.1 21.6 - - - +
452H ARG* 4.0 29.3 - - - +
453H ASP* 5.0 14.2 + - - +
456H THR* 6.2 2.0 - - - +
461H LEU* 3.2 36.8 - - + +
1M G 3.3 38.5 + - - +
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Residues in contact with GLU 351 (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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347G GLY 3.3 8.7 + - - +
348G ARG* 2.7 20.6 + - - +
350G ARG* 1.3 76.6 - - - +
352G GLN* 1.3 71.6 + - - +
353G LYS 3.1 1.7 + - - -
354G PHE* 3.3 10.3 + - - +
355G ARG* 2.9 41.5 + - + +
458H SER* 4.8 7.9 - - - +
461H LEU* 4.5 1.3 - - - +
462H GLU* 3.6 37.6 - - + +
463H SER* 3.2 21.7 + - - -
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Residues in contact with GLN 352 (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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333G GLU* 2.5 36.3 + - - +
335G LYS* 3.2 27.4 + - - +
343G SER* 4.6 1.0 + - - -
348G ARG* 2.8 39.5 + - + +
349G PHE* 4.4 3.3 - - - +
351G GLU* 1.3 81.6 - - + +
353G LYS* 1.3 60.6 + - - +
355G ARG* 3.1 30.0 - - - +
356G LEU* 3.1 18.5 - - + +
366G TYR* 2.9 24.4 + - - +
54P G 4.1 17.4 + - - +
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Residues in contact with LYS 353 (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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349G PHE* 3.3 54.3 + - + +
350G ARG* 3.8 13.5 - - - +
351G GLU 3.1 0.4 - - - -
352G GLN* 1.3 78.8 - - - +
354G PHE* 1.3 66.6 + - - +
356G LEU* 3.2 23.3 + - - +
357G LYS* 3.5 8.2 + - - +
366G TYR* 3.6 22.9 - - + -
391G THR* 4.1 5.6 + - + -
395G ASP* 2.4 40.4 + - - +
397G PHE* 3.7 20.8 - - + -
453H ASP* 5.6 1.8 + - - -
1M G 4.2 15.0 + - - -
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Residues in contact with PHE 354 (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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350G ARG 3.4 8.4 + - - +
351G GLU* 3.3 9.4 + - - +
353G LYS* 1.3 76.7 - - - +
355G ARG* 1.3 64.6 + - + +
357G LYS* 3.0 37.6 + - + +
358G ARG* 3.5 48.1 - - + +
453H ASP* 4.4 32.5 - - + -
454H GLU* 6.1 0.7 - - - -
458H SER* 4.1 30.3 - - - -
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Residues in contact with ARG 355 (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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304G HIS 3.1 26.0 + - - -
305G VAL* 4.1 19.3 - - + +
351G GLU* 2.9 41.6 + - + +
352G GLN* 3.1 19.0 - - - +
354G PHE* 1.3 80.3 - - + +
356G LEU* 1.3 62.6 + - - +
357G LYS 3.4 0.5 + - - -
358G ARG* 3.5 17.3 + - - +
359G CYS* 3.6 16.8 + - - +
463G ALA* 4.4 12.5 - - - +
53P T 5.9 0.4 + - - -
54P G 5.2 8.3 + - - -
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Residues in contact with LEU 356 (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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305G VAL* 3.4 26.5 - - + -
306G GLY* 4.0 17.7 - - - +
331G ILE* 4.8 11.0 - - + -
333G GLU* 4.5 12.1 - - + +
352G GLN* 3.1 22.9 - - + +
353G LYS* 3.3 20.6 - - - +
355G ARG* 1.3 80.7 - - - +
357G LYS* 1.4 58.9 + - - +
358G ARG 3.2 0.9 + - - -
359G CYS* 3.6 20.5 + - - -
361G LEU 3.9 1.7 - - - +
364G ARG* 3.6 22.9 - - + +
366G TYR* 4.1 15.0 - - + -
397G PHE* 4.0 22.4 - - + -
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Residues in contact with LYS 357 (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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353G LYS 3.5 11.2 + - - +
354G PHE* 3.0 29.4 + - + +
356G LEU* 1.4 77.3 - - - +
358G ARG* 1.3 61.3 + - + +
359G CYS 3.8 0.4 - - - -
360G GLY 5.4 0.2 + - - -
361G LEU 5.3 1.0 - - - +
362G GLU* 4.7 9.7 - - - +
364G ARG* 3.5 37.9 + - - +
394G ILE 5.5 0.4 - - - -
395G ASP* 4.0 30.8 + - - +
397G PHE* 4.7 5.6 - - + -
450H LYS* 4.5 19.8 - - - +
453H ASP* 3.7 28.2 + - - +
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Residues in contact with ARG 358 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354G PHE* 3.5 48.0 - - + +
355G ARG* 3.7 10.1 - - - +
356G LEU 3.2 0.4 - - - -
357G LYS* 1.3 83.4 - - + +
359G CYS* 1.3 57.0 + - - +
360G GLY 3.5 3.1 - - - +
362G GLU* 6.0 0.4 - - - -
433G TRP* 4.6 11.8 - - - -
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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