Contacts of the helix formed by residues 458 - 475 (chain A) in PDB entry 5QSY
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 MET 458 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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459A SER* 1.3 61.1 + - - +
460A PRO* 3.5 21.7 - - + +
461A ASN* 3.6 20.3 + - - +
462A GLY* 3.2 18.9 + - - -
498A ASP* 5.4 2.6 + - - -
501A CYS* 3.7 14.1 - - - +
504A GLU* 5.5 5.0 - - - +
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Residues in contact with SER 459 (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 MET* 1.3 77.3 - - - +
460A PRO* 1.4 70.3 - - - +
462A GLY* 3.3 4.1 + - - +
463A ASN* 3.2 31.1 + - - +
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Residues in contact with PRO 460 (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 MET* 3.5 16.2 - - + +
459A SER* 1.4 89.5 - - - +
461A ASN* 1.3 67.8 + - - +
463A ASN* 3.1 19.1 + - + +
464A LEU* 3.3 17.0 + - - +
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Residues in contact with ASN 461 (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 MET 3.6 13.1 - - - +
460A PRO* 1.3 79.3 - - - +
462A GLY* 1.3 62.7 + - - +
464A LEU* 3.3 14.9 + - - +
465A ILE* 3.0 26.9 + - - +
494A GLU 5.0 2.0 + - - -
495A LEU* 3.5 30.3 - - + +
498A ASP* 2.8 34.3 + - - +
501A CYS* 3.6 8.1 - - - -
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Residues in contact with GLY 462 (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 MET 3.2 12.7 + - - -
459A SER* 3.3 7.4 + - - -
460A PRO 3.2 1.4 - - - -
461A ASN* 1.3 76.2 - - - +
463A ASN* 1.3 57.2 + - - +
465A ILE* 3.4 1.6 + - - +
466A ARG* 2.8 35.1 + - - +
501A CYS* 3.3 17.3 - - - -
505A LEU* 3.9 15.2 - - - +
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Residues in contact with ASN 463 (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 SER* 3.2 17.9 + - - +
460A PRO* 3.1 10.9 + - - +
462A GLY* 1.3 74.0 - - - +
464A LEU* 1.3 69.2 + - + +
466A ARG* 3.2 9.7 + - - +
467A MET* 3.0 31.8 + - + +
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Residues in contact with LEU 464 (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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460A PRO 3.3 11.1 + - - +
461A ASN* 3.7 25.8 - - - +
463A ASN* 1.3 78.7 - - + +
465A ILE* 1.3 57.8 + - - +
467A MET* 3.9 4.2 - - + +
468A LEU* 2.8 30.6 + - - +
495A LEU* 3.8 27.0 - - + +
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Residues in contact with ILE 465 (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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461A ASN* 3.0 21.3 + - + +
462A GLY 3.8 2.9 - - - +
464A LEU* 1.3 75.1 - - - +
466A ARG* 1.3 59.1 + - - +
468A LEU* 3.3 10.5 + - + +
469A VAL* 2.9 35.5 + - + +
495A LEU* 3.9 33.0 - - + +
496A LEU* 6.3 0.9 - - + -
498A ASP* 4.5 1.1 - - + +
501A CYS* 3.6 24.2 - - + -
502A MET* 4.1 23.6 - - + -
505A LEU* 3.5 21.1 - - + -
525A LEU* 3.6 25.6 - - + -
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Residues in contact with ARG 466 (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 GLY 2.8 24.7 + - - +
463A ASN* 3.2 12.1 + - - +
465A ILE* 1.3 72.5 - - - +
467A MET* 1.3 62.9 + - + +
469A VAL* 3.7 7.8 + - - +
470A LEU* 3.2 22.7 + - - +
505A LEU* 4.2 18.9 - - + +
515A GLU* 3.6 35.2 + - - +
516A ALA* 3.9 15.0 + - - +
517A MET* 3.4 43.5 - - - +
521A GLN* 4.7 12.4 + - - -
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Residues in contact with MET 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A ASN* 3.0 21.6 + - + +
464A LEU* 4.0 4.9 - - + +
466A ARG* 1.3 78.5 - - + +
468A LEU* 1.3 58.1 + - - +
469A VAL 3.1 1.1 - - - -
