Contacts of the helix formed by residues 538 - 555 (chain A) in PDB entry 3AR2
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 THR 538 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A VAL* 5.5 2.8 - - + +
374A GLY 5.1 3.5 + - - -
536A PRO* 3.3 26.1 + - + +
537A MET* 1.3 77.6 - - - +
539A GLY* 1.3 65.5 + - - +
540A PRO* 3.4 15.6 - - - +
541A VAL* 3.2 22.8 + - + +
542A LYS* 3.0 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 539 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A THR* 1.3 71.3 - - - +
540A PRO* 1.3 59.5 - - - +
542A LYS* 3.2 8.5 + - - +
543A GLU* 2.7 44.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 540 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A GLY 4.3 5.2 - - - +
375A ASP* 4.0 47.6 - - + +
377A CYS* 4.4 5.0 - - + +
538A THR* 3.4 14.6 - - - +
539A GLY* 1.3 88.3 - - - +
541A VAL* 1.3 56.5 + - + +
543A GLU* 3.4 15.0 - - + +
544A LYS* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 541 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A ILE* 4.3 2.9 - - + -
372A VAL* 4.0 28.0 - - + -
374A GLY 5.8 0.7 - - - +
377A CYS* 3.9 24.7 - - + -
528A VAL* 3.4 36.6 - - + -
536A PRO 4.8 1.8 - - - +
537A MET* 4.3 1.1 - - - -
538A THR* 3.2 30.9 + - + +
540A PRO* 1.3 73.9 - - + +
542A LYS* 1.3 56.2 + - - +
544A LYS* 3.1 2.1 + - - +
545A ILE* 2.8 48.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 542 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A ILE* 3.5 27.9 + - + +
523A ASP* 2.8 38.9 + - - +
537A MET* 3.8 20.1 - - + +
538A THR 3.0 17.7 + - - +
539A GLY* 3.4 8.5 - - - +
541A VAL* 1.3 75.4 - - - +
543A GLU* 1.3 58.5 + - - +
544A LYS 3.2 0.2 + - - -
545A ILE* 3.3 5.1 + - - +
546A LEU* 2.9 49.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 543 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A GLY* 2.7 20.8 + - - +
540A PRO* 3.4 18.5 - - - +
542A LYS* 1.3 74.0 - - - +
544A LYS* 1.3 57.7 + - - +
546A LEU* 3.8 6.5 + - - +
547A SER* 3.1 28.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 544 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A CYS* 3.6 38.1 + - + +
378A SER* 4.7 0.7 - - - +
379A LEU* 3.8 36.8 - - + +
381A GLU* 5.8 1.3 - - - -
540A PRO 2.9 18.1 + - - +
541A VAL 3.5 3.8 - - - +
543A GLU* 1.3 73.7 - - - +
545A ILE* 1.3 69.9 + - - +
547A SER* 2.7 24.0 + - - +
548A VAL* 3.3 17.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 545 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A PHE* 3.7 20.9 - - + -
369A ILE* 3.1 35.7 - - + -
379A LEU* 4.0 4.7 - - + -
522A ILE* 3.9 18.2 - - + -
537A MET* 5.4 4.3 - - + -
541A VAL* 2.8 30.9 + - + +
542A LYS* 3.6 6.7 - - - +
544A LYS* 1.3 72.5 - - - +
546A LEU* 1.3 63.2 + - - +
548A VAL 3.5 0.9 + - - -
549A ILE* 3.3 28.6 + - + +
593A PHE* 3.4 43.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 546 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A PRO* 5.2 0.9 - - + +
519A GLU* 5.2 15.9 - - + +
522A ILE* 4.6 19.3 - - + -
523A ASP* 5.8 0.7 - - - +
542A LYS* 2.9 44.2 + - + +
543A GLU* 4.0 6.1 - - - +
545A ILE* 1.3 77.4 - - - +
547A SER* 1.3 57.6 + - - +
549A ILE* 2.9 24.9 + - + +
