Contacts of the helix formed by residues 517 - 535 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350D PRO 4.2 9.7 + - - -
351D GLY* 3.3 18.6 + - - -
352D THR* 5.0 4.3 - - - -
477D PRO* 4.8 6.5 - - - -
478D PRO* 3.8 13.6 - - - +
515D GLY 3.9 0.2 + - - -
516D PHE* 1.3 77.5 - - - +
518D GLY* 1.3 64.0 + - - +
519D ALA* 3.4 3.2 + - - +
520D ASP* 2.7 35.4 + - - -
521D VAL* 3.5 19.4 + - - +
465E ARG* 5.7 2.6 - - - +
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Residues in contact with GLY 518 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351D GLY 2.8 13.3 + - - -
352D THR* 4.5 1.3 - - - +
478D PRO* 3.8 7.1 - - - +
486D ILE* 4.0 20.1 - - - +
517D SER* 1.3 72.8 - - - +
519D ALA* 1.3 59.7 + - - +
520D ASP 3.3 0.6 + - - -
521D VAL* 3.7 5.7 + - - +
522D ALA 3.7 13.0 + - - -
801D ANP 3.5 34.3 + - - -
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Residues in contact with ALA 519 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351D GLY* 3.1 14.9 + - - +
517D SER* 3.5 2.0 + - - +
518D GLY* 1.3 74.1 - - - +
520D ASP* 1.3 64.1 + - - +
521D VAL 3.5 0.2 - - - -
522D ALA* 3.8 6.8 + - + +
523D ASN* 3.5 12.0 + - - +
801D ANP 3.4 26.6 + - - +
465E ARG* 4.0 15.5 - - - +
466E PRO* 3.3 34.2 - - - +
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Residues in contact with ASP 520 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516D PHE* 3.4 38.5 - - + -
517D SER* 2.7 32.9 + - - +
518D GLY 3.3 1.0 - - - -
519D ALA* 1.3 77.0 - - - +
521D VAL* 1.3 59.3 + - - +
522D ALA 3.2 0.2 - - - -
523D ASN* 2.9 8.2 + - - +
524D VAL* 2.9 33.9 + - - +
552D VAL* 5.4 5.3 - - + +
466E PRO* 3.2 28.0 - - + +
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Residues in contact with VAL 521 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483D ARG* 3.7 28.9 - - + -
486D ILE* 3.8 31.6 - - + +
487D PHE* 3.6 47.3 - - + +
490D HIS* 4.8 0.4 - - + -
513D THR* 5.2 0.7 - - - +
516D PHE* 4.8 5.6 - - + -
517D SER 3.5 16.8 - - - +
518D GLY* 3.7 1.8 + - - +
519D ALA 3.5 0.2 - - - -
520D ASP* 1.3 75.2 - - - +
522D ALA* 1.3 61.3 + - - +
524D VAL* 4.1 2.6 - - - +
525D CYS* 3.1 27.8 + - - -
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Residues in contact with ALA 522 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490D HIS* 3.8 26.7 + - + +
518D GLY 3.7 8.7 + - - +
519D ALA* 4.0 9.9 - - + +
520D ASP 3.2 0.6 - - - -
521D VAL* 1.3 78.9 - - - +
523D ASN* 1.3 57.0 + - - +
525D CYS* 4.1 1.3 - - - +
526D ASN* 3.3 24.4 + - - +
801D ANP 3.8 24.7 - - - +
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Residues in contact with ASN 523 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519D ALA 3.5 1.6 + - - +
520D ASP 2.9 10.4 + - - +
522D ALA* 1.3 78.0 - - - +
524D VAL* 1.3 58.8 + - - +
525D CYS 3.3 0.2 - - - -
526D ASN* 4.3 5.1 - - - +
527D GLU* 2.9 52.6 + - - +
552D VAL* 3.7 19.5 - - + +
466E PRO* 3.4 40.0 - - + +
470E ASP* 3.5 28.6 + - - +
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Residues in contact with VAL 524 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487D PHE* 4.4 15.5 - - + -
509D LEU* 5.2 0.9 - - + -
513D THR* 4.5 4.9 - - + -
516D PHE* 3.9 27.1 - - + -
520D ASP 2.9 20.5 + - - +
521D VAL* 4.1 4.9 - - - +
523D ASN* 1.3 75.7 - - - +
525D CYS* 1.3 61.4 + - - +
528D ALA* 3.1 25.6 + - - +
545D PHE* 4.3 15.4 - - + -
548D ALA* 3.9 19.3 - - + +
549D ILE* 3.8 27.4 - - + -
552D VAL* 4.8 7.6 - - + -
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Residues in contact with CYS 525 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487D PHE* 3.5 30.3 - - - -
490D HIS* 3.8 41.3 - - + +
491D LEU* 4.1 11.4 - - - -
494D LEU* 3.7 25.7 - - + +
521D VAL* 3.1 21.7 + - - +
522D ALA 4.4 2.2 - - - +
524D VAL* 1.3 76.3 - - - +
526D ASN* 1.3 63.0 + - - +
528D ALA* 4.3 0.7 - - - +
529D ALA 3.8 5.5 + - - -
545D PHE* 4.4 8.3 - - - -
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Residues in contact with ASN 526 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494D LEU* 5.7 0.7 - - - -
522D ALA 3.3 17.1 + - - +
523D ASN* 3.3 11.2 + - - +
525D CYS* 1.3 79.2 - - - +
527D GLU* 1.3 59.3 + - + +
529D ALA* 3.0 19.2 + - - +
530D LEU* 3.2 15.3 + - - +
337E GLY 5.3 0.4 + - - -
338E ALA* 4.2 4.0 - - - +
339E LYS* 3.2 57.4 + - - +
