Contacts of the helix formed by residues 541 - 555 (chain B) 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 ASN 541 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497B ASP* 4.2 14.6 - - + +
500B LEU* 3.9 11.7 - - + -
537B SER* 5.6 1.2 + - - -
539B SER 3.5 4.4 + - - +
540B ILE* 1.3 74.2 - - - +
542B GLN* 1.3 63.3 + - - +
543B LYS* 4.0 19.3 - - - +
544B HIS* 3.1 42.8 + - - +
545B PHE* 3.3 18.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 542 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500B LEU* 3.9 24.1 - - + +
505B LEU* 4.4 15.9 - - + +
508B LYS* 3.1 39.2 - - - +
509B LEU* 6.2 1.6 - - + -
512B LEU* 5.7 0.8 - - - +
541B ASN* 1.3 74.7 - - - +
543B LYS* 1.3 65.8 + - + +
545B PHE* 3.3 10.2 + - + +
546B GLU* 3.2 42.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 543 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541B ASN* 3.3 19.1 + - - +
542B GLN* 1.3 78.9 - - + +
544B HIS* 1.3 65.0 + - + +
546B GLU* 3.6 15.1 + - - +
547B GLN* 3.3 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 544 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528B ALA* 3.3 26.2 - - - +
531B ILE* 4.2 17.5 + - + +
532B ALA* 3.4 37.5 - - + +
535B HIS* 5.1 8.3 - + - +
537B SER* 3.9 21.9 - - - -
539B SER 4.2 2.2 - - - -
540B ILE* 3.8 4.8 - - + -
541B ASN* 3.1 39.6 + - - +
542B GLN 3.2 1.0 - - - -
543B LYS* 1.3 82.2 - - + +
545B PHE* 1.3 63.1 + - - +
547B GLN* 3.4 10.9 + - - +
548B ALA* 3.2 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 545 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491B LEU* 3.6 28.0 - - + -
494B LEU* 3.7 8.1 - - + -
496B LEU* 3.7 20.9 - - + -
500B LEU* 5.2 0.4 - - + -
505B LEU* 4.0 19.3 - - + -
509B LEU* 3.7 31.6 - - + -
524B VAL* 4.0 11.1 - - + +
525B CYS* 4.0 17.0 - - - -
528B ALA* 3.6 17.5 - - + -
540B ILE* 3.6 21.3 - - + -
541B ASN 3.3 20.9 - - - -
542B GLN* 3.3 9.2 + - + +
544B HIS* 1.3 76.5 - - - +
546B GLU* 1.3 63.7 + - + +
548B ALA* 3.3 1.8 + - - +
549B ILE* 3.2 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 546 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508B LYS* 4.9 2.3 + - - -
509B LEU* 6.0 0.7 - - + -
512B LEU* 4.4 22.0 - - + +
542B GLN* 3.2 44.5 + - + +
543B LYS* 3.6 14.8 + - - +
544B HIS 3.3 0.4 - - - -
545B PHE* 1.3 76.3 - - + +
547B GLN* 1.3 58.3 + - + +
549B ILE* 4.3 8.2 - - - +
550B GLU* 3.3 12.6 + - - +
593B LYS* 3.2 30.0 + - - +
607B GLN* 5.5 0.3 - - - +
737B ASP* 4.3 16.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 547 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531B ILE* 3.4 31.6 - - + +
535B HIS* 5.5 2.1 + - - -
543B LYS* 3.3 20.4 + - - +
544B HIS* 3.4 11.8 + - - +
545B PHE 3.1 0.6 - - - -
546B GLU* 1.3 78.7 - - + +
548B ALA* 1.3 54.3 + - - +
549B ILE 3.3 1.6 - - - -
550B GLU* 3.3 16.8 - - - +
551B ARG* 2.6 36.0 + - - +
557B GLU* 5.1 12.2 + - - +
593B LYS* 5.5 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 548 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B VAL* 3.6 20.2 - - + +
527B GLU* 3.8 10.5 - - + +
528B ALA* 3.6 29.6 - - + +
531B ILE* 3.9 7.5 - - + +