550A LYS* 2.8 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 547 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A GLU 3.1 16.7 + - - -
544A LYS* 2.7 31.4 + - - +
546A LEU* 1.3 74.9 - - - +
548A VAL* 1.3 57.6 + - - +
550A LYS* 3.2 12.3 + - - +
551A GLU* 2.9 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 548 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A PHE* 3.6 29.2 - - + -
379A LEU* 3.4 22.7 - - + -
381A GLU* 4.2 13.7 - - - +
544A LYS* 3.3 23.5 + - + +
545A ILE 4.0 1.6 - - - +
547A SER* 1.3 74.6 + - - +
549A ILE* 1.3 65.9 + - - +
551A GLU* 4.2 13.2 - - - +
552A TRP* 3.2 48.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 549 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A PHE* 4.5 2.2 - - + -
518A PRO* 3.5 30.3 - - + -
519A GLU* 5.7 0.4 - - - +
522A ILE* 4.6 2.0 - - + -
545A ILE* 3.3 26.0 + - + +
546A LEU* 2.9 22.4 + - + +
548A VAL* 1.3 77.4 - - - +
550A LYS* 1.3 64.8 + - - +
552A TRP* 3.5 2.2 + - - +
553A GLY* 3.0 22.3 + - - -
561A CYS* 4.1 25.5 - - + -
596A VAL* 3.9 35.7 - - + -
628A ASN* 5.4 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 550 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546A LEU 2.8 12.1 + - - +
547A SER* 3.4 13.2 - - - +
549A ILE* 1.3 79.3 - - - +
551A GLU* 1.3 55.7 + - - +
553A GLY* 5.1 0.9 - - - -
554A THR* 2.8 55.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 551 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A LYS* 5.4 3.1 + - - -
381A GLU* 5.2 3.9 - - - +
547A SER 2.9 15.0 + - - +
548A VAL* 3.7 15.4 - - - +
549A ILE 3.2 0.2 - - - -
550A LYS* 1.3 76.4 - - - +
552A TRP* 1.3 75.6 + - - +
554A THR* 3.8 2.4 + - - -
555A GLY* 2.7 38.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 552 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A LYS* 3.4 55.9 - - + +
366A MET* 3.4 27.4 - - - -
367A PHE* 3.6 28.9 - + - -
381A GLU* 3.8 26.8 + - + -
548A VAL* 3.2 26.8 + - + +
549A ILE* 4.0 3.8 - - - +
551A GLU* 1.3 101.1 + - - +
553A GLY* 1.3 58.2 + - - +
555A GLY* 3.9 3.3 + - - -
557A ASP* 4.6 0.7 + - - +
558A THR* 3.8 5.5 + - - -
559A LEU* 2.9 37.5 + - + +
561A CYS* 4.3 12.3 - - - -
596A VAL* 4.5 5.4 - - + -
597A VAL 4.5 0.9 - - - -
598A GLY* 3.9 17.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 553 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549A ILE* 3.0 17.7 + - - -
550A LYS* 3.9 1.1 - - - -
552A TRP* 1.3 76.9 - - - +
554A THR* 1.3 58.6 + - - +
558A THR* 3.1 26.2 - - - -
559A LEU 3.5 5.2 - - - -
561A CYS* 5.1 1.1 - - - -
631A THR* 3.2 37.3 - - - +
634A ALA* 3.9 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 554 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550A LYS* 2.8 46.6 + - + +
551A GLU* 3.8 3.1 + - - -
553A GLY* 1.3 71.2 - - - +
555A GLY* 1.3 68.3 + - - +
630A GLY* 4.0 27.6 - - - +
634A ALA* 4.0 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 555 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A GLU* 2.7 25.7 + - - -
552A TRP* 3.9 3.6 + - - -
553A GLY 3.3 2.4 - - - -
554A THR* 1.3 82.1 + - - +
556A ARG* 1.3 60.5 + - - -
557A ASP 3.3 2.9 - - - -
558A THR* 3.0 23.8 + - - +
----------------------------------------------------------
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