340E ILE 4.2 7.3 - - - +
341E PRO* 4.9 4.0 - - - +
470E ASP* 5.5 1.9 - - - +
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Residues in contact with GLU 527 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523D ASN* 2.9 37.7 + - - +
526D ASN* 1.3 74.6 - - + +
528D ALA* 1.3 60.0 + - - +
530D LEU* 3.6 12.4 - - + +
531D ILE* 2.8 35.5 + - + +
548D ALA* 4.1 13.0 - - + +
551D ARG* 4.3 13.6 - - + +
552D VAL* 3.4 21.9 - - - +
341E PRO* 5.6 1.6 - - + -
470E ASP* 3.2 17.5 - - + +
471E ARG* 2.9 40.8 + - - +
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Residues in contact with ALA 528 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524D VAL 3.1 20.7 + - - +
525D CYS 4.3 2.0 - - - +
526D ASN 3.2 0.4 - - - -
527D GLU* 1.3 76.5 - - - +
529D ALA* 1.3 57.1 + - - +
531D ILE* 4.1 0.6 - - - +
532D ALA* 3.2 25.3 + - - +
540D ILE* 3.7 9.8 - - + +
544D HIS* 3.5 28.0 - - - +
545D PHE* 3.5 33.0 - - + -
548D ALA* 3.8 3.2 - - + +
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Residues in contact with ALA 529 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494D LEU* 3.9 16.4 - - + -
525D CYS 3.8 2.2 + - - +
526D ASN* 3.0 12.4 + - - +
528D ALA* 1.3 78.0 - - - +
530D LEU* 1.3 59.9 + - - +
532D ALA* 3.4 2.4 + - - +
533D ALA* 3.0 27.5 + - - +
540D ILE* 3.7 25.5 - - + +
336E LEU* 3.8 6.7 - - + +
337E GLY 4.4 0.7 - - - +
338E ALA* 3.7 24.8 - - + +
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Residues in contact with LEU 530 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526D ASN* 3.2 17.9 + - - +
527D GLU* 3.2 14.1 + - + +
529D ALA* 1.3 73.9 - - - +
531D ILE* 1.3 65.3 + - + +
533D ALA* 3.4 3.8 + - - +
534D ARG* 3.1 28.4 + - - +
322E GLU* 4.5 13.2 - - + +
326E PHE* 5.3 3.6 - - + -
333E TYR* 3.6 31.5 - - + -
338E ALA* 4.1 5.6 - - + -
339E LYS 3.9 18.6 - - - +
341E PRO* 3.7 26.9 - - + -
471E ARG* 3.4 29.4 - - - +
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Residues in contact with ILE 531 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527D GLU* 2.8 24.3 + - + +
528D ALA 4.1 3.4 - - - +
530D LEU* 1.3 76.6 - - + +
532D ALA* 1.3 62.1 + - - +
534D ARG* 3.3 36.4 + - - +
535D HIS* 3.2 32.3 - - + +
544D HIS* 4.0 18.8 - - + +
547D GLN* 3.3 60.8 - - + +
548D ALA* 3.7 10.8 - - + +
551D ARG* 5.1 5.8 - - + -
471E ARG* 6.2 0.9 - - - +
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Residues in contact with ALA 532 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528D ALA 3.2 18.1 + - - +
529D ALA 3.7 5.8 - - - +
530D LEU 3.3 0.4 - - - -
531D ILE* 1.3 77.5 - - - +
533D ALA* 1.3 58.1 + - - +
534D ARG 3.4 0.2 - - - -
535D HIS* 3.7 1.4 + - - -
536D LEU 3.6 2.1 + - - -
537D SER* 3.1 30.9 + - - +
539D SER 4.8 1.6 - - - +
540D ILE* 3.7 21.1 - - + -
544D HIS* 3.3 32.5 - - + +
336E LEU* 3.8 7.6 - - + -
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Residues in contact with ALA 533 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529D ALA 3.0 16.7 + - - +
530D LEU 3.4 1.3 + - - +
531D ILE 3.2 0.4 - - - -
532D ALA* 1.3 76.5 - - - +
534D ARG* 1.3 63.5 + - - +
535D HIS 3.3 0.2 - - - -
536D LEU* 3.6 9.1 + - - +
537D SER 4.9 0.2 - - - +
332E GLN* 3.5 32.0 + - + +
333E TYR* 3.6 36.3 + - + -
336E LEU* 3.8 13.5 - - + -
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Residues in contact with ARG 534 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530D LEU 3.1 17.9 + - - +
531D ILE* 3.3 41.4 + - - +
533D ALA* 1.3 79.8 - - - +
535D HIS* 1.3 70.3 + - + +
536D LEU* 3.2 10.5 + - - +
547D GLN* 5.2 2.2 + - - -
318E LEU* 4.4 33.1 - - - +
319E GLU* 3.8 19.8 + - - -
322E GLU* 2.3 47.0 + - + +
333E TYR* 5.5 5.2 - - + +
471E ARG* 5.1 2.6 - - - +
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Residues in contact with HIS 535 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531D ILE* 3.2 33.5 + - + +
532D ALA 3.7 4.0 + - - +
533D ALA 3.3 0.2 - - - -
534D ARG* 1.3 88.4 + - + +
536D LEU* 1.3 69.0 + - - +
537D SER* 3.2 6.8 + - - +
544D HIS* 4.5 16.6 - + - +
547D GLN* 4.2 16.7 + - - -
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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
------------------------------------------------------------
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