Contacts of the helix formed by residues 533 - 546 (chain D) in PDB entry 3T6A
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 GLU 533 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526D PRO* 4.2 12.6 - - - +
528D GLU* 4.7 4.2 - - - +
529D ASN* 4.3 2.6 - - - +
530D LYS* 3.4 44.8 + - + +
531D PRO 3.1 5.8 + - - -
532D LEU* 1.3 73.8 - - - +
534D THR* 1.3 71.5 + - + +
535D ALA* 3.2 9.2 - - + +
536D LEU* 2.9 46.3 + - + +
537D LEU* 3.0 11.3 + - - +
786D LEU* 4.5 1.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 534 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532D LEU 2.8 8.6 + - - -
533D GLU* 1.3 74.7 - - + +
535D ALA* 1.3 68.7 + - + +
537D LEU* 3.3 8.6 + - - +
538D LYS* 2.9 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 535 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533D GLU* 3.2 7.3 - - + +
534D THR* 1.3 84.9 - - + +
536D LEU* 1.3 68.5 + - + +
538D LYS* 3.1 12.8 + - - +
539D ARG* 3.0 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 536 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524D PHE 4.7 7.6 - - - +
525D LEU* 3.8 5.2 - - + -
526D PRO* 3.6 39.0 - - + -
529D ASN* 3.7 22.4 - - - +
533D GLU* 2.9 31.8 + - + +
535D ALA* 1.3 81.6 - - + +
537D LEU* 1.3 57.5 + - - +
539D ARG* 3.3 22.5 + - - +
540D ALA* 3.0 27.0 + - - +
782D PHE* 6.5 0.2 - - + -
786D LEU* 3.4 29.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 537 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532D LEU* 3.7 47.1 - - + +
533D GLU 3.0 15.0 + - - +
534D THR* 3.6 8.5 - - - +
536D LEU* 1.3 76.1 - - - +
538D LYS* 1.3 65.7 + - - +
540D ALA* 3.1 6.1 + - + +
541D LYS* 2.8 27.0 + - - +
611D VAL* 4.7 10.1 - - + -
615D GLY* 6.0 2.2 - - - -
616D CYS* 3.9 31.1 - - - +
786D LEU* 4.5 24.0 - - + -
787D LEU* 5.8 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 538 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534D THR* 2.9 16.7 + - - +
535D ALA* 3.4 13.7 - - - +
537D LEU* 1.3 75.4 - - - +
539D ARG* 1.3 58.6 + - - +
541D LYS* 3.4 6.2 + - - +
542D GLU* 3.0 53.5 + - - +
616D CYS* 6.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 539 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524D PHE* 3.8 34.0 + - - +
526D PRO* 6.1 0.6 - - - +
535D ALA 3.0 12.5 + - - +
536D LEU* 3.4 24.1 - - - +
538D LYS* 1.3 77.6 - - - +
540D ALA* 1.3 61.8 + - - +
542D GLU* 3.5 11.8 + - - +
543D LEU* 3.1 21.5 + - - +
773D GLU* 3.7 21.8 + - - +
782D PHE* 6.2 0.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 540 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536D LEU 3.0 16.1 + - - +
537D LEU* 3.8 6.3 - - + +
539D ARG* 1.3 73.9 - - - +
541D LYS* 1.3 64.6 + - - +
543D LEU* 3.2 10.5 + - - +
544D PHE* 3.1 29.0 + - + -
616D CYS* 6.2 0.7 - - - -
777D ILE* 3.7 26.9 - - + +
782D PHE* 5.7 1.6 - - + -
786D LEU* 4.5 14.1 - - + -
841D UNX 4.5 8.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 541 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537D LEU 2.8 18.1 + - - +
538D LYS* 3.6 7.0 - - - +
540D ALA* 1.3 76.5 - - - +
542D GLU* 1.3 57.8 + - + +
544D PHE* 3.2 9.1 + - + +
545D THR* 2.9 40.3 + - - +
612D ASP* 3.0 30.4 + - - +
616D CYS* 3.1 36.7 - - + +
617D THR* 4.5 0.9 - - - -
626D THR* 2.7 46.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 542 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538D LYS* 3.0 44.4 + - - +
539D ARG* 3.9 12.1 - - - +
541D LYS* 1.3 77.2 - - + +
543D LEU* 1.3 57.2 + - - +
545D THR* 3.6 7.6 - - + -
546D ASN* 2.9 47.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 543 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539D ARG 3.1 14.2 + - - +
540D ALA* 3.2 12.3 + - - +
542D GLU* 1.3 78.4 - - - +
544D PHE* 1.3 61.9 + - + +
546D ASN* 3.4 2.9 + - + +
547D ASN* 2.7 48.8 + - - +
771D ASP* 4.5 7.6 - - - +
773D GLU* 3.7 57.4 - - + +
774D MET* 3.7 22.4 - - + +
777D ILE* 4.1 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 544 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540D ALA* 3.1 15.7 + - + -
541D LYS* 3.8 6.5 - - + +
543D LEU* 1.3 76.2 - - + +
545D THR* 1.3 61.8 + - - +
547D ASN 3.2 7.8 - - - +
552D ILE* 3.8 21.9 - - + +
612D ASP* 4.1 19.5 - - - +
629D LYS* 2.8 26.4 - - - +
774D MET* 3.9 25.6 - - - -
777D ILE* 3.2 40.2 - - + -
778D CYS* 6.0 1.3 - - - -
834D UNX 3.1 17.5 - - - -
835D UNX 3.8 10.8 - - - -
836D UNX 4.3 6.1 - - - -
837D UNX 4.1 8.5 - - - -
838D UNX 4.0 6.5 - - - -
839D UNX 4.0 17.0 - - - -
840D UNX 4.5 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 545 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541D LYS* 2.9 32.7 + - - +
542D GLU* 3.6 10.5 - - + -
544D PHE* 1.3 79.9 - - - +
546D ASN* 1.3 68.6 + - - +
547D ASN 3.2 2.1 + - - -
629D LYS* 4.0 14.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 546 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542D GLU* 2.9 31.4 + - - +
543D LEU* 3.4 5.5 + - + +
544D PHE 3.4 0.2 - - - -
545D THR* 1.3 83.8 - - - +
547D ASN* 1.3 67.3 + - - +
----------------------------------------------------------
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