Contacts of the helix formed by residues 403 - 420 (chain G) in PDB entry 4D1Q
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 VAL 403 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353G ASN* 5.5 4.7 - - - +
355G SER* 5.6 5.6 - - - +
356G ILE* 5.1 21.1 - - + -
402G ASP* 1.3 78.6 - - - +
404G ALA* 1.3 71.6 + - + +
405G ASP* 3.1 24.1 + - + +
406G ILE* 3.2 28.4 + - + +
407G ALA* 3.3 10.2 + - - +
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Residues in contact with ALA 404 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402G ASP 4.0 1.0 + - - -
403G VAL* 1.3 77.9 - - + +
405G ASP* 1.3 64.5 + - - +
407G ALA* 3.9 7.1 + - - +
408G LYS* 3.5 21.5 + - - +
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Residues in contact with ASP 405 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281G THR* 4.3 4.7 - - - +
283G GLU* 3.0 44.6 - - + +
284G LEU* 4.2 19.7 - - + +
356G ILE* 5.0 11.4 - - + +
403G VAL* 3.1 17.0 + - + +
404G ALA* 1.3 78.8 - - - +
406G ILE* 1.3 65.8 + - - +
408G LYS* 3.1 17.4 + - - +
409G LEU* 3.1 13.0 + - - +
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Residues in contact with ILE 406 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284G LEU* 5.6 4.3 - - + -
356G ILE* 4.2 26.9 - - + +
359G THR* 3.3 42.0 - - + +
360G MET* 5.0 5.8 - - + -
363G ILE* 4.0 6.7 - - + -
402G ASP* 4.1 11.0 - - + +
403G VAL* 3.2 30.2 + - + +
405G ASP* 1.3 73.7 - - - +
407G ALA* 1.3 56.8 + - - +
409G LEU* 2.8 39.8 + - + +
410G LYS* 3.1 30.3 + - - +
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Residues in contact with ALA 407 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399G ASP 6.1 0.7 - - - +
400G VAL* 5.7 3.1 - - - +
402G ASP* 4.1 20.5 - - + +
403G VAL 3.3 13.0 + - - +
404G ALA* 3.9 7.4 - - - +
406G ILE* 1.3 78.6 - - - +
408G LYS* 1.3 58.9 + - - +
410G LYS* 3.8 8.1 + - - +
411G VAL* 2.9 31.2 + - + +
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Residues in contact with LYS 408 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280G GLU 4.7 6.7 - - - +
281G THR* 4.8 4.9 - - + +
283G GLU* 3.5 44.0 - - + +
404G ALA 3.5 12.7 + - - +
405G ASP* 3.1 13.5 + - - +
407G ALA* 1.3 75.8 - - - +
409G LEU* 1.3 66.6 + - - +
411G VAL* 3.4 9.6 + - + +
412G ASN* 2.8 35.9 + - - +
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Residues in contact with LEU 409 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274G LEU* 6.3 0.2 - - + -
277G SER* 3.1 29.2 - - - +
278G PHE* 4.3 25.8 - - + -
281G THR* 3.6 21.5 + - + +
284G LEU* 4.2 17.9 - - + -
360G MET* 4.7 8.5 - - + -
363G ILE* 5.0 18.4 - - + -
405G ASP 3.1 10.2 + - - +
406G ILE* 2.8 16.0 + - + +
408G LYS* 1.3 75.5 - - - +
410G LYS* 1.3 64.8 + - + +
412G ASN* 2.9 15.2 + - - +
413G ILE* 3.0 33.8 + - + +
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Residues in contact with LYS 410 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359G THR* 6.0 0.4 - - - +
363G ILE* 3.7 30.8 - - + +
395G ILE 3.6 16.5 + - - -
396G CYS* 3.6 37.5 - - + +
397G SER 4.2 11.5 + - - +
398G PRO* 5.2 4.0 - - + -
399G ASP* 4.3 4.6 + - - +
402G ASP* 3.3 32.1 + - - +
406G ILE* 3.1 22.4 + - + +
407G ALA* 3.9 8.3 - - - +
408G LYS 3.4 0.2 - - - -
409G LEU* 1.3 75.4 - - + +
411G VAL* 1.3 65.9 + - + +
412G ASN 2.9 2.1 + - - -
413G ILE* 2.9 19.1 + - + +
414G ILE* 3.0 18.9 + - - +
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Residues in contact with VAL 411 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398G PRO* 5.6 10.5 - - + +
407G ALA* 2.9 24.0 - - + +
408G LYS* 3.4 11.2 - - + +
409G LEU 3.3 0.2 - - - -
410G LYS* 1.3 76.6 - - + +
412G ASN* 1.3 62.4 + - - +
414G ILE* 3.9 10.4 - - - +
415G LYS* 3.4 26.9 + - - +
