Contacts of the helix formed by residues 517 - 535 (chain E) in PDB entry 6NYY
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 517 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350E PRO 3.9 21.0 + - - -
351E GLY* 4.0 5.6 - - - -
352E THR* 4.8 4.5 - - - -
477E PRO* 5.8 2.9 - - - -
478E PRO* 4.6 7.4 - - - -
515E GLY 3.8 1.2 + - - -
516E PHE* 1.3 78.3 - - - +
518E GLY* 1.3 64.0 + - - +
519E ALA* 3.6 6.4 + - - +
520E ASP* 2.9 40.4 + - - -
521E VAL* 3.4 15.6 + - - +
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Residues in contact with GLY 518 (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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351E GLY 3.1 10.5 + - - -
352E THR* 4.4 4.7 - - - +
478E PRO* 4.4 5.2 - - - +
486E ILE* 4.3 17.9 - - - +
517E SER* 1.3 75.8 - - - +
519E ALA* 1.3 60.5 + - - +
521E VAL* 3.5 5.0 + - - +
522E ALA* 3.4 15.8 + - - +
801E ADP 3.5 32.2 + - - -
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Residues in contact with ALA 519 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351E GLY* 2.9 24.4 + - - +
517E SER* 3.3 3.7 + - - +
518E GLY* 1.3 75.3 - - - +
520E ASP* 1.3 65.6 + - - +
521E VAL 3.4 0.2 - - - -
522E ALA* 3.4 4.4 + - - +
523E ASN* 2.9 30.7 + - - +
801E ADP 3.4 30.3 - - + +
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Residues in contact with ASP 520 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516E PHE* 3.7 25.2 - - + +
517E SER* 2.9 34.0 + - - +
518E GLY 3.3 0.6 - - - -
519E ALA* 1.3 78.4 - - - +
521E VAL* 1.3 59.4 + - - +
523E ASN* 3.0 11.9 + - - +
524E VAL* 2.9 32.8 + - - +
552E VAL* 4.1 19.0 - - + +
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Residues in contact with VAL 521 (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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483E ARG* 4.4 18.6 - - + -
486E ILE* 3.9 23.6 - - + +
487E PHE* 3.6 50.5 - - + +
490E HIS* 4.9 0.9 - - + -
513E THR* 4.9 0.2 - - - +
516E PHE* 4.2 14.6 - - + -
517E SER 3.4 15.2 + - - +
518E GLY* 3.8 7.9 - - - +
519E ALA 3.4 0.4 - - - -
520E ASP* 1.3 75.8 - - - +
522E ALA* 1.3 61.8 + - - +
524E VAL* 3.3 8.9 + - - +
525E CYS* 3.2 24.5 + - - -
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Residues in contact with ALA 522 (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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490E HIS* 3.7 38.3 + - + +
518E GLY 3.4 9.4 + - - +
519E ALA* 3.6 9.4 - - - +
520E ASP 3.2 0.4 - - - -
521E VAL* 1.3 80.1 - - - +
523E ASN* 1.3 58.0 + - - +
525E CYS* 4.1 2.6 + - - +
526E ASN* 3.4 21.5 + - - +
801E ADP 3.9 15.7 - - + +
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Residues in contact with ASN 523 (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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519E ALA* 2.9 22.0 + - - +
520E ASP* 3.0 13.6 + - - +
522E ALA* 1.3 79.7 + - - +
524E VAL* 1.3 56.5 + - - +
525E CYS 3.2 0.7 - - - -
526E ASN* 3.4 14.6 - - - +
527E GLU* 2.5 52.3 + - + +
552E VAL* 4.4 12.3 - - + -
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Residues in contact with VAL 524 (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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487E PHE* 4.0 20.2 - - + -
509E LEU* 5.4 3.1 - - + -
513E THR* 4.6 2.7 - - + -
516E PHE* 3.8 23.1 - - + -
520E ASP 2.9 19.2 + - - +
521E VAL* 3.7 9.6 - - - +
523E ASN* 1.3 75.4 - - - +
525E CYS* 1.3 60.9 + - - +
526E ASN 3.4 0.9 + - - -
528E ALA* 3.4 20.6 + - - +
545E PHE* 4.3 11.4 - - + +
548E ALA* 3.5 24.4 - - + +
549E ILE* 4.3 15.5 - - + -
552E VAL* 3.8 19.1 - - + -
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Residues in contact with CYS 525 (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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487E PHE* 3.6 32.5 - - - -
490E HIS* 3.7 39.5 - - + +
491E LEU* 3.7 20.6 - - - -
494E LEU* 3.4 32.4 - - + +
521E VAL 3.2 8.6 + - - +
522E ALA 4.4 2.7 - - - +
524E VAL* 1.3 76.1 - - - +
526E ASN* 1.3 57.5 + - - +
528E ALA* 4.5 1.8 - - - -
529E ALA* 3.8 5.1 + - - +
545E PHE* 4.7 3.6 - - - -
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Residues in contact with ASN 526 (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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522E ALA 3.4 17.2 + - - +
