Contacts of the helix formed by residues 359 - 376 (chain S) in PDB entry 5JPQ
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 ILE 359 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264S ASN* 5.0 7.2 - - + +
351S VAL* 5.9 8.4 - - + +
357S ARG 3.4 5.7 + - - +
358S PHE* 1.3 73.6 - - - +
360S GLY* 1.3 61.4 + - - +
361S ASP* 3.2 5.0 + - - -
362S GLN* 3.6 8.2 + - + +
363S LEU* 3.5 18.3 + - - +
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Residues in contact with GLY 360 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264S ASN* 4.6 13.6 - - - +
267S ALA* 3.8 29.8 - - - +
268S LEU* 5.9 0.5 - - - -
358S PHE* 3.7 4.2 - - - +
359S ILE* 1.3 76.0 - - - +
361S ASP* 1.3 57.8 + - - +
363S LEU* 3.5 8.3 + - - +
364S ASN* 3.0 29.1 + - - +
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Residues in contact with ASP 361 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359S ILE 3.2 1.5 - - - -
360S GLY* 1.3 74.4 - - - +
362S GLN* 1.3 61.9 + - - +
364S ASN* 3.4 7.2 + - - +
365S GLU* 3.1 26.0 + - - +
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Residues in contact with GLN 362 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359S ILE* 3.6 8.7 + - + +
361S ASP* 1.3 74.8 - - - +
363S LEU* 1.3 60.8 + - - +
365S GLU* 3.6 7.3 - - - +
366S GLN* 2.8 31.8 + - - +
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Residues in contact with LEU 363 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264S ASN 6.0 1.1 - - - +
268S LEU* 6.0 6.3 - - + -
344S LYS* 5.0 18.6 - - + +
348S ALA* 5.9 6.5 - - + -
359S ILE 3.5 12.6 + - - +
360S GLY* 3.6 12.3 - - - +
361S ASP 3.2 0.4 - - - -
362S GLN* 1.3 79.4 - - - +
364S ASN* 1.3 56.9 + - - +
366S GLN* 3.4 6.3 + - - +
367S LEU* 2.9 29.7 + - - +
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Residues in contact with ASN 364 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267S ALA* 5.0 11.7 - - + +
268S LEU* 5.8 6.2 - - - +
360S GLY 3.0 18.8 + - - +
361S ASP* 3.6 6.7 - - - +
363S LEU* 1.3 75.4 - - - +
365S GLU* 1.3 52.0 + - - +
367S LEU* 3.2 7.3 + - - +
368S LYS* 2.8 36.7 + - - +
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Residues in contact with GLU 365 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361S ASP 3.1 16.3 + - - +
362S GLN* 3.6 8.7 - - - +
363S LEU 3.3 0.2 - - - -
364S ASN* 1.3 74.4 - - - +
366S GLN* 1.3 65.4 + - - +
368S LYS* 3.4 4.6 + - - +
369S LYS* 3.0 24.6 + - - +
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Residues in contact with GLN 366 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344S LYS* 6.5 0.4 - - + -
362S GLN 2.8 21.4 + - - +
363S LEU* 3.5 7.9 - - - +
365S GLU* 1.3 72.0 - - - +
367S LEU* 1.3 61.8 + - - +
369S LYS* 3.5 6.7 - - - +
370S ARG* 3.2 21.7 + - - +
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Residues in contact with LEU 367 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340S ALA* 5.8 5.6 - - + +
341S LEU* 6.0 4.5 - - - -
344S LYS* 5.1 12.3 - - + -
363S LEU 2.9 18.9 + - - +
364S ASN* 3.5 7.9 - - - +
366S GLN* 1.3 74.1 - - - +
368S LYS* 1.3 60.9 + - - +
370S ARG* 3.1 9.8 + - - +
371S ILE* 2.9 28.2 + - - +
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Residues in contact with LYS 368 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364S ASN 2.8 19.9 + - - +
365S GLU* 4.1 5.4 - - - +
367S LEU* 1.3 74.0 - - - +
369S LYS* 1.3 57.4 + - - +
371S ILE* 3.8 7.5 - - - +
372S ASP* 2.9 29.8 + - - +
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Residues in contact with LYS 369 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365S GLU 3.0 17.4 + - - +
366S GLN* 3.5 9.0 - - - +
368S LYS* 1.3 73.4 - - - +
370S ARG* 1.3 65.0 + - - +
372S ASP* 3.2 7.0 + - - +
373S GLU* 3.1 23.2 + - - +
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Residues in contact with ARG 370 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340S ALA* 4.6 20.2 - - + -
366S GLN 3.2 9.1 + - - +
367S LEU* 3.1 11.8 + - - +
369S LYS* 1.3 79.6 - - - +
371S ILE* 1.3 61.9 + - - +
373S GLU* 3.5 6.9 + - - +
374S ILE* 3.2 22.3 + - - +
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Residues in contact with ILE 371 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325S ALA* 5.5 11.0 - - + -
337S ILE* 5.8 9.6 - - + +
367S LEU 2.9 15.0 + - - +
368S LYS* 3.8 8.7 - - - +
370S ARG* 1.3 75.1 - - - +
372S ASP* 1.3 65.0 + - - +
374S ILE* 3.1 10.0 + - - +
375S LYS* 3.0 23.6 + - - +
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Residues in contact with ASP 372 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368S LYS 2.9 19.4 + - - +
369S LYS* 3.2 8.0 + - - +
371S ILE* 1.3 74.6 - - - +
373S GLU* 1.3 61.9 + - - +
375S LYS* 3.6 6.4 + - - +
376S GLU* 3.4 21.1 + - - +
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Residues in contact with GLU 373 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369S LYS 3.1 12.6 + - - +
370S ARG* 3.7 10.3 - - - +
371S ILE 3.2 0.2 - - - -
372S ASP* 1.3 75.7 - - - +
374S ILE* 1.3 66.2 + - - +
376S GLU* 3.2 22.1 + - - +
377S LYS* 5.0 1.2 - - - +
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Residues in contact with ILE 374 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333S GLN* 5.4 16.4 - - + +
336S LYS* 5.0 16.2 - - + -
337S ILE* 5.7 6.1 - - + +
370S ARG 3.2 10.9 + - - +
371S ILE* 3.1 13.4 + - - +
373S GLU* 1.3 78.9 - - - +
375S LYS* 1.3 61.3 - - - +
376S GLU 3.3 0.7 + - - -
377S LYS* 4.0 14.9 + - - +
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Residues in contact with LYS 375 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333S GLN* 6.1 3.1 - - - -
371S ILE 3.0 14.4 + - - +
372S ASP* 3.6 7.4 + - - +
373S GLU 3.2 0.2 - - - -
374S ILE* 1.3 77.0 - - - +
376S GLU* 1.3 56.9 + - - +
377S LYS 3.1 9.6 + - - +
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Residues in contact with GLU 376 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372S ASP 3.4 13.7 + - - +
373S GLU* 3.2 14.0 + - - +
375S LYS* 1.3 74.6 - - - +
377S LYS* 1.3 59.9 + - - +
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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
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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