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Residues in contact with ASN 412 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277G SER* 3.7 10.8 - - - +
280G GLU* 2.9 38.6 + - - +
281G THR* 3.8 7.5 + - - +
408G LYS* 2.8 27.1 + - - +
409G LEU 2.9 8.8 + - - +
411G VAL* 1.3 78.8 - - - +
413G ILE* 1.3 67.0 + - - +
414G ILE 3.1 1.3 - - - -
415G LYS* 2.8 41.9 + - - +
416G ASN* 2.5 26.4 - - - +
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Residues in contact with ILE 413 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273G VAL* 4.5 9.2 - - + -
274G LEU* 5.2 6.5 - - + -
277G SER* 3.2 22.4 + - - -
363G ILE* 4.3 9.4 - - + -
367G PHE* 3.8 34.5 - - + -
392G VAL* 4.1 1.8 - - + -
396G CYS* 3.5 28.9 - - - -
409G LEU* 3.0 33.0 + - + +
410G LYS* 2.9 7.7 + - + +
412G ASN* 1.3 75.1 - - - +
414G ILE* 1.3 53.5 + - - +
416G ASN* 3.0 2.8 + - - +
417G VAL* 2.8 49.0 + - + +
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Residues in contact with ILE 414 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392G VAL* 5.3 1.1 - - + -
393G LYS* 4.7 26.7 - - + +
396G CYS* 2.8 48.7 - - + +
398G PRO* 4.4 11.7 - - + -
410G LYS 3.0 14.1 + - - +
411G VAL* 3.9 9.9 - - - +
413G ILE* 1.3 81.7 - - + +
415G LYS* 1.3 61.2 + - - +
417G VAL* 3.7 13.2 - - - +
418G ARG* 3.6 21.4 - - - +
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Residues in contact with LYS 415 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280G GLU* 3.2 12.7 + - - +
411G VAL* 3.4 16.9 + - - +
412G ASN* 2.8 39.2 + - - +
414G ILE* 1.3 76.1 - - - +
416G ASN* 1.3 64.5 + - - +
418G ARG* 3.1 36.8 + - - +
419G ILE* 3.1 33.9 - - + +
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Residues in contact with ASN 416 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273G VAL* 3.8 7.4 - - + +
276G ASN* 3.5 30.3 - - - +
277G SER* 3.4 19.8 + - - +
280G GLU* 3.4 23.4 + - - +
412G ASN* 2.5 29.1 + - - +
413G ILE 3.6 1.8 - - - +
415G LYS* 1.3 76.8 + - - +
417G VAL* 1.3 60.2 + - - +
418G ARG 2.9 2.2 - - - -
419G ILE* 3.5 15.8 - - - +
420G ILE* 2.8 54.4 + - + +
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Residues in contact with VAL 417 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273G VAL* 4.2 9.6 - - + +
389G ILE* 3.6 31.6 - - + -
392G VAL* 3.6 29.4 - - + -
393G LYS* 4.4 8.5 - - + -
413G ILE* 2.8 35.1 + - + +
414G ILE* 3.7 10.8 - - - +
415G LYS 3.3 0.2 - - - -
416G ASN* 1.3 76.0 - - - +
418G ARG* 1.3 52.2 + - - +
421G TRP* 3.1 26.2 - - + +
422G GLU* 2.8 37.0 + - - +
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Residues in contact with ARG 418 (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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393G LYS* 4.6 8.3 - - - +
414G ILE* 3.6 18.2 - - - +
415G LYS* 3.1 30.9 + - - +
416G ASN 2.9 0.8 - - - -
417G VAL* 1.3 79.5 - - - +
419G ILE* 1.3 71.0 + - - +
422G GLU* 3.4 27.0 + - - +
423G GLU* 2.8 33.6 + - - +
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Residues in contact with ILE 419 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415G LYS* 3.1 40.6 - - + +
416G ASN* 3.5 19.7 - - - +
418G ARG* 1.3 92.7 - - - +
420G ILE* 1.3 64.1 + - + +
423G GLU* 3.2 23.7 - - + +
424G ASN* 4.1 3.5 + - - -
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Residues in contact with ILE 420 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249G ARG* 3.2 28.4 + - - +
269G LEU* 3.8 6.7 - - - +
272G ASN* 3.9 12.8 - - + +
273G VAL* 3.4 26.0 - - + +
276G ASN* 3.9 19.3 - - + +
416G ASN* 2.8 49.8 + - + +
419G ILE* 1.3 82.5 - - + +
421G TRP* 1.3 66.8 + - - +
424G ASN* 3.0 28.5 + - - +
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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