Contacts of the helix formed by residues 530 - 539 (chain B) in PDB entry 3PLZ
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 530 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B ASP* 4.2 2.2 + - - -
354B PHE* 5.0 8.6 - - + -
528B TYR* 4.0 24.0 + - - -
529B ASN* 1.3 81.6 + - - +
531B LEU* 1.3 64.8 + - - +
533B ILE* 3.2 16.2 - - - +
534B GLU* 3.3 15.8 - - - +
744D LEU* 3.9 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 531 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B ASP* 3.2 11.2 + - - +
353B LEU* 3.6 19.3 - - + +
354B PHE* 3.6 47.3 - - + +
357B VAL* 4.6 4.0 - - + -
530B ASN* 1.3 76.9 - - - +
532B LEU* 1.3 67.0 + - - +
534B GLU* 3.1 5.3 + - + -
535B MET* 2.9 48.4 + - + +
744D LEU* 3.9 15.0 - - + -
745D LEU* 5.2 7.9 - - + +
748D LEU* 3.8 31.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
1B 470 5.2 0.2 - - + -
346B CYS* 3.7 35.0 - - + +
349B ALA* 4.4 12.3 - - + -
350B ASP* 2.9 24.3 + - + +
353B LEU* 3.9 14.5 - - + +
382B TRP* 3.8 28.9 - - + -
386B LEU* 5.1 0.2 - - + -
517B LEU* 4.6 17.7 - - + -
526B VAL* 4.4 8.3 - - + -
529B ASN* 3.3 19.5 + - - +
531B LEU* 1.3 72.0 - - - +
533B ILE* 1.3 58.0 + - - +
535B MET* 3.3 1.4 + - - -
536B LEU* 2.9 39.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 533 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518B TYR* 4.9 1.8 - - + -
521B HIS* 3.3 50.7 - - + +
526B VAL* 6.4 0.2 - - + -
529B ASN* 2.9 33.2 + - - +
530B ASN* 3.2 15.0 - - - +
532B LEU* 1.3 77.1 - - - +
534B GLU* 1.3 74.1 + - - +
536B LEU* 3.3 18.7 + - + -
537B HIS* 3.1 45.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 534 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530B ASN 3.3 14.8 - - - +
531B LEU* 3.1 12.3 + - + +
533B ILE* 1.3 85.4 - - - +
535B MET* 1.3 65.4 + - - +
537B HIS* 3.2 24.1 + - - +
538B ALA* 3.5 9.0 + - - +
742D ASN* 2.7 45.0 + - - +
744D LEU* 4.2 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 535 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B LEU* 4.1 17.0 - - + -
357B VAL* 6.0 2.0 - - + -
378B LEU* 3.9 12.6 - - + +
379B GLN* 4.0 14.6 - - + -
382B TRP* 3.2 59.5 + - + -
514B GLU* 4.7 0.3 - - - +
531B LEU* 2.9 40.1 + - + +
532B LEU 3.7 3.8 - - - +
534B GLU* 1.3 80.2 - - - +
536B LEU* 1.3 62.6 - - - +
538B ALA* 2.9 21.6 + - + +
539B LYS 4.4 0.5 + - - -
742D ASN* 5.8 1.1 - - - +
745D LEU* 4.1 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 536 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B 470 4.7 0.9 - - + -
382B TRP* 3.6 25.3 - - + -
514B GLU* 3.6 40.8 - - + +
517B LEU* 4.0 32.8 - - + +
518B TYR* 4.3 10.8 - - + +
521B HIS* 5.0 2.2 - - + -
526B VAL* 5.8 3.6 - - + -
532B LEU* 2.9 32.1 + - + +
533B ILE* 3.3 26.7 + - + +
535B MET* 1.3 75.3 - - - +
537B HIS* 1.3 61.0 + - - +
538B ALA 3.4 0.7 + - - -
539B LYS 4.3 2.6 + - - -
540B ARG* 3.5 20.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 537 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518B TYR* 3.6 31.6 + + - -
521B HIS* 4.9 4.3 - + - -
533B ILE* 3.1 43.3 + - + +
534B GLU* 3.2 20.5 + - - +
535B MET 3.1 0.8 - - - -
536B LEU* 1.3 76.9 - - - +
538B ALA* 1.3 61.1 + - - +
539B LYS 3.4 0.4 - - - -
540B ARG* 3.1 18.6 + - - +
740D LYS* 2.8 29.9 + - - +
742D ASN* 5.9 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 538 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B GLN* 3.7 46.1 + - + +
382B TRP* 4.5 1.8 - - - +
534B GLU 3.5 5.6 + - - +
535B MET* 2.9 22.5 + - + +
537B HIS* 1.3 79.3 - - - +
539B LYS* 1.3 61.3 + - - +
540B ARG 4.2 0.5 - - - +
740D LYS* 3.4 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 539 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A GLN* 4.9 7.8 - - - +
379B GLN 2.9 29.6 + - - +
380B ASN* 2.9 29.2 + - - +
382B TRP* 3.6 8.7 - - - +
383B SER* 4.1 4.0 + - - -
384B GLU* 5.0 0.6 + - - -
507B ARG* 3.9 9.6 - - - +
511B MET* 3.6 37.7 - - + -
514B GLU* 2.8 39.1 + - - +
535B MET 4.4 0.6 + - - -
536B LEU 4.3 2.4 + - - -
537B HIS 3.4 0.4 - - - -
538B ALA* 1.3 75.5 - - + +
540B ARG* 1.3 64.9 + - + +
----------------------------------------------------------
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