Contacts of the helix formed by residues 342 - 356 (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 ARG 342 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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306G GLN* 4.8 1.4 + - - +
309G GLY* 3.2 26.9 + - - +
310G GLY* 3.5 28.5 + - - +
311G ALA 5.4 2.0 + - - -
312G GLY* 5.1 11.9 - - - -
340G GLN 3.7 8.5 - - - +
341G GLU* 1.3 73.6 + - + +
343G GLU* 1.3 57.0 + - - +
344G LEU* 3.3 2.0 - - - +
345G PHE* 3.5 10.1 - - - +
346G GLN* 3.0 27.5 + - - +
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Residues in contact with GLU 343 (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 GLN* 5.9 3.4 - - + -
341G GLU 2.2 23.9 + - - +
342G ARG* 1.3 68.3 - - - +
344G LEU* 1.3 81.5 + - + +
346G GLN* 3.1 9.8 + - + +
347G GLU* 2.9 28.2 + - - +
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Residues in contact with LEU 344 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302G HIS* 6.4 0.2 - - - +
306G GLN* 3.8 17.7 - - + +
339G GLY* 5.2 4.7 - - - +
341G GLU* 3.4 35.6 + - - +
342G ARG 3.3 0.2 - - - -
343G GLU* 1.3 90.9 + - + +
345G PHE* 1.3 54.7 - - - +
347G GLU* 3.0 9.9 + - + +
348G THR* 2.8 36.9 + - - +
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Residues in contact with PHE 345 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303G ILE* 5.2 7.9 - - + -
306G GLN* 3.2 43.9 - - + +
307G LEU* 4.0 12.6 - - + -
310G GLY* 3.2 30.5 - - - -
311G ALA* 3.7 14.1 - - + -
315G LEU* 4.1 8.1 - - + -
342G ARG* 3.5 9.8 - - - +
344G LEU* 1.3 78.0 - - - +
346G GLN* 1.3 72.5 + - - +
348G THR* 3.1 9.5 + - - -
349G LEU* 3.0 59.0 + - + +
366G LEU* 3.6 28.3 - - + -
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Residues in contact with GLN 346 (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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310G GLY 5.0 2.9 - - - +
342G ARG 3.0 15.1 + - - +
343G GLU* 3.1 14.6 + - + +
345G PHE* 1.3 89.2 - - - +
347G GLU* 1.3 62.3 + - - +
349G LEU* 3.3 23.4 + - - +
350G GLU* 3.5 11.1 + - - +
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Residues in contact with GLU 347 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240G GLN* 4.1 18.5 + - - +
243G PRO* 5.5 8.5 - - + +
343G GLU* 2.9 22.5 + - - +
344G LEU* 3.0 13.2 + - + +
346G GLN* 1.3 75.5 - - - +
348G THR* 1.3 59.2 + - - +
350G GLU* 3.3 14.4 + - - +
351G SER* 2.9 28.4 + - - -
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Residues in contact with THR 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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243G PRO* 4.2 24.2 + - - +
244G ILE* 4.3 9.2 - - + -
247G ALA* 4.3 11.5 - - + +
248G PHE* 6.4 0.9 - - + -
303G ILE* 5.4 6.3 - - + -
306G GLN* 3.5 17.5 + - - +
344G LEU* 2.8 19.3 + - - +
345G PHE* 3.1 9.6 + - - -
347G GLU* 1.3 75.6 - - - +
349G LEU* 1.3 65.8 + - + +
351G SER* 2.2 32.0 + - - +
352G LEU* 2.9 18.2 + - + +
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Residues in contact with LEU 349 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315G LEU* 4.7 12.1 - - + -
345G PHE* 3.0 67.6 + - + +
346G GLN* 3.7 19.7 - - - +
347G GLU 3.2 0.8 - - - -
348G THR* 1.3 77.3 - - + +
350G GLU* 1.3 62.8 + - - +
352G LEU* 3.1 17.2 + - + +
353G ARG* 2.9 21.8 + - - +
359G HIS* 5.3 11.7 - - + +
362G ILE* 4.6 17.0 - - + +
366G LEU* 4.8 4.3 - - + -
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Residues in contact with GLU 350 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240G GLN* 5.5 2.7 - - - +
346G GLN 3.5 7.1 + - - +
347G GLU* 3.3 20.3 + - - +
349G LEU* 1.3 78.2 - - - +
351G SER* 1.3 65.3 + - - +
353G ARG* 2.9 28.9 + - - +
354G VAL* 3.0 29.4 + - + +
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Residues in contact with SER 351 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240G GLN* 2.8 38.8 - - - +
243G PRO* 4.1 8.7 - - - +
244G ILE* 3.1 19.0 - - - +
347G GLU* 2.9 15.5 + - - -
348G THR* 2.2 35.5 + - - +
350G GLU* 1.3 77.0 - - - +
352G LEU* 1.3 57.9 + - - +
354G VAL* 3.1 7.3 - - - +
355G LEU* 3.1 24.4 - - - +
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Residues in contact with LEU 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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244G ILE* 3.4 34.1 - - + -
248G PHE* 6.2 2.9 - - + -
348G THR* 2.9 25.2 + - + +
349G LEU* 3.3 14.6 - - + +
351G SER* 1.3 74.5 + - - +
353G ARG* 1.3 66.8 + - - +
355G LEU* 3.1 22.0 + - + +
356G GLY 3.2 4.3 + - - -
357G PHE* 3.5 18.9 + - + -
362G ILE* 3.2 46.4 - - + -
365G MET* 4.4 18.4 - - + -
366G LEU* 5.0 6.5 - - + -
455G LEU* 5.1 1.8 - - + -
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Residues in contact with ARG 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 LEU 2.9 12.4 + - - +
350G GLU* 2.9 23.6 + - - +
352G LEU* 1.3 76.8 - - - +
354G VAL* 1.3 58.7 + - - +
356G GLY* 2.7 25.6 + - - -
357G PHE 3.9 15.6 + - - +
359G HIS* 4.9 26.1 - - - +
362G ILE* 5.8 2.5 - - + -
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Residues in contact with VAL 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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237G GLN* 5.1 3.8 - - + +
240G GLN* 3.5 28.7 - - + +
350G GLU* 3.0 24.9 + - - +
351G SER 3.1 17.7 - - - +
353G ARG* 1.3 77.3 - - - +
355G LEU* 1.3 66.2 + - + +
356G GLY* 3.1 2.6 + - - -
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Residues in contact with LEU 355 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237G GLN* 3.6 46.3 - - + +
240G GLN* 4.0 15.7 - - + +
241G ALA* 5.0 0.7 - - - +
244G ILE* 3.8 27.8 - - + -
351G SER 3.1 21.8 - - - +
352G LEU* 3.1 12.5 + - + +
354G VAL* 1.3 81.9 - - + +
356G GLY* 1.3 57.2 + - - +
357G PHE* 3.6 15.7 - - + -
459G LEU* 4.0 23.8 - - + -
462G ALA* 3.5 25.1 - - + +
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Residues in contact with GLY 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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352G LEU 3.2 0.6 + - - -
353G ARG 2.7 14.1 + - - -
354G VAL 3.0 3.1 - - - -
355G LEU* 1.3 81.5 - - - +
357G PHE* 1.3 70.3 + - - +
358G SER* 3.8 1.4 + - - -
361G GLU* 4.6 0.5 - - - +
458G ARG* 4.8 5.5 + - - -
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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
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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