470A LEU* 2.8 25.8 + - + +
471A PHE* 2.7 61.2 + - + -
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Residues in contact with LEU 468 (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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464A LEU 2.8 18.4 + - - +
465A ILE* 3.5 11.4 - - + +
467A MET* 1.3 75.5 - - - +
469A VAL* 1.3 62.0 + - + +
471A PHE* 3.5 14.9 + - + +
472A PHE* 3.1 22.3 + - - +
484A LEU* 4.4 17.0 - - + -
488A LEU* 3.7 28.0 - - + -
492A SER* 6.5 0.2 - - - -
495A LEU* 4.6 15.5 - - + -
496A LEU* 3.6 30.7 - - + -
528A LEU* 4.8 11.7 - - + -
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Residues in contact with VAL 469 (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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465A ILE* 2.9 22.9 + - + +
466A ARG* 3.7 8.5 - - - +
468A LEU* 1.3 77.7 - - + +
470A LEU* 1.3 57.7 + - - +
472A PHE* 3.6 1.9 - - - +
473A LEU* 3.1 27.3 + - + +
517A MET* 4.7 5.2 - - + -
521A GLN* 3.6 36.8 - - + +
524A ALA* 3.8 15.5 - - + -
525A LEU* 3.9 27.1 - - + -
528A LEU* 3.8 23.6 - - + -
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Residues in contact with LEU 470 (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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466A ARG 3.2 14.0 + - - +
467A MET* 2.8 30.9 + - + +
469A VAL* 1.3 74.6 - - - +
471A PHE* 1.3 76.5 + - + +
472A PHE 3.1 0.2 + - - -
473A LEU* 3.3 3.0 + - + -
474A GLU* 2.9 53.7 + - + +
521A GLN* 3.4 28.3 - - - +
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Residues in contact with PHE 471 (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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467A MET* 2.7 50.1 + - + +
468A LEU* 4.0 14.8 - - + +
470A LEU* 1.3 84.0 - - + +
472A PHE* 1.3 60.6 + - - +
474A GLU* 4.9 2.5 - - - -
475A SER* 2.5 35.2 + - - +
484A LEU* 5.5 0.7 - - + -
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Residues in contact with PHE 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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468A LEU 3.1 14.3 + - - +
469A VAL* 3.6 5.6 - - - +
470A LEU 3.1 0.2 - - - -
471A PHE* 1.3 78.9 - - - +
473A LEU* 1.3 69.5 + - + +
475A SER 3.6 10.6 - - - +
478A HIS* 3.7 26.0 - - + +
479A GLU 4.1 8.3 - - - -
480A HIS 4.0 2.2 - - - -
481A ALA* 3.6 40.6 - - + -
484A LEU* 3.4 31.8 - - + +
520A ARG* 5.5 4.3 - - - -
524A ALA* 4.1 27.8 - - + -
527A GLU* 4.8 10.5 - - - -
528A LEU* 4.3 13.5 - - + -
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Residues in contact with LEU 473 (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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469A VAL* 3.1 15.7 + - + +
470A LEU* 4.0 3.4 - - + +
472A PHE* 1.3 83.7 - - + +
474A GLU* 1.3 73.7 + - + +
475A SER 4.1 2.9 - - - +
520A ARG* 3.3 55.6 - - + +
521A GLN* 3.5 45.1 - - + +
524A ALA* 3.9 14.6 - - + -
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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
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470A LEU* 2.9 47.9 + - + +
471A PHE* 4.5 1.6 - - - +
473A LEU* 1.3 88.7 - - + +
475A SER* 1.3 61.9 + - - +
521A GLN* 5.2 2.4 + - - -
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Residues in contact with SER 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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471A PHE* 2.5 29.1 + - - +
472A PHE 3.6 13.3 + - - +
473A LEU 4.1 3.1 - - - +
474A GLU* 1.3 80.7 - - - +
476A GLU* 1.3 59.9 + - - +
477A LEU* 3.3 29.8 + - - +
478A HIS* 4.6 5.5 + - - +
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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