Contacts of the helix formed by residues 542 - 555 (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 GLN 542 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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500D LEU* 3.8 25.7 - - + +
505D LEU* 4.5 14.4 - - + -
508D LYS* 3.4 41.5 - - - +
509D LEU* 5.7 2.5 - - + -
512D LEU* 4.8 2.6 - - + +
541D ASN* 1.3 82.6 + - - +
543D LYS* 1.3 58.5 + - - +
545D PHE* 3.0 28.0 + - + +
546D GLU* 3.2 28.9 + - + +
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Residues in contact with LYS 543 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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541D ASN* 3.2 19.3 - - + +
542D GLN* 1.3 79.0 - - - +
544D HIS* 1.3 64.4 + - + +
546D GLU* 3.3 27.0 + - + +
547D GLN* 3.2 41.1 + - + +
737D ASP* 5.3 6.5 + - - -
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Residues in contact with HIS 544 (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* 3.5 30.5 - - - +
531D ILE* 4.0 24.0 - - + +
532D ALA* 3.3 29.0 - - + +
535D HIS* 4.5 15.5 - + + +
537D SER* 3.9 24.9 - - - -
540D ILE* 4.1 2.2 - - + -
541D ASN* 3.3 39.0 + - + +
542D GLN 3.2 0.4 - - - -
543D LYS* 1.3 82.8 - - + +
545D PHE* 1.3 62.1 + - - +
547D GLN* 3.9 5.1 + - - -
548D ALA* 3.7 10.4 + - - +
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Residues in contact with PHE 545 (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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491D LEU* 3.6 26.5 - - + -
494D LEU* 4.1 4.5 - - + -
496D LEU* 3.8 11.4 - - + -
505D LEU* 3.7 21.3 - - + -
509D LEU* 3.6 40.4 - - + -
524D VAL* 4.3 14.8 - - + +
525D CYS* 4.4 9.2 - - - -
528D ALA* 3.5 19.3 - - + -
540D ILE* 3.7 21.8 - - + -
541D ASN 3.3 20.4 - - - -
542D GLN* 3.0 16.1 + - + +
544D HIS* 1.3 76.9 - - - +
546D GLU* 1.3 61.2 + - + +
547D GLN 3.2 0.2 - - - -
548D ALA* 2.9 17.7 + - - +
549D ILE* 3.0 19.5 + - + +
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Residues in contact with GLU 546 (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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508D LYS* 5.5 1.2 - - - -
512D LEU* 4.2 25.9 - - + +
542D GLN* 3.2 28.2 + - + +
543D LYS* 3.3 35.2 + - + +
545D PHE* 1.3 76.9 - - + +
547D GLN* 1.3 60.4 + - - +
548D ALA 3.2 0.2 - - - -
549D ILE* 4.1 9.1 - - + +
550D GLU* 3.5 24.8 + - - +
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Residues in contact with GLN 547 (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* 3.3 36.2 - - + +
534D ARG* 5.2 2.9 + - - -
535D HIS* 4.2 13.2 + - - -
543D LYS* 3.2 34.1 + - + +
544D HIS* 4.3 5.6 - - - +
545D PHE 3.2 0.8 - - - -
546D GLU* 1.3 76.5 - - + +
548D ALA* 1.3 58.1 + - - +
550D GLU* 4.1 12.7 - - - +
551D ARG* 3.3 23.2 + - - +
593D LYS* 6.1 1.3 - - - +
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Residues in contact with ALA 548 (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* 3.9 16.2 - - + +
527D GLU* 4.1 8.7 - - + -
528D ALA* 3.8 26.0 - - + +
531D ILE* 3.8 8.3 - - + -
544D HIS 3.7 7.7 + - - +
545D PHE* 2.9 10.5 + - - +
547D GLN* 1.3 78.0 - - - +
549D ILE* 1.3 64.4 + - - +
550D GLU 3.3 1.3 - - - -
551D ARG* 4.0 3.3 - - - +
552D VAL* 3.2 30.0 + - - +
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Residues in contact with ILE 549 (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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509D LEU* 4.3 16.4 - - + -
