Contacts of the helix formed by residues 572 - 580 (chain B) in PDB entry 2WSC
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 ALA 572 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B PRO* 4.4 3.8 - - + +
537B GLY* 3.4 22.4 - - - +
540B ASP 5.4 0.6 + - - -
541B ALA* 3.2 38.6 - - + +
550B LYS* 5.1 3.0 - - - +
554B GLY 5.4 1.2 + - - -
555B TYR* 3.4 29.6 + - + +
570B ILE 4.3 0.6 + - - -
571B SER* 1.3 69.6 - - - +
573B TRP* 1.4 58.3 + - - +
574B ASP 3.4 0.2 - - - -
575B ASP* 3.6 11.7 + - - +
576B PHE* 3.3 13.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 573 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555B TYR* 3.1 29.7 + + + -
556B SER* 2.8 32.0 + - - +
558B PRO* 3.8 6.1 - - + -
571B SER 2.8 2.8 + - - -
572B ALA* 1.4 72.4 - - - +
574B ASP* 1.3 94.4 + - - +
575B ASP 3.0 4.9 - - - -
576B PHE* 3.0 16.0 - + - +
577B TYR* 2.3 41.9 + + + -
703B VAL* 3.7 21.3 - - + -
706B ARG* 3.8 15.0 - - + -
707B LEU* 3.5 43.5 - - + -
1759B CLA 3.1 37.1 - - + +
1783B LMG 4.3 17.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 574 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558B PRO* 3.1 14.1 - - - +
569B ASP* 3.5 26.2 - - + +
571B SER* 1.9 43.0 + - - +
573B TRP* 1.3 87.0 - - - +
575B ASP* 1.3 65.5 + - - +
577B TYR* 3.4 13.3 - - + -
578B LEU* 3.3 24.8 + - - +
706B ARG* 2.4 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 575 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699A TYR* 3.3 18.5 - - + -
702A GLU* 4.0 14.9 - - - +
533B ILE* 2.8 30.0 - - + +
534B LEU* 4.5 1.8 - - - -
536B LYS* 5.4 1.1 - - - -
537B GLY* 3.8 21.5 - - - +
540B ASP 5.7 0.7 - - - +
569B ASP 2.9 24.5 - - - +
570B ILE* 4.3 0.6 - - - -
571B SER 2.9 24.6 + - - +
572B ALA* 3.6 6.3 + - - +
574B ASP* 1.3 81.4 - - - +
576B PHE* 1.3 54.0 + - - +
578B LEU* 3.7 0.9 - - - +
579B ALA* 2.4 33.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 576 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B THR* 4.4 15.3 - - + -
388B ALA* 3.3 25.4 - - + -
534B LEU* 3.9 9.4 - - + +
537B GLY* 5.3 0.4 - - - -
555B TYR* 3.2 19.7 - - - +
572B ALA 3.3 6.4 + - - +
573B TRP* 3.0 28.7 + + - +
575B ASP* 1.3 73.0 - - - +
577B TYR* 1.3 74.4 + - - +
579B ALA* 2.9 17.6 + - - +
580B VAL* 3.1 18.3 + - + +
710B LEU* 5.9 2.2 - - + -
1759B CLA 3.2 31.2 - - + -
1783B LMG 3.1 53.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 577 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694A PHE* 2.9 20.3 + - - +
569B ASP* 4.1 11.0 - - - -
573B TRP* 2.3 42.9 + + + +
574B ASP* 3.4 20.2 - - - -
576B PHE* 1.3 77.6 - - - +
578B LEU* 1.3 92.0 + - + +
580B VAL* 3.4 21.5 - - - +
581B PHE* 3.7 20.3 - + - -
664B LEU* 3.4 21.0 - - + +
667B TRP* 5.1 4.2 - - - -
706B ARG* 2.8 54.4 - - + +
707B LEU* 4.3 1.1 - - - -
709B GLY 4.4 0.7 - - - -
710B LEU* 4.9 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 578 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694A PHE 4.1 1.6 - - - +
695A SER* 3.6 38.8 - - - +
696A GLY 4.3 4.7 - - - +
699A TYR* 4.3 20.2 - - + -
700A TRP* 4.6 1.1 - - + -
1813A CLA 2.9 48.0 - - + +
533B ILE* 4.0 3.4 - - + -
569B ASP* 4.6 1.6 - - + +
574B ASP 3.3 13.9 + - - +
575B ASP* 3.0 9.3 + - - +
576B PHE 3.0 0.8 - - - -
577B TYR* 1.3 107.8 - - + +
579B ALA* 1.3 66.6 + - - +
580B VAL 3.4 0.3 + - - -
581B PHE* 3.5 23.4 + - + +
582B TRP* 4.5 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 579 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B THR* 4.3 6.1 - - + -
530B THR* 4.4 6.0 - - + +
533B ILE* 3.8 13.4 - - + +
534B LEU* 3.0 47.1 - - + -
575B ASP 2.4 23.3 + - - +
576B PHE* 2.9 5.8 + - - +
578B LEU* 1.3 69.4 - - - +
580B VAL* 1.3 52.5 + - - +
581B PHE 2.8 13.0 + - - -
582B TRP* 2.8 20.5 + - - +
583B MET 3.6 6.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 580 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B PHE* 5.1 11.9 - - + -
384B THR* 4.4 16.2 - - + -
576B PHE* 3.1 13.8 + - + +
577B TYR* 3.4 14.1 - - - +
579B ALA* 1.3 76.6 - - - +
581B PHE* 1.3 59.4 + - + +
582B TRP 3.5 0.4 - - - -
583B MET* 4.0 19.4 - - - -
584B LEU* 3.2 28.3 + - + +
710B LEU* 3.3 46.2 - - + +
714B SER* 5.3 3.4 - - - +
1759B CLA 6.1 2.0 - - + -
1783B LMG 5.1 10.5 - - + -
----------------------------------------------------------
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