Contacts of the helix formed by residues 358 - 375 (chain G) in PDB entry 5JLH
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 SER 358 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356G GLY 3.8 2.2 + - - -
357G PHE* 1.3 75.2 - - - +
359G HIS* 1.3 72.3 + - - +
360G GLU* 3.2 17.7 + - - +
361G GLU* 3.1 24.0 + - - +
362G ILE* 3.1 24.9 + - - +
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Residues in contact with HIS 359 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315G LEU* 5.4 10.6 - - + +
349G LEU* 5.3 13.0 - - + +
353G ARG* 4.9 26.0 - - - +
357G PHE 4.0 0.4 + - - -
358G SER* 1.3 76.3 + - - +
360G GLU* 1.3 57.8 + - - +
362G ILE* 3.2 14.4 + - + +
363G ILE* 2.9 46.0 + - + +
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Residues in contact with GLU 360 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358G SER* 3.5 13.5 + - - +
359G HIS* 1.3 79.7 + - - +
361G GLU* 1.3 58.0 + - + +
363G ILE* 2.7 30.6 - - + +
364G SER* 2.9 18.3 + - - +
632G ARG* 3.2 35.8 + - - +
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Residues in contact with GLU 361 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357G PHE* 3.2 41.5 - - + +
358G SER* 3.1 22.1 + - - +
360G GLU* 1.3 81.3 - - + +
362G ILE* 1.3 57.7 + - - +
364G SER* 3.2 9.0 + - - -
365G MET* 2.9 37.9 + - - +
454G TRP* 5.1 14.6 - - + -
458G ARG* 3.5 27.3 + - - -
632G ARG* 5.7 5.8 - - - +
633G LEU* 4.8 1.9 - - + +
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Residues in contact with ILE 362 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315G LEU* 5.7 2.9 - - + -
349G LEU* 4.6 19.1 - - + +
352G LEU* 3.2 46.2 - - + -
353G ARG* 5.8 1.6 - - + +
357G PHE* 4.0 16.4 - - + +
358G SER 3.1 17.7 + - - +
359G HIS* 3.4 16.4 - - + +
361G GLU* 1.3 75.9 - - - +
363G ILE* 1.3 63.3 + - - +
365G MET* 3.0 18.3 + - - +
366G LEU* 2.9 47.9 + - + +
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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
----------------------------------------------------------
315G LEU* 5.0 12.8 - - + -
318G ASP* 3.3 30.3 - - + +
319G LEU* 4.1 14.5 - - + +
359G HIS* 2.9 30.6 + - + +
360G GLU* 2.7 35.4 - - + +
362G ILE* 1.3 78.1 - - - +
364G SER* 1.3 57.9 + - - +
366G LEU* 3.5 6.1 + - - +
367G ARG* 2.9 53.2 + - - +
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Residues in contact with SER 364 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360G GLU* 2.9 18.9 + - - +
361G GLU* 3.2 10.6 + - - -
363G ILE* 1.3 79.1 - - - +
365G MET* 1.3 63.3 + - - +
367G ARG* 3.2 17.1 + - - +
368G MET* 3.1 18.2 + - - +
632G ARG* 4.6 11.1 + - - -
633G LEU* 3.4 36.1 - - - +
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Residues in contact with MET 365 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248G PHE* 3.8 30.3 - - + -
352G LEU* 4.4 16.6 - - + -
357G PHE* 5.5 5.6 - - - -
361G GLU* 2.9 23.0 + - - +
362G ILE* 3.0 27.8 + - - +
364G SER* 1.3 76.8 - - - +
366G LEU* 1.3 64.1 + - + +
368G MET* 3.1 9.1 + - - +
369G VAL* 2.9 31.5 + - - +
451G LEU* 4.7 7.8 - - + +
454G TRP* 4.0 30.1 - - + -
455G LEU* 4.3 19.5 - - + -
633G LEU* 3.8 9.6 - - + -
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Residues in contact with LEU 366 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248G PHE* 5.7 3.1 - - + -
303G ILE* 5.5 11.4 - - + -
307G LEU* 3.6 16.7 - - + +
315G LEU* 3.9 19.3 - - + -
319G LEU* 3.1 21.8 - - + +
345G PHE* 3.6 37.2 - - + -
349G LEU* 4.8 2.0 - - + -
352G LEU* 5.0 8.1 - - + -
362G ILE* 2.9 38.0 + - + +
363G ILE* 4.0 4.3 - - - +
365G MET* 1.3 85.7 - - + +
367G ARG* 1.3 56.9 + - - +
369G VAL* 3.2 11.1 + - + +
370G SER 2.9 23.2 + - - -
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Residues in contact with ARG 367 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318G ASP* 4.1 23.1 + - - +
319G LEU* 3.6 19.0 - - + +
363G ILE* 2.9 46.7 + - - +
364G SER* 3.3 18.8 + - - +
366G LEU* 1.3 75.4 - - - +
368G MET* 1.3 57.3 + - - +
370G SER* 3.0 7.8 + - - -
371G ALA 2.9 20.8 + - - -
402G ARG 5.9 0.4 - - - -
403G LEU* 3.3 40.6 - - + +
631G ASP* 5.2 9.4 + - - -