544B HIS 3.2 13.1 + - - +
545B PHE 3.3 3.8 + - - +
547B GLN* 1.3 73.6 - - - +
549B ILE* 1.3 63.9 + - - +
551B ARG* 3.7 5.4 - - - +
552B VAL* 3.3 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 549 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509B LEU* 4.2 17.9 - - + -
512B LEU* 4.0 29.2 - - + +
513B THR* 3.7 33.4 - - + -
516B PHE* 4.8 8.0 - - + -
524B VAL* 3.7 19.7 - - + -
545B PHE 3.2 19.7 + - - +
546B GLU* 4.3 5.4 - - - +
548B ALA* 1.3 74.2 - - - +
550B GLU* 1.3 62.5 + - - +
551B ARG 3.4 0.7 + - - -
552B VAL* 3.4 9.0 + - - +
553B ILE* 3.4 21.6 + - + +
607B GLN* 3.5 24.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 550 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546B GLU 3.3 12.7 + - - +
547B GLN* 3.1 19.3 + - - +
549B ILE* 1.3 79.0 - - - +
551B ARG* 1.3 56.9 + - - +
553B ILE* 4.8 1.8 - - - -
554B GLY* 3.2 15.5 + - - -
557B GLU* 4.8 4.9 - - - +
593B LYS* 2.6 40.0 + - + +
599B ARG* 2.7 39.0 + - - +
605B TYR* 2.3 37.7 + - + +
607B GLN* 4.4 10.7 + - - +
735B VAL* 4.7 10.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 551 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B GLU* 4.9 15.5 + - + +
531B ILE* 5.0 7.9 - - + -
547B GLN 2.6 19.0 + - - +
548B ALA* 3.7 9.9 - - - +
549B ILE 3.2 0.4 - - - -
550B GLU* 1.3 74.0 - - - +
552B VAL* 1.3 70.9 + - + +
555B GLY* 2.6 48.3 + - - +
556B LEU* 3.4 12.3 - - - +
557B GLU 5.6 2.0 - - - +
599B ARG* 4.8 2.0 - - - +
319C GLU* 2.8 41.9 + - - -
471C ARG* 4.0 22.8 - - - +
472C GLN 3.9 21.4 + - - +
473C ILE* 4.2 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 552 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516B PHE* 4.7 10.8 - - + -
520B ASP* 4.6 17.0 - - + +
523B ASN* 4.0 25.4 - - + +
524B VAL* 4.6 12.1 - - + -
527B GLU* 4.9 7.0 - - + -
548B ALA 3.3 18.6 + - - +
549B ILE* 3.4 4.9 + - - +
551B ARG* 1.3 84.7 + - + +
553B ILE* 1.3 69.8 + - + +
555B GLY* 4.8 1.6 + - - -
466C PRO* 5.4 2.9 - - + -
470C ASP 5.7 0.4 - - - +
1H ALA* 5.7 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 553 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516B PHE* 3.7 28.7 - - + -
549B ILE* 3.4 15.5 - - + +
550B GLU* 4.7 1.6 - - - +
552B VAL* 1.3 79.1 - - + +
554B GLY* 1.3 66.1 + - - +
607B GLN* 3.4 42.4 - - + +
1H ALA* 3.8 11.4 - - + +
2H ALA* 3.7 39.0 - - + +
3H ALA 4.3 7.6 - - - +
4H ALA* 4.2 17.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 554 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550B GLU 3.2 17.6 + - - -
553B ILE* 1.3 84.1 - - - +
555B GLY* 1.3 57.2 + - - +
599B ARG* 3.4 32.1 - - - +
605B TYR* 5.4 11.4 - - - +
4H ALA* 5.8 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 555 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550B GLU 4.0 2.0 + - - -
551B ARG* 2.6 47.6 + - - +
552B VAL 4.8 1.0 + - - -
553B ILE 3.9 0.2 - - - -
554B GLY* 1.3 78.5 - - - +
556B LEU* 1.3 60.9 + - - -
557B GLU 4.1 0.8 + - - -
599B ARG* 4.1 9.5 + - - +
600B GLY* 5.1 1.1 - - - -
472C GLN 5.8 1.6 - - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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