523E ASN* 2.9 18.1 + - - +
525E CYS* 1.3 79.4 - - - +
527E GLU* 1.3 66.5 + - - +
528E ALA 3.3 0.9 - - - -
529E ALA* 3.3 9.2 + - - +
530E LEU* 3.2 30.9 + - - +
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Residues in contact with GLU 527 (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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523E ASN* 2.5 40.1 + - + +
526E ASN* 1.3 71.9 - - + +
528E ALA* 1.3 57.1 + - - +
530E LEU* 3.0 24.9 + - - +
531E ILE* 2.9 32.0 + - + +
548E ALA* 4.0 21.3 - - + +
551E ARG* 3.9 39.3 + - + +
552E VAL* 4.7 4.0 - - + -
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Residues in contact with ALA 528 (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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524E VAL 3.4 10.6 + - - +
525E CYS 5.1 0.2 - - - +
526E ASN 3.3 0.6 - - - -
527E GLU* 1.3 76.2 - - - +
529E ALA* 1.3 60.9 + - - +
531E ILE* 3.7 8.0 - - - +
532E ALA* 3.0 28.8 + - - +
540E ILE* 4.0 7.2 - - + +
544E HIS* 3.6 22.5 - - + +
545E PHE* 3.5 36.6 - - + -
548E ALA* 3.7 4.6 - - + +
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Residues in contact with ALA 529 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494E LEU* 3.8 26.4 - - + +
525E CYS 3.8 7.5 + - - +
526E ASN* 3.3 17.8 + - - +
527E GLU 3.2 0.6 - - - -
528E ALA* 1.3 78.2 - - - +
530E LEU* 1.3 62.4 + - + +
532E ALA* 4.0 2.2 + - - +
533E ALA* 3.2 21.8 + - - +
540E ILE* 4.4 10.2 - - + +
338F ALA* 4.5 17.0 - - - +
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Residues in contact with LEU 530 (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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526E ASN* 3.2 23.0 + - - +
527E GLU* 3.0 31.4 + - - +
529E ALA* 1.3 77.8 - - + +
531E ILE* 1.3 55.5 + - + +
533E ALA* 3.0 8.8 + - + +
534E ARG* 2.7 47.4 + - + +
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Residues in contact with ILE 531 (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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527E GLU* 2.9 21.1 + - + +
528E ALA* 3.5 5.8 + - - +
529E ALA 3.4 0.2 - - - -
530E LEU* 1.3 77.7 - - + +
532E ALA* 1.3 57.5 + - - +
534E ARG* 3.3 5.8 + - - +
535E HIS* 3.0 40.6 + - + +
544E HIS* 3.7 32.5 - - + +
547E GLN* 3.8 52.3 - - + +
548E ALA* 3.9 7.6 - - - +
551E ARG* 4.9 20.9 - - + +
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Residues in contact with ALA 532 (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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528E ALA 3.0 15.6 + - - +
529E ALA 4.3 2.9 - - - +
531E ILE* 1.3 77.4 - - - +
533E ALA* 1.3 57.8 + - - +
535E HIS 4.6 0.2 - - - +
536E LEU* 3.0 5.9 + - - -
537E SER* 3.0 41.2 + - - +
540E ILE* 3.8 24.7 - - + -
544E HIS* 3.5 28.2 + - + +
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Residues in contact with ALA 533 (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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529E ALA 3.2 18.8 + - - +
530E LEU* 3.0 13.7 + - + +
532E ALA* 1.3 76.9 - - - +
534E ARG* 1.3 66.7 + - + +
535E HIS 3.2 0.2 - - - -
536E LEU* 3.4 25.3 + - - +
537E SER 5.6 0.2 - - - -
333F TYR* 4.0 22.7 - - - +
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Residues in contact with ARG 534 (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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530E LEU* 2.7 31.2 + - + +
531E ILE* 3.3 7.2 + - - +
533E ALA* 1.3 75.3 - - + +
535E HIS* 1.3 70.4 + - + +
536E LEU* 3.4 4.9 - - - +
321F MET* 4.2 6.1 - - - +
322F GLU* 1.0 130.4 - - - +
323F PHE* 3.6 14.6 - - - +
325F ASN* 3.0 30.2 - - - +
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Residues in contact with HIS 535 (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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531E ILE* 3.0 29.2 + - + +
532E ALA 4.5 1.3 - - - +
534E ARG* 1.3 88.4 - - + +
536E LEU* 1.3 71.2 + - - +
537E SER* 3.6 3.1 - - - +
544E HIS* 3.9 24.4 + + + +
547E GLN* 4.6 11.2 - - - -
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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