Contacts of the helix formed by residues 545 - 551 (chain A) in PDB entry 2Q8J
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 545 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A LEU* 3.0 22.6 + - + +
436A VAL* 3.8 15.6 - - + +
544A LYS* 1.3 72.8 - - - +
546A ASP* 1.3 68.1 + - - +
547A THR 3.2 1.0 + - - -
548A VAL* 3.3 13.7 + - - +
549A TRP* 3.5 20.4 + - - -
571A LEU* 5.4 0.9 - - - +
581A VAL* 4.2 1.9 - - - +
584A ALA* 3.4 29.8 - - + +
1C NAG 1.5 64.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 546 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A ARG* 3.5 29.8 + - - -
433A TYR* 4.1 13.6 - - - +
434A LEU 4.8 1.2 + - - -
544A LYS* 3.2 21.6 - - - +
545A ASN* 1.3 80.5 + - - +
547A THR* 1.3 56.7 + - - +
549A TRP* 3.4 3.0 + - - +
550A GLU* 3.0 44.5 + - - +
644A ASN* 3.8 9.4 + - - +
1C NAG 2.7 38.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 547 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A TYR* 3.5 42.5 - - + +
527A THR* 4.5 0.7 - - - +
530A PHE* 3.8 15.6 - - + -
543A VAL* 4.2 8.5 - - + -
544A LYS* 3.1 32.9 + - - +
546A ASP* 1.3 76.6 - - - +
548A VAL* 1.3 67.4 + - - +
550A GLU* 4.6 5.4 - - - -
551A ASN* 3.1 43.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
436A VAL* 4.8 1.3 - - + -
438A VAL* 3.8 34.8 - - + -
530A PHE* 4.2 19.1 - - + -
543A VAL* 5.0 1.1 - - + -
544A LYS 3.9 5.1 + - - +
545A ASN* 3.3 11.4 + - - +
547A THR* 1.3 77.7 - - - +
549A TRP* 1.3 64.0 + - + +
551A ASN* 3.5 0.5 + - - +
552A THR* 2.9 44.1 + - + +
566A ARG* 5.1 1.1 - - + -
569A PHE* 4.6 7.0 - - + -
571A LEU* 4.6 5.4 - - + -
581A VAL* 3.7 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 549 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A ASN* 3.5 31.2 + - - -
546A ASP 3.4 1.9 + - - +
547A THR 3.3 0.6 - - - -
548A VAL* 1.3 84.3 - - + +
550A GLU* 1.3 63.0 + - - +
551A ASN 3.2 1.0 + - - -
552A THR 3.4 6.2 + - - +
555A GLU* 3.6 3.7 - - - +
566A ARG* 3.1 63.3 + - - +
581A VAL* 3.6 15.8 + - + +
582A THR* 3.7 38.1 - - + -
1C NAG 3.7 41.9 + - - -
2C NAG 3.4 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 550 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A LYS* 5.5 4.0 + - - -
546A ASP* 3.0 26.7 + - + +
547A THR* 4.3 3.5 - - - +
549A TRP* 1.3 76.0 - - - +
551A ASN* 1.3 72.9 + - - +
555A GLU* 3.2 31.1 - - - +
556A SER* 3.8 1.7 + - - -
636A THR* 4.7 4.5 + - - +
638A ASN* 4.9 13.2 + - - +
643A ASP* 5.4 3.9 - - - +
644A ASN* 2.9 45.5 + - - +
1C NAG 4.4 8.3 + - - +
2C NAG 5.4 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 551 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A THR* 4.1 10.7 + - - +
530A PHE* 4.2 7.3 - - + -
547A THR* 3.1 41.3 + - - +
549A TRP 3.2 0.8 - - - -
550A GLU* 1.3 84.8 + - - +
552A THR* 1.3 65.0 + - - +
556A SER* 3.8 15.5 + - - -
560A TRP* 3.9 30.8 - - + -
561A ALA* 3.4 22.1 - - + +
564A LEU* 3.7 6.8 - - - +
636A THR* 3.0 25.4 + - - -
----------------------------------------------------------
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