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Residues in contact with MET 368 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364G SER 3.1 11.3 + - - +
365G MET* 3.1 12.1 + - - +
367G ARG* 1.3 72.4 - - - +
369G VAL* 1.3 63.7 + - - +
371G ALA* 2.8 26.3 + - + +
372G VAL* 2.9 15.4 + - - +
403G LEU* 5.3 0.6 + - - -
404G LEU* 5.3 9.6 - - + -
447G THR* 3.3 43.2 - - + +
451G LEU* 3.6 28.2 - - + +
633G LEU* 4.4 8.7 - - + -
634G THR* 5.1 13.0 - - - +
637G ILE* 3.4 34.5 - - + -
638G TRP* 5.4 2.2 - - - +
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Residues in contact with VAL 369 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248G PHE* 4.5 15.9 - - + -
303G ILE* 4.5 13.2 - - + -
304G PHE* 3.8 28.7 - - + -
307G LEU* 3.7 20.6 - - + -
365G MET 2.9 21.6 + - - +
366G LEU* 3.2 12.8 + - + +
368G MET* 1.3 74.4 - - - +
370G SER* 1.3 62.5 + - - +
372G VAL* 3.0 22.9 - - - +
373G LEU* 3.5 7.6 - - - +
448G TYR* 5.1 3.6 - - + -
451G LEU* 3.6 22.4 - - + -
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Residues in contact with SER 370 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307G LEU* 4.4 1.0 - - - +
319G LEU* 3.7 13.8 + - - -
321G LEU* 3.3 33.7 - - - +
327G TYR* 4.3 0.9 + - - -
366G LEU 2.9 11.4 + - - -
367G ARG 3.0 10.1 + - - -
369G VAL* 1.3 77.9 - - - +
371G ALA* 1.3 50.2 + - - +
373G LEU* 2.9 10.2 + - - +
374G GLN* 2.8 51.4 + - - +
403G LEU* 3.7 7.8 - - - +
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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
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367G ARG 2.9 6.6 + - - +
368G MET* 2.8 25.9 + - + +
370G SER* 1.3 75.6 - - - +
372G VAL* 1.3 59.4 + - - +
374G GLN* 3.0 14.6 + - - +
375G PHE* 2.8 27.4 + - + -
400G LEU* 4.5 14.2 - - + +
403G LEU* 3.6 19.5 - - + -
404G LEU* 4.8 11.0 - - + -
447G THR* 5.6 2.5 - - + -
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Residues in contact with VAL 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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291G ALA* 5.2 9.6 - - + -
304G PHE* 4.2 21.5 - - + -
329G PHE* 3.6 11.5 - - + -
368G MET 2.9 10.2 + - - +
369G VAL* 3.0 29.2 - - - +
371G ALA* 1.3 75.7 - - - +
373G LEU* 1.3 67.4 + - + +
375G PHE* 3.3 25.5 + - - +
444G ALA* 3.2 38.6 - - + +
447G THR* 4.5 8.2 - - + +
448G TYR* 4.2 16.6 - - + -
451G LEU* 6.1 0.4 - - + -
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Residues in contact with LEU 373 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291G ALA 5.7 2.0 - - - +
304G PHE* 4.4 32.8 - - + +
307G LEU* 4.8 9.4 - - + -
308G LEU* 4.8 15.0 - - + -
321G LEU* 5.2 1.3 - - + -
327G TYR* 3.3 33.4 - - + -
329G PHE* 4.4 14.1 - - + +
330G LEU* 3.9 38.4 - - + -
369G VAL 3.5 15.0 - - - +
370G SER* 2.9 11.7 + - - +
372G VAL* 1.3 85.7 - - + +
374G GLN* 1.3 65.7 + - - +
376G GLY* 3.0 14.6 + - - -
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Residues in contact with GLN 374 (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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319G LEU 4.7 1.2 + - - -
320G LEU 3.7 2.6 + - - -
322G GLU* 5.8 0.2 - - - +
327G TYR* 3.5 21.4 + - - -
370G SER* 2.8 31.8 + - - +
371G ALA* 3.0 10.7 + - - +
373G LEU* 1.3 71.5 - - - +
375G PHE* 1.3 65.0 + - - +
376G GLY 3.0 2.7 - - - -
377G ASN* 2.7 45.5 + - - +
378G ILE* 3.6 8.0 + - - +
396G ALA* 4.7 5.8 - - - +
399G LYS* 3.2 43.1 - - - +
400G LEU* 5.0 18.1 - - + +
403G LEU* 3.8 12.3 - - + +
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Residues in contact with PHE 375 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329G PHE* 3.6 21.7 - - + -
371G ALA* 2.8 42.7 + - + -
372G VAL* 3.4 19.5 - - - +
373G LEU 3.1 0.4 - - - -
374G GLN* 1.3 76.3 - - - +
376G GLY* 1.3 56.9 + - - +
378G ILE* 2.8 28.3 - - + +
400G LEU* 4.5 28.9 - - + +
404G LEU* 5.2 7.0 - - + -
411G PHE* 5.4 3.4 - + - -
440G LEU* 3.8 29.9 - - + +
443G LEU* 3.7 31.0 - - + -
444G ALA* 3.8 11.7 - - + -
447G THR* 4.1 18.8 - - + -
626G LEU* 5.8 4.5 - - + -
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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