Contacts of the helix formed by residues 524 - 537 (chain B) in PDB entry 2DB3
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 LEU 524 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522B ASP 5.5 2.0 - - - +
523B ARG* 1.3 73.6 - - - +
525B GLN* 1.3 58.4 + - - +
526B SER* 3.9 11.7 - - - +
527B GLN* 2.7 66.7 + - + +
528B ARG* 2.9 10.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 525 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B TYR* 4.0 5.2 - - + -
328B ARG* 3.0 38.1 + - - +
329B GLU* 3.0 23.6 + - - -
332B ILE* 4.6 0.8 - - - +
353B TYR* 4.0 7.5 - - + -
354B GLY 3.9 8.7 - - - +
355B GLY* 3.4 33.0 - - - +
523B ARG 3.6 2.0 + - - -
524B LEU* 1.3 72.8 - - - +
526B SER* 1.3 63.9 + - - +
528B ARG* 3.2 15.0 + - - +
529B GLU* 2.6 59.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 526 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B TYR* 3.5 46.7 + - - +
524B LEU* 3.9 12.7 - - - +
525B GLN* 1.3 78.2 - - - +
527B GLN* 1.3 62.6 + - - +
529B GLU* 3.6 1.6 + - - +
530B GLN* 3.0 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 527 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B ARG* 3.4 43.8 + - + +
524B LEU* 2.7 56.9 + - + +
526B SER* 1.3 81.9 + - - +
528B ARG* 1.3 62.6 + - - +
529B GLU 3.2 0.4 - - - -
530B GLN* 3.9 5.8 - - - +
531B ALA* 3.0 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 528 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B ARG* 3.9 13.1 - - - +
329B GLU* 2.8 46.4 + - - +
518B SER 5.1 1.3 - - - -
519B ILE* 3.8 29.1 - - + +
520B HIS 3.7 22.4 + - - +
521B GLY* 4.1 14.9 + - - -
523B ARG* 3.9 17.9 - - + -
524B LEU 2.9 11.5 + - - +
525B GLN* 3.2 26.5 + - - +
527B GLN* 1.3 76.7 - - - +
529B GLU* 1.3 63.2 + - - +
531B ALA* 3.4 11.9 + - - +
532B LEU* 3.5 10.2 + - - +
548B VAL* 3.4 15.3 - - - +
5F U 2.9 41.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 529 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B TYR* 2.7 29.4 + - - +
204B PRO* 3.7 6.4 - - - +
205B PRO* 4.5 3.3 - - - +
329B GLU* 4.6 5.6 - - + +
332B ILE* 3.5 16.9 - - + +
353B TYR* 2.9 27.8 + - - -
525B GLN* 2.6 47.2 + - - +
526B SER 4.0 4.0 - - - +
528B ARG* 1.3 79.5 - - - +
530B GLN* 1.3 56.2 + - - +
532B LEU* 3.5 7.2 + - - +
533B ARG* 3.1 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 530 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526B SER 3.0 18.6 + - - +
527B GLN* 3.9 7.2 - - - +
528B ARG 3.3 0.2 - - - -
529B GLU* 1.3 74.1 - - - +
531B ALA* 1.3 55.3 + - - +
533B ARG* 4.0 28.8 + - - +
534B ASP* 2.6 77.2 + - - +
537B ASN* 5.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 531 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517B THR* 3.5 31.6 - - + +
518B SER 3.4 25.6 - - - +
519B ILE* 4.7 4.3 - - + -
523B ARG* 4.1 1.1 - - - +
527B GLN 3.0 17.6 + - - +
528B ARG* 3.6 7.2 - - - +
529B GLU 3.3 0.2 - - - -
530B GLN* 1.3 79.3 - - - +
532B LEU* 1.3 57.3 + - - +
534B ASP* 3.8 2.8 + - - +
535B PHE* 3.1 26.2 + - - +
543B LEU* 4.8 2.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 532 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B GLU* 3.7 33.4 - - + -
519B ILE* 4.1 15.3 - - + -
528B ARG 3.5 9.8 + - - +
529B GLU* 3.5 7.7 + - - +
530B GLN 3.2 0.2 - - - -
531B ALA* 1.3 74.8 - - - +
533B ARG* 1.3 59.1 + - - +
534B ASP 3.1 0.2 - - - -
535B PHE* 3.5 4.1 - - + +
536B LYS* 2.7 58.7 + - + +
543B LEU* 4.1 22.9 - - + -
553B LEU* 4.4 15.9 - - + -
555B ILE* 4.0 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 533 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B PRO* 4.2 30.1 - - - +
529B GLU 3.1 18.0 + - - +
530B GLN* 3.5 30.8 + - - +
532B LEU* 1.3 77.7 - - - +
534B ASP* 1.3 56.2 + - - +
536B LYS* 3.6 8.7 + - - +
537B ASN* 3.1 37.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 534 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517B THR* 5.0 3.1 + - - -
530B GLN* 2.6 57.3 + - - +
531B ALA* 4.1 5.3 - - - +
533B ARG* 1.3 70.3 - - - +
535B PHE* 1.3 63.3 + - - +
536B LYS 3.2 0.2 - - - -
537B ASN* 3.0 28.7 + - - +
539B SER* 3.1 13.0 + - - -
540B MET* 3.1 40.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 535 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491B GLY* 3.7 9.6 - - - -
492B THR 3.4 34.1 - - - -
493B ILE* 4.6 0.7 - - - -
517B THR* 5.0 0.7 - - + -
531B ALA 3.1 18.7 + - - +
532B LEU* 3.1 8.4 + - - +
534B ASP* 1.3 77.3 - - - +
536B LYS* 1.3 57.6 + - - +
538B GLY* 3.7 4.4 + - - -
540B MET* 4.2 19.3 - - + +
541B LYS* 3.3 22.4 - - - -
542B VAL 4.2 3.8 - - - -
543B LEU* 3.5 33.4 - - + -
555B ILE* 4.1 17.9 - - + -
557B ASN* 2.8 30.0 + - + +
558B ILE* 3.7 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 536 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B GLN* 5.7 4.8 + - - +
532B LEU* 2.7 38.6 + - - +
533B ARG* 3.9 7.4 - - - +
535B PHE* 1.3 75.6 - - + +
537B ASN* 1.3 58.1 + - - +
538B GLY 3.1 5.5 + - - -
554B ASP 5.1 4.3 + - - -
555B ILE* 4.1 36.6 - - + +
557B ASN* 2.5 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 537 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533B ARG* 3.1 25.1 + - - +
534B ASP* 3.0 13.7 + - - +
536B LYS* 1.3 76.2 - - - +
538B GLY* 1.3 54.4 + - - +
539B SER* 2.5 48.1 + - - -
----------------------------------------------------------
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