Contacts of the helix formed by residues 471 - 485 (chain A) in PDB entry 5SUY
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 GLU 471 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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463A TYR* 3.4 17.9 - - - +
469A PHE* 4.0 1.4 - - - +
470A PRO* 1.3 82.2 - - + +
472A ARG* 1.3 67.1 + - - +
473A ARG* 3.8 22.8 - - + +
474A GLU* 3.1 28.8 + - + +
475A ALA 3.8 1.9 + - - -
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Residues in contact with ARG 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456A SER* 3.7 5.5 + - - +
459A VAL* 3.4 26.2 - - + +
460A ASP* 2.9 30.1 + - - +
463A TYR* 3.5 38.3 + - + -
471A GLU* 1.3 73.5 - - - +
473A ARG* 1.3 57.6 + - - +
475A ALA* 3.0 18.6 + - - +
476A ARG* 3.1 19.4 + - - +
499A GLU* 3.0 40.8 + - - -
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Residues in contact with ARG 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A GLU* 3.1 21.8 + - + +
472A ARG* 1.3 78.4 - - - +
474A GLU* 1.3 61.3 + - - +
476A ARG* 2.9 44.5 + - - +
477A LYS* 3.0 51.9 + - - +
101C SO4 2.8 29.3 + - - -
476C ARG* 4.9 1.0 - - - +
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Residues in contact with GLU 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A PHE* 3.8 18.3 - - + -
470A PRO* 3.9 24.5 - - + -
471A GLU* 3.1 19.3 + - + +
473A ARG* 1.3 78.6 - - - +
475A ALA* 1.3 60.5 + - - +
477A LYS* 3.4 37.8 + - - +
478A TYR* 3.0 26.9 + - - +
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Residues in contact with ALA 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459A VAL* 4.1 11.0 - - + +
462A LEU* 3.7 9.8 - - + +
463A TYR* 4.0 27.8 - - + +
469A PHE* 3.8 33.2 - - + -
471A GLU 3.8 1.6 + - - -
472A ARG 3.0 11.8 + - - +
474A GLU* 1.3 76.7 - - - +
476A ARG* 1.3 58.6 + - - +
478A TYR* 3.3 4.0 + - - +
479A ALA* 3.0 23.7 + - - +
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Residues in contact with ARG 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A VAL* 3.9 16.4 - - + +
472A ARG* 3.1 19.6 + - - +
473A ARG* 2.9 52.9 - - - +
475A ALA* 1.3 76.6 - - - +
477A LYS* 1.3 61.9 + - + +
479A ALA* 3.2 3.6 + - - +
480A SER* 3.0 22.4 + - - -
497A PHE* 4.2 21.0 - - + -
499A GLU* 2.8 34.1 + - - +
101C SO4 3.2 36.4 + - - -
500C GLN* 3.8 3.4 - - - +
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Residues in contact with LYS 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A ARG* 3.0 38.4 + - - +
474A GLU* 3.6 39.4 + - - +
475A ALA 3.3 0.4 - - - -
476A ARG* 1.3 74.6 - - + +
478A TYR* 1.3 56.7 + - - +
480A SER* 3.3 10.4 + - - -
481A GLY* 3.0 23.6 + - - -
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Residues in contact with TYR 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462A LEU* 3.7 32.1 - - + -
466A VAL* 5.3 3.1 - - + -
469A PHE* 3.8 26.9 - + + -
474A GLU 3.0 13.9 + - - +
475A ALA 3.4 8.5 - - - +
477A LYS* 1.3 76.3 - - - +
479A ALA* 1.3 61.8 + - - +
481A GLY* 3.1 5.2 + - - +
482A LEU* 3.0 31.9 + - + -
418B SER 5.0 0.9 + - - -
419B VAL* 5.0 18.8 - - + -
421B THR 4.5 4.0 + - - -
423B MET* 3.6 42.2 + - + +
426B VAL* 3.4 31.6 - - + +
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Residues in contact with ALA 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458A VAL* 4.1 8.7 - - + -
459A VAL* 4.0 11.7 - - + -
462A LEU* 3.9 14.6 - - + +
475A ALA 3.0 12.8 + - - +
476A ARG 3.4 9.2 - - - +
478A TYR* 1.3 74.2 - - - +
480A SER* 1.3 61.8 + - - +
482A LEU* 3.1 20.2 + - - +
483A LEU* 3.1 13.0 + - - +
488A ILE* 4.1 5.5 - - + +
497A PHE* 3.7 27.6 - - + -
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Residues in contact with SER 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476A ARG* 3.0 12.5 + - - -
477A LYS* 3.3 13.4 + - - -
479A ALA* 1.3 76.0 - - - +
481A GLY* 1.3 62.4 + - - +
483A LEU* 3.2 5.0 + - - +
484A LYS* 3.1 43.7 + - - +
497A PHE* 3.9 29.4 + - - +
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Residues in contact with GLY 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477A LYS 3.0 13.1 + - - -
478A TYR* 3.1 6.4 + - - -
480A SER* 1.3 75.5 - - - +
482A LEU* 1.3 60.7 + - - +
484A LYS* 3.3 15.3 + - - +
485A ALA* 3.1 24.8 + - - +
423B MET* 4.2 16.6 - - - +
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Residues in contact with LEU 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458A VAL* 4.8 4.0 - - + -
462A LEU* 4.5 9.4 - - + -
478A TYR* 3.0 38.7 + - + +
479A ALA* 3.1 13.9 + - - +
481A GLY* 1.3 77.5 - - - +
483A LEU* 1.3 59.4 + - - +
485A ALA* 3.5 2.8 + - - -
486A GLY 3.3 2.6 + - - -
487A LEU* 3.0 47.4 + - + +
488A ILE* 3.4 15.1 + - + -
423B MET* 4.0 20.0 - - + +
426B VAL* 5.8 0.7 - - + -
427B THR* 3.4 27.4 - - - +
430B MET* 4.4 20.6 - - + -
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Residues in contact with LEU 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479A ALA 3.1 10.6 + - - +
480A SER* 3.2 7.8 + - - +
482A LEU* 1.3 74.0 - - - +
484A LYS* 1.3 64.4 + - + +
486A GLY* 3.1 14.2 + - - -
488A ILE* 3.6 31.2 - - + +
489A ARG* 4.0 1.3 - - - -
490A HIS* 3.8 37.5 - - + +
495A ILE 3.4 25.8 - - - +
497A PHE* 3.8 29.6 - - + +
503A TYR* 4.0 9.9 - - + -
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Residues in contact with LYS 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480A SER* 3.1 37.2 + - - +
481A GLY* 3.3 12.3 + - - +
483A LEU* 1.3 77.3 - - + +
485A ALA* 1.3 61.6 + - - +
486A GLY* 3.4 0.9 + - - -
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Residues in contact with ALA 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481A GLY 3.1 14.8 + - - +
482A LEU 3.9 3.8 - - - +
483A LEU 3.3 0.2 - - - -
484A LYS* 1.3 78.5 - - - +
486A GLY* 1.3 60.1 + - - +
487A LEU* 3.5 23.7 + - + +
423B MET* 5.4 5.6 - - - -
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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