Contacts of the helix formed by residues 457 - 472 (chain A) in PDB entry 5OQN
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 SER 457 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399A ARG* 5.5 0.9 - - - -
400A TYR* 3.3 10.0 + - - -
419A GLU* 3.4 26.2 + - - +
455A THR 3.4 3.3 + - - -
456A LEU* 1.3 74.9 - - - +
458A GLU* 1.3 66.4 + - - +
459A PRO* 3.5 14.8 - - - +
460A LEU* 3.0 28.4 + - - +
461A ILE* 3.0 9.7 + - - +
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Residues in contact with GLU 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A LEU 3.8 1.2 + - - -
457A SER* 1.3 71.1 - - - +
459A PRO* 1.3 72.3 - - + +
461A ILE* 2.9 15.4 + - + +
462A LYS* 2.9 22.2 + - - +
580A THR* 4.9 15.8 - - - +
584A TYR* 3.2 33.7 + - + +
624A LYS* 5.3 4.5 + - - -
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Residues in contact with PRO 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A GLU* 5.9 0.7 - - - +
423A GLU* 3.9 27.5 - - - +
457A SER* 3.4 16.4 - - - +
458A GLU* 1.3 94.7 - - + +
460A LEU* 1.3 61.7 + - + +
462A LYS* 3.6 12.5 + - + +
463A ILE* 3.4 21.8 + - - +
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Residues in contact with LEU 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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400A TYR* 3.0 33.0 - - + +
419A GLU* 3.4 41.1 - - + +
422A ILE* 4.0 14.6 - - + -
423A GLU* 3.8 26.2 - - + +
450A MET* 4.2 9.5 - - - +
456A LEU* 3.4 22.4 - - + -
457A SER* 3.0 16.2 + - - +
459A PRO* 1.3 76.6 - - + +
461A ILE* 1.3 60.1 + - - +
463A ILE* 3.4 7.2 - - + +
464A GLY* 2.8 29.3 + - - -
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Residues in contact with ILE 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A LEU* 4.1 3.7 - - + +
456A LEU* 3.2 39.9 - - + +
457A SER 3.0 11.4 + - - +
458A GLU* 2.9 17.8 + - + +
460A LEU* 1.3 76.6 - - - +
462A LYS* 1.3 64.5 + - - +
464A GLY* 3.9 0.2 - - - -
465A ILE* 3.2 26.2 + - + +
577A LEU* 5.5 3.4 - - + -
580A THR* 4.3 12.8 - - - +
581A ARG* 3.6 57.7 - - + +
584A TYR* 4.7 6.5 - - + -
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Residues in contact with LYS 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A ILE* 6.3 0.8 - - - +
458A GLU 2.9 12.7 + - - +
459A PRO* 3.8 12.1 - - + +
461A ILE* 1.3 79.1 - - - +
463A ILE* 1.3 73.9 + - - +
465A ILE* 3.4 4.3 + - - +
466A ARG* 3.1 56.6 + - - +
584A TYR* 3.3 52.2 - - + +
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Residues in contact with ILE 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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423A GLU* 4.8 10.5 - - + +
426A SER* 3.6 26.0 - - - +
427A ILE* 3.6 48.9 - - + +
430A GLU* 4.3 11.7 - - + +
450A MET* 5.5 1.3 - - + -
459A PRO 3.4 12.2 + - - +
460A LEU* 3.4 15.9 - - + +
462A LYS* 1.3 88.3 - - + +
464A GLY* 1.3 65.6 + - - +
466A ARG* 2.9 23.0 + - + +
467A VAL* 2.8 32.4 + - + +
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Residues in contact with GLY 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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447A VAL* 4.5 3.1 - - - +
450A MET* 3.7 23.6 - - - -
451A LEU* 3.8 12.5 - - - +
460A LEU 2.8 18.9 + - - -
462A LYS 3.3 0.2 - - - -
463A ILE* 1.3 78.3 - - - +
465A ILE* 1.3 62.4 + - - +
467A VAL* 3.2 7.9 + - - +
468A MET* 2.9 23.6 + - - +
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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
----------------------------------------------------------
451A LEU* 3.8 24.9 - - + -
461A ILE* 3.2 20.0 + - + +
462A LYS 3.7 6.1 - - - +
