Contacts of the helix formed by residues 395 - 409 (chain N) in PDB entry 5G04
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 395 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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391N VAL* 5.0 3.1 - - - -
392N ASN* 3.0 17.1 + - - +
393N THR* 2.9 16.5 - - - +
394N CYS* 1.3 82.2 - - - +
396N ILE* 1.3 59.9 + - - +
397N ILE* 3.0 33.7 - - + +
398N THR* 2.6 72.4 + - - +
399N LEU* 4.1 3.1 + - - +
401N ILE* 5.7 1.0 - - - +
437N GLN 4.7 9.9 - - - +
438N ILE* 5.5 1.4 - - - -
441N GLY* 6.0 0.9 - - - -
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Residues in contact with ILE 396 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386N LEU* 3.5 50.8 - - + +
387N LEU* 4.3 4.3 - - + -
391N VAL* 3.9 13.9 - - + +
392N ASN 3.6 3.0 + - - +
393N THR* 6.0 0.2 - - - -
395N ASP* 1.3 71.5 - - - +
397N ILE* 1.3 49.9 + - - +
399N LEU* 3.3 7.3 + - - +
400N TYR* 2.8 30.1 + - + +
424N ILE* 4.1 18.4 - - + -
427N TYR* 3.6 30.3 - - + -
428N LEU* 3.9 26.2 - - + -
431N ARG* 3.6 23.8 - - - +
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Residues in contact with ILE 397 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393N THR* 4.5 2.9 - - - +
395N ASP* 3.0 30.4 - - + +
396N ILE* 1.3 74.8 - - - +
398N THR* 1.3 58.0 + - - +
399N LEU 3.4 0.2 - - - -
400N TYR* 3.6 17.5 - - + -
401N ILE* 2.9 39.0 + - + +
428N LEU* 3.8 22.9 - - + -
434N THR* 4.2 18.2 - - + +
437N GLN 5.8 0.4 - - - -
438N ILE* 4.0 19.5 - - + +
504N LEU* 3.8 27.4 - - + -
508N ILE* 3.8 26.0 - - + -
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Residues in contact with THR 398 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350N ASP 5.9 0.2 - - - -
394N CYS 4.0 6.4 + - - +
395N ASP* 2.6 48.0 + - - +
397N ILE* 1.3 72.8 - - - +
399N LEU* 1.3 59.7 + - - +
401N ILE* 3.6 12.7 + - + +
402N SER* 3.1 26.3 + - - -
451N ASP* 6.0 6.1 - - + -
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Residues in contact with LEU 399 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345N PHE* 3.8 27.6 - - + -
348N VAL* 3.7 28.9 - - + +
349N ARG* 3.8 27.1 - - + +
350N ASP 5.2 1.6 - - - -
382N LEU* 4.9 6.7 - - + -
386N LEU* 3.7 29.2 - - + -
395N ASP 5.0 2.2 - - - +
396N ILE 3.3 10.0 + - - +
398N THR* 1.3 79.8 + - - +
400N TYR* 1.3 52.0 + - - +
402N SER* 3.2 9.0 + - - -
403N ALA* 2.7 37.5 + - + +
424N ILE* 6.3 1.3 - - + -
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Residues in contact with TYR 400 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386N LEU* 5.5 0.2 - - - +
396N ILE* 2.8 21.1 + - + +
397N ILE* 3.7 24.2 - - + +
398N THR 3.3 0.4 - - - -
399N LEU* 1.3 70.7 - - - +
401N ILE* 1.3 58.3 + - - +
403N ALA* 3.2 4.9 + - - +
404N ILE* 2.8 58.5 + - + +
417N LEU* 5.7 1.7 - - - +
421N CYS* 3.7 28.9 - - + +
424N ILE* 3.7 40.2 - - + -
425N ARG* 3.6 14.1 + - - -
428N LEU* 4.3 10.3 - - + -
503N SER* 4.2 3.1 + - - -
504N LEU* 4.6 9.0 - - + -
507N SER* 2.9 37.2 + - - -
508N ILE* 5.6 0.7 - - + -
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Residues in contact with ILE 401 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395N ASP* 5.7 0.9 - - - +
397N ILE* 2.9 30.8 + - + +
398N THR* 3.9 12.6 - - + +
400N TYR* 1.3 71.8 - - - +
402N SER* 1.3 56.8 + - - +
404N ILE* 3.0 12.5 + - + +
405N LYS* 3.0 50.2 + - + +
451N ASP* 6.1 3.8 - - + -
452N LEU* 4.8 20.9 - - + +
455N GLU* 5.8 5.2 - - + -
500N ASP* 5.1 8.1 - - + +
504N LEU* 3.7 46.7 - - + -
