Contacts of the strand formed by residues 531 - 539 (chain E) in PDB entry 6IWQ
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 531 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481E TYR 4.3 0.2 + - - -
482E ALA* 3.0 36.4 + - - +
485E PRO* 3.0 25.3 - - - +
529E PRO 4.3 2.6 - - - +
530E LYS* 1.3 79.2 - - - +
532E VAL* 1.3 64.3 + - - +
533E ASP* 4.1 10.8 - - - +
534E TRP* 4.6 5.3 - - + +
572E ARG* 4.0 20.8 + - - +
573E ILE 3.4 11.7 - - - +
574E ASN* 4.1 8.0 - - - +
575E GLU* 4.6 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 532 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530E LYS 3.7 1.2 + - - -
531E ASN* 1.3 73.5 - - - +
533E ASP* 1.3 69.6 + - + +
573E ILE* 2.9 16.1 + - + +
574E ASN 3.6 19.7 - - - +
575E GLU* 3.8 20.4 - - + -
610E TYR* 5.0 18.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 533 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531E ASN* 3.2 4.7 - - - +
532E VAL* 1.3 85.6 - - + +
534E TRP* 1.3 88.9 + - - +
572E ARG* 3.4 1.0 - - - +
573E ILE* 2.7 35.1 + - + +
610E TYR* 3.5 29.1 - - + -
612E LYS* 2.4 35.1 + - - -
651E MET* 4.0 14.5 - - - +
653E ASN* 3.8 9.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 534 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485E PRO* 3.4 39.3 + - + +
486E GLU* 3.7 20.2 - - + -
488E GLN* 5.4 8.4 - - + +
531E ASN* 4.6 7.4 - - + +
533E ASP* 1.3 92.6 + - - +
535E GLY* 1.3 71.8 + - - +
570E LEU* 4.1 13.2 - - + -
571E PHE 3.4 9.2 - - - +
572E ARG* 3.8 10.5 - - + -
651E MET* 3.4 14.6 - - - -
652E ASN 3.8 2.8 + - - -
653E ASN* 2.7 66.9 + - + +
654E ILE* 3.5 19.5 - - + -
655E HIS* 3.6 31.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 535 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534E TRP* 1.3 92.3 - - - +
536E GLU* 1.3 67.7 + - - -
537E ILE 3.8 0.3 + - - -
570E LEU* 3.9 9.2 - - - -
571E PHE* 3.0 29.6 + - - +
651E MET* 3.3 5.3 - - - +
652E ASN 2.8 13.9 - - - -
653E ASN* 4.0 0.4 - - - -
654E ILE 4.2 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 536 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535E GLY* 1.3 76.3 - - - -
537E ILE* 1.3 62.3 + - - +
538E ARG* 2.8 47.1 + - + -
545E CYS* 4.9 2.7 - - + -
562E CYS* 4.1 2.1 - - - +
564E ARG* 3.8 8.9 + - - +
569E GLN* 3.0 47.7 + - + +
570E LEU* 4.3 1.8 - - - +
650E GLU 3.7 0.3 - - - +
651E MET* 3.1 8.5 - - - +
652E ASN* 2.8 57.4 + - - +
654E ILE* 4.0 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 537 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536E GLU* 1.3 75.2 - - - +
538E ARG* 1.3 58.2 + - - +
539E GLY 4.1 0.2 + - - -
545E CYS* 3.4 3.3 - - - +
546E ILE* 3.1 56.6 + - + +
569E GLN 4.0 6.3 + - - -
571E PHE* 3.6 36.3 - - + -
579E LEU* 3.8 24.9 - - + -
586E LEU* 6.2 0.2 - - + -
617E PHE* 3.6 32.5 - - + -
626E LEU* 5.2 0.4 - - + -
649E TRP* 4.1 11.6 - - + -
650E GLU 3.6 5.2 - - - +
651E MET* 3.8 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 538 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536E GLU* 2.8 42.8 + - - +
537E ILE* 1.3 72.9 - - - +
539E GLY* 1.3 69.5 + - - +
542E THR 3.3 30.9 + - - +
543E ALA* 3.9 13.9 - - - +
544E TYR 3.6 7.6 - - - +
545E CYS* 4.2 2.7 - - - +
562E CYS* 3.8 18.4 + - - +
564E ARG* 2.8 48.6 - - - +
649E TRP* 3.1 20.5 - - - +
650E GLU* 3.1 35.9 + - + +
652E ASN* 4.1 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 539 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537E ILE 4.1 0.4 + - - -
538E ARG* 1.3 74.9 - - - +
540E PHE* 1.3 60.5 + - - -
541E GLU 3.1 0.5 + - - -
542E THR* 2.3 43.5 + - - +
544E TYR 2.7 17.3 + - - -
628E ARG* 3.5 20.6 - - - -
649E TRP* 4.1 8.4 - - - -
----------------------------------------------------------
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