464A GLY* 1.3 75.0 - - - +
466A ARG* 1.3 58.5 + - + +
468A MET* 3.2 13.6 + - + +
469A LYS* 2.8 29.3 + - - +
478A PHE* 3.5 26.0 - - + -
482A ALA* 5.0 8.1 - - + -
581A ARG* 4.4 21.5 - - + +
584A TYR* 4.0 15.0 - - + +
585A MET* 4.0 14.6 - - + +
588A LEU* 3.8 10.8 - - + -
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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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430A GLU* 3.7 35.2 + - - +
462A LYS* 3.1 54.2 + - - +
463A ILE* 2.9 25.2 + - + +
465A ILE* 1.3 77.7 - - - +
467A VAL* 1.3 61.2 + - - +
469A LYS* 3.4 8.5 + - - +
470A SER* 3.3 15.1 + - - -
584A TYR* 5.0 5.4 + - - -
587A GLU* 4.2 23.7 + - - -
588A LEU* 4.4 25.0 - - - +
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Residues in contact with VAL 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A LEU* 6.1 0.7 - - + -
426A SER* 3.2 36.3 - - - +
429A ALA* 4.4 13.7 - - + +
430A GLU* 3.7 15.7 - - + +
443A MET* 4.4 10.8 - - + -
447A VAL* 3.9 22.4 - - + -
463A ILE* 2.8 22.5 + - + +
464A GLY* 3.6 7.0 - - - +
466A ARG* 1.3 71.2 - - - +
468A MET* 1.3 61.7 + - - +
470A SER* 2.8 21.0 + - - -
471A LEU* 3.1 25.3 + - + +
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Residues in contact with MET 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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444A LEU* 4.2 13.9 - - + +
447A VAL* 4.2 14.3 - - + +
448A ARG* 4.4 10.3 - - - -
451A LEU* 3.7 23.1 - - + -
464A GLY 2.9 16.3 + - - +
465A ILE* 3.8 6.5 - - + +
467A VAL* 1.3 76.6 - - - +
469A LYS* 1.3 61.6 + - - +
471A LEU* 3.8 9.2 - - - +
472A SER* 3.2 23.4 + - - -
478A PHE* 3.6 29.1 - - + +
481A MET* 4.2 17.7 - - + -
482A ALA* 3.6 33.0 - - + +
485A ILE* 4.2 9.4 - - - -
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Residues in contact with LYS 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 2.8 18.3 + - - +
466A ARG* 3.5 6.7 - - - +
467A VAL 3.1 0.2 - - - -
468A MET* 1.3 78.6 - - - +
470A SER* 1.3 61.3 + - - +
471A LEU 3.6 0.2 + - - -
472A SER* 3.8 12.9 + - - +
474A ASN 5.6 0.8 - - - -
475A GLU* 4.1 27.3 - - - +
478A PHE* 3.6 33.3 - - + +
588A LEU* 3.7 47.4 + - + -
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Residues in contact with SER 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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430A GLU* 2.9 30.1 + - - -
431A ARG* 5.1 0.2 - - - -
432A TYR 5.3 1.6 + - - -
434A TYR* 4.5 13.2 - - - -
466A ARG 3.3 8.3 + - - -
467A VAL* 2.8 11.2 + - - -
469A LYS* 1.3 79.5 - - - +
471A LEU* 1.3 68.1 + - - +
472A SER 4.0 4.0 - - - +
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Residues in contact with LEU 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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434A TYR* 3.1 41.5 - - + +
440A ARG* 3.5 41.4 + - + +
443A MET* 4.1 9.0 - - + -
444A LEU* 3.3 57.0 - - + +
447A VAL* 4.5 8.7 - - + -
467A VAL* 3.1 21.7 + - + +
468A MET* 3.3 5.6 + - - +
469A LYS 3.3 0.4 - - - -
470A SER* 1.3 76.1 - - - +
472A SER* 1.3 70.4 + - - +
473A ILE* 3.4 2.4 + - - +
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Residues in contact with SER 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A ARG* 5.5 1.1 - - - +
444A LEU* 5.5 1.1 - - - +
468A MET 3.2 10.5 + - - -
469A LYS* 4.1 8.5 - - - +
470A SER 3.5 6.0 - - - +
471A LEU* 1.3 82.7 - - - +
473A ILE* 1.3 63.0 + - - +
474A ASN 2.3 32.7 + - - -
477A ASP* 3.2 14.9 + - - -
478A PHE* 3.0 31.0 + - - -
481A MET* 5.3 4.0 - - - -
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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