Contacts of the helix formed by residues 537 - 552 (chain A) in PDB entry 3TT9
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 GLY 537 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A ILE* 4.2 7.6 - - - -
494A TRP* 4.0 27.1 - - - -
535A CYS 3.1 1.2 + - - -
536A ASP* 1.3 72.2 - - - +
538A LEU* 1.3 62.0 + - - +
539A ILE 3.6 1.5 - - - +
540A ASP* 4.1 10.3 + - - +
541A SER* 2.9 30.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 538 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A LEU* 4.1 16.4 - - + -
484A THR* 3.8 31.2 - - + +
488A ILE* 4.1 11.2 - - + -
518A LEU* 3.9 18.6 - - + -
532A MET* 3.6 35.7 - - + +
535A CYS* 3.0 16.7 + - + +
536A ASP 3.3 2.4 + - - -
537A GLY* 1.3 77.5 - - - +
539A ILE* 1.3 67.1 + - + +
541A SER* 3.8 2.7 - - - -
542A LEU* 3.1 49.0 + - + +
566A ILE* 5.5 0.7 - - + -
570A LEU* 4.4 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 539 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533A ARG* 3.8 45.7 + - + +
535A CYS 4.7 0.8 + - - -
537A GLY 3.6 0.2 - - - -
538A LEU* 1.3 80.6 - - + +
540A ASP* 1.3 70.6 + - - +
542A LEU* 3.2 3.9 + - + +
543A VAL* 3.0 35.3 + - + +
567A LEU* 3.9 25.4 - - + -
570A LEU* 4.4 23.8 - - + +
571A SER* 4.4 12.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 540 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A TRP* 3.4 43.5 - - + +
537A GLY* 3.7 9.5 + - - +
538A LEU 3.3 0.6 - - - -
539A ILE* 1.3 83.5 - - - +
541A SER* 1.3 56.9 + - - +
543A VAL* 3.5 6.4 + - - +
544A HIS* 3.0 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 541 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A ILE* 3.9 17.3 - - - -
489A ILE* 3.4 10.0 - - - +
492A SER* 3.4 29.8 + - - -
494A TRP* 3.2 29.2 - - - -
537A GLY 2.9 22.3 + - - -
538A LEU 3.8 2.7 - - - -
540A ASP* 1.3 74.2 - - - +
542A LEU* 1.3 61.8 + - - +
544A HIS* 3.4 0.9 + - - +
545A TYR* 3.0 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 542 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A ILE* 3.9 28.9 - - + -
511A PHE* 5.0 1.6 - - + -
515A THR* 4.6 1.6 - - + -
518A LEU* 5.2 0.2 - - + -
538A LEU* 3.1 40.0 + - + +
539A ILE* 3.8 4.3 - - + +
541A SER* 1.3 75.5 - - - +
543A VAL* 1.3 63.9 + - - +
545A TYR* 3.2 5.4 + - - +
546A VAL* 3.0 27.7 + - - +
563A CYS* 3.7 26.3 - - + +
566A ILE* 3.5 45.8 - - + -
567A LEU* 4.1 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 543 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A ILE* 3.0 29.6 + - + +
540A ASP* 3.8 6.7 - - - +
542A LEU* 1.3 75.3 - - - +
544A HIS* 1.3 62.8 + - - +
546A VAL* 3.3 5.4 + - + +
547A ARG* 3.0 62.3 + - + +
567A LEU* 3.8 27.4 - - + -
571A SER* 5.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 544 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A SER 3.0 29.0 + - - -
493A GLY* 3.7 11.2 + - - -
494A TRP* 3.7 25.8 - - + -
496A GLU* 3.6 48.9 + - + +
540A ASP 3.0 17.9 + - - +
541A SER 3.7 3.6 - - - +
542A LEU 3.2 0.2 - - - -
543A VAL* 1.3 79.1 - - - +
545A TYR* 1.3 56.8 + - - +
547A ARG* 3.3 8.6 + - - +
548A GLY* 2.9 31.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 545 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A PHE* 3.9 16.2 - + - -
492A SER* 4.5 17.9 - - - -
508A PHE* 3.5 17.0 - - - -
511A PHE* 3.7 42.8 - + + -
541A SER 3.0 14.8 + - - +
542A LEU* 3.2 8.9 + - - +
544A HIS* 1.3 80.4 - - - +
546A VAL* 1.3 63.1 + - - +
548A GLY* 3.1 3.4 + - - -
549A THR* 3.0 33.5 + - + +
557A ASP* 2.6 27.5 + - - -
559A ALA* 4.0 0.2 - - + -
560A THR* 3.4 26.2 - - - -
563A CYS* 4.1 10.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 546 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A LEU 3.0 19.5 + - - +
543A VAL* 3.6 8.5 - - - +
545A TYR* 1.3 76.5 - - - +
547A ARG* 1.3 65.4 + - + +
549A THR* 2.8 24.5 + - - -
550A ILE* 3.2 22.4 + - + +
560A THR* 4.0 24.2 - - + +
563A CYS* 3.4 26.0 - - + -
564A VAL* 4.2 16.6 - - + +
567A LEU* 4.4 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 547 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A VAL* 3.0 45.4 + - - +
544A HIS* 3.8 7.2 - - - +
546A VAL* 1.3 80.1 - - + +
548A GLY* 1.3 62.8 + - - +
550A ILE* 3.2 15.4 + - + +
551A ALA* 3.1 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 548 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A GLU* 6.1 0.9 - - - -
544A HIS* 2.9 21.1 + - - -
545A TYR* 3.1 4.4 + - - -
547A ARG* 1.3 77.9 - - - +
549A THR* 1.3 56.1 + - - +
551A ALA* 3.4 5.3 + - - +
552A ASP* 2.9 42.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 549 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A TYR* 3.0 32.6 + - + +
546A VAL 2.8 17.3 + - - -
548A GLY* 1.3 73.2 - - - +
550A ILE* 1.3 65.2 + - - +
552A ASP* 4.5 3.1 - - - +
553A TYR 3.2 2.6 + - - -
554A GLN* 2.9 52.7 + - + -
557A ASP* 3.4 11.7 - - - +
560A THR* 2.9 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 550 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546A VAL* 3.2 28.0 + - + +
547A ARG* 3.2 14.8 + - + +
549A THR* 1.3 81.6 + - - +
551A ALA* 1.3 63.9 + - - +
553A TYR* 3.1 21.0 + - - -
555A PRO* 6.4 0.9 - - - -
560A THR* 6.0 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 551 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A ARG 3.1 15.0 + - - +
548A GLY* 3.9 6.7 - - - +
550A ILE* 1.3 79.3 - - - +
552A ASP* 1.3 63.3 + - - +
553A TYR* 3.2 21.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 552 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A GLY* 2.9 25.1 + - - +
549A THR* 3.6 4.5 + - - +
550A ILE 3.2 0.2 - - - -
551A ALA* 1.3 82.7 - - - +
553A TYR* 1.3 72.6 + - - +
554A GLN* 3.4 17.6 + - + +
----------------------------------------------------------
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