Contacts of the helix formed by residues 441 - 454 (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 ALA 441 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434X TYR* 6.0 0.2 - - - -
437X LEU* 3.8 20.4 - - + +
438X GLY 4.1 3.9 + - - +
439X ALA 3.3 4.2 - - - +
440X ASN* 1.3 77.5 - - - +
442X GLN* 1.3 66.8 + - - +
443X THR* 3.4 2.5 - - - +
444X LEU* 3.7 34.0 + - + +
445X THR* 3.4 22.9 + - - +
471X GLN* 3.8 4.3 + - - +
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Residues in contact with GLN 442 (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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284X ALA 5.4 3.3 - - - +
440X ASN 3.6 16.5 + - - +
441X ALA* 1.3 72.5 - - - +
443X THR* 1.3 61.8 + - + +
445X THR* 2.6 22.0 + - - -
446X LEU* 3.0 19.2 + - + +
468X ALA* 4.2 10.9 - - + +
471X GLN* 4.1 22.8 + - + +
472X ARG* 3.7 32.4 - - + +
475X TYR* 4.1 24.0 - - + -
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Residues in contact with THR 443 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284X ALA 5.4 1.3 - - - +
407X LEU* 3.4 43.0 - - + +
437X LEU* 4.2 11.3 - - - +
441X ALA* 4.7 0.5 - - - +
442X GLN* 1.3 78.6 + - + +
444X LEU* 1.3 54.3 + - - +
446X LEU* 3.3 15.2 + - + +
447X LEU* 2.7 46.9 + - - +
475X TYR* 3.3 29.4 - - + +
477X LYS* 6.4 0.2 - - + -
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Residues in contact with LEU 444 (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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433X VAL* 3.3 45.8 - - + +
434X TYR* 3.4 42.0 - - + +
437X LEU* 3.5 23.8 - - + -
438X GLY 3.2 26.9 - - - +
441X ALA* 3.7 19.0 + - + +
442X GLN 3.4 0.6 - - - -
443X THR* 1.3 77.3 + - - +
445X THR* 1.3 57.4 + - - +
447X LEU* 3.3 10.1 + - + +
448X ALA* 2.8 30.5 + - - +
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Residues in contact with THR 445 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434X TYR* 4.0 21.1 - - + +
441X ALA 3.4 10.1 + - - +
442X GLN* 2.6 26.3 + - - -
444X LEU* 1.3 78.6 - - - +
446X LEU* 1.3 54.5 + - - +
448X ALA* 3.5 6.8 + - - +
449X THR* 2.9 34.5 + - - +
464X LEU* 4.0 24.5 - - + +
467X LYS* 5.5 5.2 - - + -
468X ALA* 3.3 24.4 - - + +
471X GLN* 4.7 10.4 + - - +
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Residues in contact with LEU 446 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442X GLN 3.0 18.3 + - - +
443X THR* 3.4 14.1 - - + +
445X THR* 1.3 74.1 - - - +
447X LEU* 1.3 70.9 + - + +
449X THR* 2.5 26.1 + - - -
450X VAL 3.4 3.8 + - - -
465X LEU* 4.9 5.8 - - + -
468X ALA* 4.5 4.8 - - + +
475X TYR* 4.0 15.3 - - + -
477X LYS* 3.7 20.6 - - + -
478X ALA* 3.5 38.1 - - + +
481X LYS* 3.4 46.0 + - + +
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Residues in contact with LEU 447 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407X LEU* 5.3 4.3 - - + +
410X TYR* 5.0 7.0 - - + -
411X GLU* 3.9 21.1 - - + +
414X ILE* 3.7 34.2 - - + +
430X ALA* 5.2 4.9 - - + -
433X VAL* 4.2 26.2 - - + -
443X THR* 2.7 37.5 + - - +
444X LEU* 3.5 14.6 - - + +
446X LEU* 1.3 80.0 - - + +
448X ALA* 1.3 59.3 + - - +
450X VAL* 3.1 8.7 + - + +
451X CYS* 2.9 32.6 + - - -
481X LYS* 4.6 6.7 - - - +
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Residues in contact with ALA 448 (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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430X ALA* 5.2 4.2 - - + +