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Residues in contact with SER 402 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348N VAL* 3.9 9.8 - - - +
350N ASP 3.5 23.5 + - - -
351N PHE* 3.4 25.6 + - - -
398N THR 3.1 15.9 + - - -
399N LEU 3.2 9.8 + - - -
401N ILE* 1.3 74.5 - - - +
403N ALA* 1.3 57.2 + - - +
405N LYS* 3.7 9.2 + - - +
406N ALA* 3.1 30.7 + - - +
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Residues in contact with ALA 403 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348N VAL* 3.6 17.0 - - + +
382N LEU* 6.3 1.8 - - + -
399N LEU* 2.7 20.2 + - + +
400N TYR* 3.2 13.9 + - + +
402N SER* 1.3 71.8 - - - +
404N ILE* 1.3 58.9 + - - +
406N ALA* 4.7 2.0 - - - -
407N LEU* 3.0 41.7 + - + +
417N LEU* 3.8 1.7 - - - +
421N CYS* 4.6 15.0 - - - -
424N ILE* 5.2 4.9 - - + -
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Residues in contact with ILE 404 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400N TYR* 2.8 60.7 + - + +
401N ILE* 3.0 15.9 + - + +
403N ALA* 1.3 74.5 - - - +
405N LYS* 1.3 58.4 + - - +
408N ARG* 3.1 29.3 + - + +
414N MET* 5.7 3.4 - - + -
417N LEU* 3.5 23.1 - - + +
421N CYS* 5.1 0.4 - - - -
498N SER 4.9 2.9 - - - +
500N ASP* 3.4 45.8 - - + +
503N SER* 4.6 10.8 - - - +
504N LEU* 4.7 7.0 - - + -
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Residues in contact with LYS 405 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351N PHE* 3.9 29.1 + - + +
355N ARG* 5.7 3.1 + - - +
401N ILE* 3.0 34.3 + - - +
402N SER* 4.4 7.7 + - - +
404N ILE* 1.3 75.5 - - - +
406N ALA* 1.3 61.5 + - - +
408N ARG* 3.3 35.0 + - - +
409N VAL* 3.5 11.1 + - - +
451N ASP* 4.4 24.5 + - - +
455N GLU* 5.2 11.5 - - - +
500N ASP* 3.4 15.7 - - - +
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Residues in contact with ALA 406 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348N VAL* 4.6 17.3 - - + -
351N PHE* 4.0 15.7 - - + -
358N ILE* 3.5 30.8 - - + +
402N SER 3.1 17.2 + - - +
403N ALA 4.3 1.6 - - - +
405N LYS* 1.3 79.1 - - - +
407N LEU* 1.3 60.8 + - + +
409N VAL* 3.0 27.8 - - - +
410N LEU* 5.1 1.9 - - - +
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Residues in contact with LEU 407 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344N LEU* 5.3 12.6 - - + -
348N VAL* 6.2 2.2 - - + -
374N LEU* 6.1 4.5 - - + -
378N LEU* 4.8 15.7 - - + -
403N ALA* 3.0 27.5 + - + +
406N ALA* 1.3 74.5 - - + +
408N ARG* 1.3 57.5 + - - +
409N VAL 2.9 16.5 - - - +
410N LEU* 4.6 10.5 - - + -
413N SER 3.3 12.1 - - - +
414N MET* 4.0 5.4 - - - -
416N ILE* 4.1 23.0 - - + +
417N LEU* 3.5 38.9 - - + +
420N ALA* 4.2 13.0 - - + -
421N CYS* 4.2 13.0 - - - -
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Residues in contact with ARG 408 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404N ILE* 3.1 17.7 + - + +
405N LYS* 3.3 25.9 + - - +
406N ALA 3.3 0.2 - - - -
407N LEU* 1.3 74.4 - - - +
409N VAL* 1.3 63.4 + - - +
410N LEU 3.4 3.6 + - - +
413N SER* 3.3 30.4 - - - +
414N MET* 4.6 8.7 - - + -
417N LEU* 4.0 0.6 - - + +
498N SER* 4.4 21.2 + - - -
500N ASP* 2.8 42.1 + - - +
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Residues in contact with VAL 409 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351N PHE* 6.4 0.4 - - + -
355N ARG* 4.0 29.6 - - - +
358N ILE* 3.9 23.6 - - + +
359N GLU* 4.0 14.8 - - + +
362N LYS* 3.9 20.6 - - + -
405N LYS 3.5 9.4 + - - +
406N ALA* 3.0 21.9 + - - +
407N LEU* 2.9 14.6 - - - +
408N ARG* 1.3 75.0 - - - +
410N LEU* 1.3 73.9 + - + +
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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