Contacts of the helix formed by residues 475 - 490 (chain X) 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 TYR 475 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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284X ALA 4.9 8.7 + - - -
285X GLY* 4.7 18.3 - - - -
442X GLN* 4.1 33.2 - - + -
443X THR* 3.3 26.6 - - + +
446X LEU* 4.0 6.7 - - + -
468X ALA 5.8 1.8 - - - +
469X LEU* 4.1 3.2 - - + +
472X ARG* 3.8 19.1 + - + +
473X PRO 3.5 2.8 + - - -
474X ASP* 1.3 73.4 - - - +
476X ILE* 1.3 71.8 + - + +
477X LYS* 3.2 41.5 + - + +
478X ALA* 3.5 22.0 - - + -
479X VAL* 3.1 25.2 + - - +
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Residues in contact with ILE 476 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287X ASN* 5.8 8.5 - - + -
288X LYS* 6.5 0.4 - - - -
474X ASP 3.5 3.3 + - - +
475X TYR* 1.3 76.6 - - + +
477X LYS* 1.3 69.3 + - + +
479X VAL* 3.6 2.5 + - - +
480X VAL* 3.2 27.6 + - + +
507X SER* 3.7 36.6 - - - +
508X ASP 5.3 3.6 - - - +
509X CYS* 6.3 0.9 - - + -
510X VAL* 4.2 24.5 - - + -
511X LEU* 4.5 14.8 - - + +
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Residues in contact with LYS 477 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313X TYR* 5.6 3.6 + - - -
411X GLU* 3.5 30.3 + - - +
443X THR* 6.4 0.2 - - + -
446X LEU* 3.7 20.9 - - + -
475X TYR* 3.2 25.8 + - + +
476X ILE* 1.3 81.5 - - + +
478X ALA* 1.3 55.5 + - - +
480X VAL* 3.5 6.1 + - - +
481X LYS* 2.8 39.6 + - + +
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Residues in contact with ALA 478 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442X GLN* 6.5 0.7 - - + -
446X LEU* 3.5 16.7 - - + +
465X LEU* 3.5 16.7 - - + +
468X ALA* 4.7 11.2 - - + -
469X LEU* 3.7 25.5 - - + +
475X TYR* 3.5 18.3 - - + -
476X ILE 3.3 0.6 - - - -
477X LYS* 1.3 75.7 - - - +
479X VAL* 1.3 59.4 + - - +
481X LYS* 3.4 0.4 + - - -
482X LYS* 2.9 31.4 + - - +
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Residues in contact with VAL 479 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469X LEU* 3.5 25.6 - - + -
474X ASP* 4.4 4.9 - - - +
475X TYR 3.1 23.1 + - - +
476X ILE* 4.1 3.4 - - - +
478X ALA* 1.3 74.4 - - - +
480X VAL* 1.3 53.1 + - - +
482X LYS* 3.4 2.6 + - - +
483X ALA* 2.8 35.6 + - - +
498X LEU* 4.6 16.7 - - + +
499X LEU* 3.7 24.9 - - + -
502X ALA* 3.6 34.3 - - + -
511X LEU* 4.2 4.9 - - + -
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Residues in contact with VAL 480 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476X ILE* 3.2 18.8 + - + +
477X LYS* 3.8 6.7 - - - +
479X VAL* 1.3 76.9 - - - +
481X LYS* 1.3 59.1 + - + +
483X ALA* 3.3 7.4 + - - +
484X GLU* 3.0 29.5 + - + +
510X VAL* 4.0 27.4 - - + -
511X LEU* 3.8 20.2 - - + -
514X ILE* 4.3 26.3 - - + +
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Residues in contact with LYS 481 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415X GLU* 5.9 1.6 + - - +
446X LEU* 3.4 49.2 + - + +
447X LEU* 4.6 6.9 - - - +
449X THR* 4.4 2.2 - - - +
450X VAL* 3.4 38.0 - - + +
453X GLU* 5.4 3.1 - - - +
465X LEU* 3.7 20.5 - - + +
477X LYS* 2.8 27.0 + - - +
478X ALA 3.9 3.4 - - - +
480X VAL* 1.3 75.5 - - + +
482X LYS* 1.3 59.9 + - - +
484X GLU* 3.5 25.6 + - - +
485X LEU* 3.5 7.8 + - - +
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Residues in contact with LYS 482 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462X LYS* 5.1 6.1 - - - +
465X LEU* 3.6 19.8 - - + +
