Contacts of the helix formed by residues 535 - 544 (chain D) in PDB entry 1WSU
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 SER 535 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526D TYR* 4.8 0.4 - - - -
533D PRO 3.5 2.6 + - - -
534D PRO* 1.3 72.2 - - - +
536D PHE* 1.3 58.8 + - - +
537D LYS* 3.9 5.4 + - - +
538D GLU* 2.3 50.3 + - - +
539D VAL* 2.8 31.3 + - - +
569D GLU* 3.3 35.8 + - - -
570D PHE* 3.4 13.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 536 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526D TYR* 4.8 4.7 + - - -
535D SER* 1.3 69.3 - - - +
537D LYS* 1.3 69.1 - - + +
539D VAL* 3.0 17.5 + - - +
540D ALA* 3.0 15.9 + - + +
547D PRO* 3.1 38.8 - - + -
548D SER* 4.3 1.3 - - - -
550D LEU* 3.4 36.3 - - + -
551D GLU* 4.4 17.0 - - + -
554D LEU* 3.6 17.9 - - + -
568D ASP 4.3 8.7 - - - +
569D GLU* 2.5 25.0 + - + +
570D PHE* 4.4 0.4 - - - +
571D TYR* 5.2 3.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 537 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535D SER* 4.2 6.9 - - - +
536D PHE* 1.3 85.3 - - + +
538D GLU* 1.3 63.0 + - + +
540D ALA* 3.5 16.7 - - - +
541D GLY* 4.0 3.5 + - - -
569D GLU* 5.6 2.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 538 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533D PRO 4.7 0.9 - - - +
534D PRO* 3.6 13.0 - - + +
535D SER* 2.3 45.1 + - - +
536D PHE 3.0 0.6 - - - -
537D LYS* 1.3 78.9 - - + +
539D VAL* 1.3 63.6 + - - +
540D ALA 3.4 0.3 + - - -
541D GLY* 3.4 8.8 + - - -
542D SER* 3.2 17.5 + - - +
569D GLU* 4.7 2.1 - - - +
570D PHE* 5.7 0.6 - - - -
607D LYS* 4.1 20.0 + - - -
608D TYR* 5.6 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 539 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522D LEU* 3.9 28.0 - - + -
525D LYS* 5.2 3.6 - - + -
526D TYR* 3.6 21.5 - - + +
534D PRO* 3.4 33.7 - - + -
535D SER 2.8 24.8 + - - +
536D PHE 3.7 3.1 - - - +
538D GLU* 1.3 70.6 - - - +
540D ALA* 1.3 66.1 + - - +
541D GLY 3.2 0.9 + - - -
542D SER* 3.2 15.4 + - - -
543D PHE* 3.3 23.2 + - + +
550D LEU* 4.4 14.4 - - + +
554D LEU* 6.2 0.4 - - + -
----------------------------------------------------------
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 PHE* 3.0 16.3 + - + +
537D LYS* 3.5 15.7 - - - +
538D GLU 3.2 0.4 - - - -
539D VAL* 1.3 76.2 - - - +
541D GLY* 1.3 56.9 + - - +
543D PHE* 5.8 0.2 - - - -
544D ASN* 3.0 20.1 + - - -
545D LEU* 3.0 31.0 + - - +
546D ASP 5.0 3.4 - - - +
547D PRO* 5.8 2.5 - - + -
550D LEU* 4.3 13.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 541 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537D LYS 4.0 3.8 + - - -
538D GLU 3.4 5.6 + - - -
539D VAL 3.1 0.4 - - - -
540D ALA* 1.3 78.9 - - - +
542D SER* 1.3 60.1 + - - +
543D PHE 3.2 2.2 - - - -
544D ASN* 2.6 29.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 542 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525D LYS* 5.3 11.1 - - - -
534D PRO* 6.1 1.2 - - - +
538D GLU* 3.2 15.1 + - - +
539D VAL* 3.2 12.1 + - - -
541D GLY* 1.3 76.8 - - - +
543D PHE* 1.3 72.6 + - - +
544D ASN* 4.8 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 543 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518D LEU* 3.3 22.8 - - + +
521D ASP* 3.0 50.9 - - + -
522D LEU* 3.5 32.3 - - + -
525D LYS* 4.1 24.0 - - + -
539D VAL* 3.3 14.1 + - + +
540D ALA 5.0 0.2 - - - +
542D SER* 1.3 91.1 - - - +
544D ASN* 1.3 79.0 + - - +
545D LEU* 4.1 17.8 - - + +
550D LEU* 5.9 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 544 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540D ALA 3.0 11.6 + - - -
541D GLY* 2.6 30.3 + - - -
542D SER 4.9 1.6 - - - +
543D PHE* 1.3 84.5 - - - +
545D LEU* 1.3 70.7 + - - +
----------------------------------------------------------
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