Contacts of the helix formed by residues 472 - 485 (chain E) in PDB entry 6T8O
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 LYS 472 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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464E VAL* 3.7 20.4 - - + -
465E ALA 4.1 8.5 - - - +
466E GLY 5.2 3.6 - - - +
470E SER* 3.9 6.3 - - - +
471E GLY* 1.3 74.2 - - - +
473E SER* 1.3 65.2 + - - +
474E VAL 3.3 1.6 - - - -
475E GLY* 3.2 3.6 + - - -
476E VAL* 3.0 36.4 + - + +
595E ASP* 3.1 37.4 + - - -
596E GLU* 3.4 16.2 + - - +
629E ALA* 3.9 16.8 - - + -
630E THR 3.6 22.0 - - - +
631E GLN* 3.9 18.4 - - - +
652E PHE* 4.1 8.6 - - + -
801E ADP 2.6 19.2 + - - +
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Residues in contact with SER 473 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472E LYS* 1.3 85.9 + - - +
474E VAL* 1.3 56.5 + - - -
476E VAL* 3.3 8.0 + - - +
477E ASN* 2.9 36.8 + - - -
502E LEU* 4.7 3.7 - - - +
503E GLU* 3.7 33.9 - - - +
595E ASP* 5.1 3.1 + - - -
596E GLU* 5.6 0.2 + - - -
631E GLN* 5.0 0.3 + - - -
801E ADP 2.5 38.1 + - - -
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Residues in contact with VAL 474 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471E GLY 5.0 0.7 - - - +
472E LYS 3.3 0.4 - - - -
473E SER* 1.3 75.2 - - - +
475E GLY* 1.3 59.2 + - - +
477E ASN* 3.4 8.0 + - - +
478E ALA* 2.9 27.9 + - - +
694E ALA 4.1 3.1 - - - +
695E PHE* 3.8 13.0 - - + -
696E VAL* 3.6 41.2 - - + +
801E ADP 3.5 59.4 + - + +
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Residues in contact with GLY 475 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471E GLY 4.1 4.0 + - - -
472E LYS 3.2 9.0 + - - -
474E VAL* 1.3 79.7 - - - +
476E VAL* 1.3 56.8 + - - +
478E ALA* 3.2 7.3 + - - +
479E MET* 3.0 40.2 + - - +
652E PHE* 4.6 15.3 - - - -
678E MET* 5.3 6.3 - - - -
693E GLY* 6.0 3.1 - - - -
694E ALA 5.3 2.0 - - - -
801E ADP 5.5 0.2 + - - -
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Residues in contact with VAL 476 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464E VAL* 5.0 11.0 - - + -
472E LYS* 3.0 31.8 + - + +
473E SER* 3.3 9.4 + - - +
475E GLY* 1.3 75.7 - - - +
477E ASN* 1.3 58.9 + - - +
479E MET* 3.2 11.6 + - + +
480E LEU* 3.0 45.4 + - + +
504E LEU* 4.9 9.6 - - + -
593E VAL* 5.7 5.4 - - + -
595E ASP* 4.6 13.5 - - - +
627E ILE* 5.3 10.3 - - + -
629E ALA* 4.5 12.8 - - + -
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Residues in contact with ASN 477 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473E SER 2.9 26.4 + - - +
474E VAL* 3.7 8.8 - - - +
475E GLY 3.3 0.2 - - - -
476E VAL* 1.3 76.0 - - - +
478E ALA* 1.3 58.9 + - - +
480E LEU* 3.4 0.4 + - - -
481E LEU* 2.9 34.7 + - - +
503E GLU* 3.2 31.5 + - - +
504E LEU* 4.5 8.0 - - - +
506E ILE* 5.4 3.2 - - - +
507E TYR* 3.3 29.4 + - - +
696E VAL* 4.0 15.9 + - + +
698E ASP* 5.1 4.2 + - - -
701E VAL* 4.7 15.1 - - + +
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Residues in contact with ALA 478 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423E PHE* 3.9 23.0 - - + -
442E ALA 4.3 9.4 - - - +
443E LEU* 5.3 2.5 - - - +
474E VAL 2.9 17.4 + - - +
475E GLY* 3.2 7.6 + - - +
477E ASN* 1.3 73.8 - - - +
479E MET* 1.3 60.9 + - - +
481E LEU* 3.5 1.2 + - - -
482E SER* 2.8 33.0 + - - -
694E ALA* 3.9 19.3 - - + +
696E VAL* 3.8 8.9 - - + +
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Residues in contact with MET 479 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441E LEU* 3.7 25.9 - - + +
442E ALA 5.2 2.2 - - - +
443E LEU* 3.8 30.5 - - + -