512D LEU* 3.8 39.0 - - + +
513D THR* 3.7 28.3 - - + -
516D PHE* 4.6 3.8 - - + -
524D VAL* 3.8 15.3 - - + -
545D PHE* 3.0 18.3 + - + +
546D GLU* 3.9 9.6 + - + +
548D ALA* 1.3 75.6 - - - +
550D GLU* 1.3 61.4 + - - +
552D VAL* 3.7 1.9 + - - +
553D ILE* 3.3 42.1 + - + +
592D LEU* 6.1 2.5 - - + -
607D GLN* 4.8 5.6 - - - +
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Residues in contact with GLU 550 (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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546D GLU 3.5 17.2 + - - +
547D GLN* 4.4 10.1 - - - +
548D ALA 3.3 0.6 - - - -
549D ILE* 1.3 79.1 - - - +
551D ARG* 1.3 59.1 + - - +
554D GLY* 2.8 28.8 + - - -
593D LYS* 2.6 42.0 + - - -
595D SER* 5.8 0.7 - - - -
599D ARG* 2.4 41.2 + - - +
605D TYR* 4.2 8.7 - - + -
607D GLN* 3.9 25.8 - - + +
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Residues in contact with ARG 551 (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* 4.3 14.4 - - - +
531D ILE* 5.1 5.8 - - + -
547D GLN 3.3 18.1 + - - +
548D ALA* 4.0 6.5 - - - +
549D ILE 3.4 0.2 - - - -
550D GLU* 1.3 77.2 - - - +
552D VAL* 1.3 64.7 + - - +
555D GLY* 3.2 39.5 + - - -
556D LEU* 3.4 15.8 - - - +
557D GLU* 5.3 2.0 - - - +
599D ARG* 4.8 4.7 - - - +
319E GLU* 3.5 45.5 + - - +
471E ARG* 4.3 12.5 - - - +
472E GLN* 3.5 24.9 + - - +
473E ILE* 3.9 11.1 - - - +
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Residues in contact with VAL 552 (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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516D PHE* 4.8 16.6 - - + -
520D ASP* 5.4 5.8 - - + +
523D ASN* 3.7 28.0 - - + +
524D VAL* 4.8 9.2 - - + -
527D GLU* 3.4 21.3 - - - +
548D ALA 3.2 18.0 + - - +
549D ILE* 4.3 3.4 - - - +
551D ARG* 1.3 77.8 - - - +
553D ILE* 1.3 68.0 + - + +
555D GLY* 4.5 1.7 + - - -
466E PRO* 4.9 10.5 - - + -
470E ASP 5.6 0.4 - - - +
472E GLN* 5.8 0.2 - - - +
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Residues in contact with ILE 553 (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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512D LEU 5.8 0.7 - - - +
514D PRO* 6.1 3.6 - - + -
516D PHE* 3.8 33.0 - - + -
549D ILE* 3.3 26.1 + - + +
550D GLU 4.2 0.2 - - - +
552D VAL* 1.3 80.8 - - + +
554D GLY* 1.3 62.5 + - - +
605D TYR* 3.4 17.7 - - - +
607D GLN* 3.6 19.7 - - - +
608D TYR 5.3 1.3 - - - +
610D PRO* 6.3 0.2 - - + -
2J ALA* 3.9 34.3 - - + +
3J ALA* 4.1 10.8 - - + +
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Residues in contact with GLY 554 (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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550D GLU 2.8 20.5 + - - -
553D ILE* 1.3 77.4 - - - +
555D GLY* 1.3 57.1 + - - +
599D ARG* 3.7 21.2 - - - +
600D GLY* 4.9 2.3 - - - -
605D TYR* 3.4 29.6 + - - -
3J ALA* 5.3 0.2 - - - -
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Residues in contact with GLY 555 (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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551D ARG* 3.2 38.4 + - - +
552D VAL 4.5 1.3 + - - -
553D ILE 3.7 1.0 - - - -
554D GLY* 1.3 79.4 - - - +
556D LEU* 1.3 66.9 + - - -
599D ARG* 3.5 14.6 + - - -
600D GLY* 5.2 3.4 - - - -
472E GLN* 4.6 6.7 - - - -
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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