434X TYR* 4.8 13.2 - - + -
444X LEU 2.8 20.0 + - - +
445X THR* 3.7 7.9 - - - +
447X LEU* 1.3 72.1 - - - +
449X THR* 1.3 57.8 + - - +
451X CYS* 3.3 14.2 + - - +
452X LEU* 2.9 36.4 + - + +
464X LEU* 4.9 12.6 - - + -
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Residues in contact with THR 449 (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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445X THR 2.9 23.5 + - - +
446X LEU* 2.5 22.5 + - - -
448X ALA* 1.3 76.1 - - - +
450X VAL* 1.3 55.6 + - - +
452X LEU 3.2 1.0 + - - -
453X GLU* 2.9 38.0 + - - +
461X ALA* 3.3 34.8 - - - +
464X LEU* 3.7 5.2 - - + -
465X LEU* 3.4 46.1 - - + +
481X LYS* 4.4 4.2 - - - +
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Residues in contact with VAL 450 (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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414X ILE* 4.2 16.4 - - + -
415X GLU* 6.0 7.4 - - + -
418X LEU* 5.2 19.1 - - + +
447X LEU* 3.1 9.9 + - + +
449X THR* 1.3 77.0 + - - +
451X CYS* 1.3 65.0 + - - +
453X GLU* 3.4 30.1 - - + +
454X ASP* 3.5 8.1 + - - +
481X LYS* 3.4 41.5 - - + +
484X GLU* 5.7 4.7 - - - +
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Residues in contact with CYS 451 (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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414X ILE* 3.4 19.7 - - - -
423X ILE 5.4 1.4 - - - +
426X ALA* 4.1 9.2 - - - -
427X MET* 4.5 25.9 - - + +
430X ALA* 3.2 34.5 - - - -
447X LEU 2.9 25.6 + - - -
448X ALA* 3.3 10.3 - - - +
450X VAL* 1.3 74.9 - - - +
452X LEU* 1.3 56.8 + - + +
454X ASP* 3.4 9.6 + - - +
455X PRO* 3.0 21.8 - - - +
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Residues in contact with LEU 452 (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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448X ALA* 2.9 19.1 + - + +
449X THR 3.2 0.6 + - - -
451X CYS* 1.3 73.9 - - + +
453X GLU* 1.3 64.3 + - - +
454X ASP 3.2 1.6 - - - -
455X PRO* 3.4 8.3 - - + +
457X THR* 2.9 73.1 + - - +
460X LYS* 3.3 37.9 - - + +
461X ALA* 3.4 17.5 - - + +
464X LEU* 5.4 7.0 - - + -
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Residues in contact with GLU 453 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449X THR* 2.9 30.2 + - - +
450X VAL* 3.4 24.9 - - + +
452X LEU* 1.3 77.3 - - - +
454X ASP* 1.3 57.2 + - - +
456X VAL* 2.9 26.3 + - - +
457X THR 5.1 0.9 - - - +
458X GLN* 5.2 2.8 - - + -
461X ALA* 3.3 20.5 - - - +
465X LEU* 4.9 3.8 - - - +
481X LYS* 5.4 2.6 - - - +
484X GLU* 5.5 4.4 - - - +
485X LEU* 3.3 25.7 - - - +
488X ARG* 3.4 36.6 + - - +
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Residues in contact with ASP 454 (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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418X LEU* 3.8 33.9 - - + +
421X ASN* 4.1 8.0 - - - +
422X SER 4.8 0.9 - - - -
423X ILE* 3.4 49.6 - - + +
426X ALA* 4.8 5.6 - - + +
450X VAL 3.5 7.0 + - - +
451X CYS* 3.4 16.0 + - - +
452X LEU 3.2 0.2 - - - -
453X GLU* 1.3 78.7 - - - +
455X PRO* 1.4 62.7 - - + +
456X VAL* 3.4 8.5 + - - +
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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