462E LEU* 3.7 32.8 - - + -
464E VAL* 4.3 13.7 - - + -
475E GLY* 3.0 25.0 + - - +
476E VAL* 3.2 12.5 + - + +
478E ALA* 1.3 77.2 - - + +
480E LEU* 1.3 60.8 + - + +
482E SER* 3.1 6.7 + - - -
483E ILE* 3.0 30.7 + - - +
627E ILE* 4.0 18.2 - - + -
650E ILE* 4.4 10.3 - - + -
652E PHE* 6.0 1.3 - - + -
678E MET* 5.3 3.4 - - + -
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Residues in contact with LEU 480 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476E VAL* 3.0 36.0 + - + +
477E ASN* 4.9 0.2 - - - -
479E MET* 1.3 80.2 - - + +
481E LEU* 1.3 57.7 + - - +
483E ILE* 3.2 11.2 + - + +
484E LEU* 2.9 32.9 + - + +
494E LEU* 4.3 25.6 - - + +
496E MET* 4.6 4.5 - - + -
504E LEU* 3.9 10.8 - - + -
507E TYR* 3.6 39.5 - - + +
591E VAL* 5.6 0.9 - - + -
593E VAL* 3.8 33.2 - - + -
627E ILE* 5.8 1.1 - - + -
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Residues in contact with LEU 481 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321E LEU* 4.4 7.2 - - + -
423E PHE* 4.2 14.6 - - + -
477E ASN 2.9 26.4 + - - +
478E ALA* 4.0 4.0 - - - +
480E LEU* 1.3 72.4 - - - +
482E SER* 1.3 60.3 + - - +
484E LEU* 3.6 12.3 - - + -
485E PHE* 2.9 61.5 + - + -
507E TYR* 3.3 25.1 - - + +
696E VAL* 4.1 21.1 - - + -
700E GLU* 4.8 3.8 - - - +
701E VAL* 4.1 19.3 - - + -
704E VAL* 4.3 15.5 - - + -
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Residues in contact with SER 482 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423E PHE* 3.9 6.6 - - - -
427E LEU* 4.7 0.8 - - - +
432E TYR* 2.9 28.0 + - - -
440E PRO* 3.8 22.1 - - - +
441E LEU* 3.9 1.6 - - - -
442E ALA* 3.1 43.3 + - - +
478E ALA 2.8 18.7 + - - -
479E MET 3.1 9.4 + - - -
481E LEU* 1.3 73.2 - - - +
483E ILE* 1.3 64.3 + - - +
485E PHE 4.1 1.0 + - - -
486E LYS* 4.4 2.1 + - - +
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Residues in contact with ILE 483 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439E VAL* 3.8 36.8 - - + -
440E PRO* 3.5 19.7 - - - +
441E LEU* 4.2 9.0 - - + -
456E LEU* 4.4 7.9 - - + -
479E MET 3.0 15.5 + - - +
480E LEU* 3.4 17.7 - - + +
481E LEU 3.2 0.2 - - - -
482E SER* 1.3 77.8 - - - +
484E LEU* 1.3 64.0 + - + +
485E PHE 3.5 0.2 + - - -
486E LYS* 3.6 0.5 + - - +
487E SER* 3.5 25.8 + - - +
492E ALA* 4.8 10.8 - - + -
494E LEU* 4.1 31.0 - - + -
512E HIS* 5.3 4.9 + - + -
591E VAL* 5.0 4.5 - - + -
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Residues in contact with LEU 484 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315E LEU* 5.5 0.2 - - - +
316E PRO* 4.7 0.5 - - - +
480E LEU* 2.9 20.9 + - + +
481E LEU* 3.0 13.8 + - + +
483E ILE* 1.3 78.9 - - + +
485E PHE* 1.3 59.1 + - + +
486E LYS 3.1 5.4 + - - -
487E SER 3.9 4.6 + - - +
494E LEU* 4.9 6.7 - - + -
496E MET* 6.5 0.4 - - + -
507E TYR* 4.2 27.4 - - + -
510E ILE* 3.9 20.2 - - + -
512E HIS* 3.7 26.7 - - + +
704E VAL* 3.9 24.2 - - + -
705E VAL* 5.7 0.9 - - + -
708E TRP* 3.3 48.1 + - + +
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Residues in contact with PHE 485 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315E LEU* 3.9 18.0 - - - +
316E PRO* 4.4 22.6 - - + +
317E PRO 3.9 23.3 - - - -
318E LEU* 4.7 19.6 - - + +
320E LEU* 4.7 4.3 - - + -
321E LEU* 3.7 30.5 - - + -
423E PHE* 4.4 0.2 - + - -
427E LEU* 3.7 18.8 - - + -
432E TYR* 3.9 13.9 + - - +
481E LEU* 2.9 53.8 + - + +
482E SER 4.1 0.4 + - - -
483E ILE 3.4 0.6 - - - -
484E LEU* 1.3 76.2 - - + +
486E LYS* 1.3 59.2 + - - +
704E VAL* 3.6 28.7 - - + -
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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