466X ASP* 2.7 35.7 + - - +
469X LEU* 3.7 23.0 - - + +
478X ALA 2.9 18.4 + - - +
479X VAL 3.7 3.8 - - - +
481X LYS* 1.3 72.6 - - - +
483X ALA* 1.3 65.5 + - - +
485X LEU* 3.3 26.6 - - + +
486X LEU* 3.4 18.1 - - + +
498X LEU* 3.7 33.5 - - + +
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Residues in contact with ALA 483 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479X VAL* 2.8 22.1 + - + +
480X VAL 3.3 6.5 + - - +
482X LYS* 1.3 72.0 - - - +
484X GLU* 1.3 63.2 + - - +
486X LEU* 3.0 14.5 + - - +
487X SER* 3.2 14.5 + - - -
495X GLY* 6.0 1.3 - - - +
498X LEU* 4.9 7.8 - - + +
499X LEU* 4.2 13.9 - - + -
514X ILE* 3.9 25.8 - - + -
518X PHE* 3.3 17.0 - - + -
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Residues in contact with GLU 484 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450X VAL* 5.7 4.3 - - - +
453X GLU* 5.5 4.7 - - - +
480X VAL* 3.0 14.5 + - + +
481X LYS* 3.5 19.3 - - - +
482X LYS 3.3 0.2 - - - -
483X ALA* 1.3 74.6 - - - +
485X LEU* 1.3 62.0 - - - +
487X SER* 3.0 23.5 + - - +
488X ARG* 3.2 26.1 + - - +
514X ILE* 5.7 0.2 - - - +
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Residues in contact with LEU 485 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453X GLU* 3.3 26.5 - - - +
458X GLN* 4.7 12.7 + - + +
462X LYS* 3.6 49.4 - - + +
465X LEU* 3.6 30.1 - - + -
481X LYS 3.5 6.0 + - - +
482X LYS* 3.3 18.8 + - + +
484X GLU* 1.3 76.4 - - - +
486X LEU* 1.3 51.5 + - - +
488X ARG* 3.0 28.3 + - - +
489X GLU* 2.6 38.7 + - - +
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Residues in contact with LEU 486 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462X LYS* 4.2 25.6 - - - +
482X LYS* 3.4 23.8 - - + +
483X ALA* 3.0 11.9 + - - +
485X LEU* 1.3 78.7 - - - +
487X SER* 1.3 56.5 + - - +
489X GLU* 3.7 8.1 - - + -
490X GLN* 2.8 28.9 + - - -
491X LYS* 3.5 18.0 + - + +
492X TYR* 4.9 0.9 - - - -
494X ASP* 3.5 25.4 - - - +
495X GLY* 3.5 31.0 - - - +
498X LEU* 4.1 15.9 - - + -
518X PHE* 4.1 8.7 - - + -
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Residues in contact with SER 487 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483X ALA 3.2 11.2 + - - -
484X GLU* 3.0 17.8 + - - +
486X LEU* 1.3 76.5 - - - +
488X ARG* 1.3 62.4 + - - +
490X GLN* 3.5 15.4 + - - +
492X TYR* 4.0 23.4 + - - -
518X PHE* 3.7 16.7 - - - -
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Residues in contact with ARG 488 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453X GLU* 3.4 41.8 + - - +
456X VAL* 4.6 8.7 - - - +
458X GLN* 3.4 36.9 + - - +
484X GLU* 3.2 26.1 + - + +
485X LEU* 3.0 32.8 + - - +
487X SER* 1.3 74.8 - - - +
489X GLU* 1.3 66.0 + - - +
490X GLN* 3.5 16.3 + - - +
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Residues in contact with GLU 489 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458X GLN* 3.8 26.1 + - - +
462X LYS* 3.5 35.1 - - - +
485X LEU* 2.6 33.6 + - - +
486X LEU* 3.3 13.7 + - + +
488X ARG* 1.3 71.5 - - - +
490X GLN* 1.3 69.6 + - - +
491X LYS* 3.2 13.7 + - + +
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Residues in contact with GLN 490 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486X LEU 2.8 8.5 + - - -
487X SER 3.5 11.6 + - - +
488X ARG 3.3 16.2 + - - +
489X GLU* 1.3 78.2 + - - +
491X LYS* 1.3 58.7 + - - +
492X TYR* 3.3 35.0 + - + +
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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